Starting phenix.real_space_refine on Sat Jun 14 19:57:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xqb_22288/06_2025/6xqb_22288.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xqb_22288/06_2025/6xqb_22288.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6xqb_22288/06_2025/6xqb_22288.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xqb_22288/06_2025/6xqb_22288.map" model { file = "/net/cci-nas-00/data/ceres_data/6xqb_22288/06_2025/6xqb_22288.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xqb_22288/06_2025/6xqb_22288.cif" } resolution = 3.4 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= 0.002 sd= 0.038 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: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 15 5.49 5 Mg 1 5.21 5 S 61 5.16 5 C 5262 2.51 5 N 1392 2.21 5 O 1603 1.98 5 H 7987 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16323 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 12682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 801, 12682 Classifications: {'peptide': 801} Link IDs: {'PTRANS': 25, 'TRANS': 775} Chain breaks: 5 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1713 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 993 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "D" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 444 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 229 Classifications: {'RNA': 7} Modifications used: {'3*END': 1, 'rna3p_pur': 4, 'rna3p_pyr': 3} Link IDs: {'rna3p': 6} Chain: "F" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 259 Classifications: {'RNA': 8} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 4} Link IDs: {'rna3p': 7} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3213 SG CYS A 301 37.207 66.986 36.975 1.00131.34 S ATOM 3290 SG CYS A 306 37.350 65.836 33.243 1.00128.23 S ATOM 3355 SG CYS A 310 40.424 66.248 34.854 1.00134.44 S ATOM 6095 SG CYS A 487 19.687 63.110 45.316 1.00126.47 S ATOM 8612 SG CYS A 645 17.972 62.844 42.341 1.00141.82 S ATOM 8622 SG CYS A 646 22.155 64.389 43.308 1.00142.48 S Time building chain proxies: 8.01, per 1000 atoms: 0.49 Number of scatterers: 16323 At special positions: 0 Unit cell: (84.55, 97.01, 108.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 S 61 16.00 P 15 15.00 Mg 1 11.99 O 1603 8.00 N 1392 7.00 C 5262 6.00 H 7987 1.00 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: 4.70 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " Number of angles added : 3 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1934 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 8 sheets defined 53.2% alpha, 11.5% beta 7 base pairs and 10 stacking pairs defined. Time for finding SS restraints: 8.37 Creating SS restraints... Processing helix chain 'A' and resid 123 through 132 Processing helix chain 'A' and resid 139 through 149 removed outlier: 3.684A pdb=" N LYS A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 159 Processing helix chain 'A' and resid 170 through 177 removed outlier: 3.520A pdb=" N VAL A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 198 removed outlier: 3.867A pdb=" N ALA A 185 " --> pdb=" O ARG A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 242 Processing helix chain 'A' and resid 243 through 246 removed outlier: 4.018A pdb=" N THR A 246 " --> pdb=" O PRO A 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 243 through 246' Processing helix chain 'A' and resid 249 through 260 removed outlier: 4.264A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A 254 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N VAL A 257 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASP A 258 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP A 260 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 315 removed outlier: 3.614A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 319 removed outlier: 3.585A pdb=" N THR A 319 " --> pdb=" O LEU A 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 316 through 319' Processing helix chain 'A' and resid 367 through 376 removed outlier: 4.455A pdb=" N ALA A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 383 removed outlier: 4.222A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 425 Processing helix chain 'A' and resid 447 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 480 removed outlier: 5.132A pdb=" N LYS A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.812A pdb=" N VAL A 493 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 508 Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.726A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 removed outlier: 3.532A pdb=" N LYS A 532 " --> pdb=" O PHE A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 573 removed outlier: 3.682A pdb=" N THR A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN A 573 " --> pdb=" O ARG A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 581 removed outlier: 3.912A pdb=" N ALA A 581 " --> pdb=" O LYS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 607 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 627 through 638 removed outlier: 3.739A pdb=" N ARG A 631 " --> pdb=" O PRO A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 662 Processing helix chain 'A' and resid 686 through 710 removed outlier: 3.893A pdb=" N SER A 709 " --> pdb=" O ASN A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 732 Processing helix chain 'A' and resid 738 through 752 removed outlier: 4.021A pdb=" N VAL A 742 " --> pdb=" O ASP A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 774 Processing helix chain 'A' and resid 778 through 789 removed outlier: 4.050A pdb=" N PHE A 782 " --> pdb=" O SER A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 843 removed outlier: 3.905A pdb=" N ILE A 837 " --> pdb=" O ASP A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 865 removed outlier: 3.834A pdb=" N ASP A 865 " --> pdb=" O SER A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 872 Processing helix chain 'A' and resid 874 through 895 removed outlier: 3.505A pdb=" N ALA A 878 " --> pdb=" O ASN A 874 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU A 894 " --> pdb=" O LYS A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 915 removed outlier: 3.703A pdb=" N SER A 913 " --> pdb=" O ASN A 909 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG A 914 " --> pdb=" O ASP A 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 94 Processing helix chain 'B' and resid 95 through 98 Processing helix chain 'B' and resid 101 through 108 removed outlier: 3.533A pdb=" N ASN B 105 " --> pdb=" O ASP B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 114 removed outlier: 4.530A pdb=" N GLY B 113 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N CYS B 114 " --> pdb=" O ARG B 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 110 through 114' Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 135 through 142 removed outlier: 3.559A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 removed outlier: 3.751A pdb=" N ASN B 179 " --> pdb=" O ASN B 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 20 removed outlier: 3.548A pdb=" N LEU C 20 " --> pdb=" O VAL C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 40 Processing helix chain 'C' and resid 44 through 62 removed outlier: 3.634A pdb=" N ALA C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 99 removed outlier: 3.515A pdb=" N THR D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 112 removed outlier: 3.610A pdb=" N ASP D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 201 through 202 Processing sheet with id=AA3, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.416A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 9.490A pdb=" N SER A 363 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N PHE A 334 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.416A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 115 " --> pdb=" O VAL A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 389 through 390 removed outlier: 6.826A pdb=" N LEU A 389 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 397 through 400 removed outlier: 7.200A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 753 through 758 Processing sheet with id=AA8, first strand: chain 'A' and resid 816 through 822 369 hydrogen bonds defined for protein. 1011 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 10 stacking parallelities Total time for adding SS restraints: 6.35 Time building geometry restraints manager: 5.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 7963 1.03 - 1.22: 42 1.22 - 1.42: 3706 1.42 - 1.62: 4725 1.62 - 1.82: 93 Bond restraints: 16529 Sorted by residual: bond pdb=" C GLY A 203 " pdb=" N VAL A 204 " ideal model delta sigma weight residual 1.332 1.273 0.059 1.73e-02 3.34e+03 1.16e+01 bond pdb=" CB VAL A 473 " pdb=" CG2 VAL A 473 " ideal model delta sigma weight residual 1.521 1.411 0.110 3.30e-02 9.18e+02 1.10e+01 bond pdb=" C GLN A 573 " pdb=" N LYS A 574 " ideal model delta sigma weight residual 1.332 1.290 0.043 1.40e-02 5.10e+03 9.28e+00 bond pdb=" CA ILE B 120 " pdb=" C ILE B 120 " ideal model delta sigma weight residual 1.524 1.494 0.030 1.05e-02 9.07e+03 8.26e+00 bond pdb=" CB VAL A 637 " pdb=" CG2 VAL A 637 " ideal model delta sigma weight residual 1.521 1.430 0.091 3.30e-02 9.18e+02 7.65e+00 ... (remaining 16524 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.39: 29219 3.39 - 6.78: 489 6.78 - 10.16: 13 10.16 - 13.55: 6 13.55 - 16.94: 2 Bond angle restraints: 29729 Sorted by residual: angle pdb=" N GLY A 503 " pdb=" CA GLY A 503 " pdb=" C GLY A 503 " ideal model delta sigma weight residual 111.85 117.17 -5.32 1.06e+00 8.90e-01 2.51e+01 angle pdb=" CA LEU A 241 " pdb=" CB LEU A 241 " pdb=" CG LEU A 241 " ideal model delta sigma weight residual 116.30 133.24 -16.94 3.50e+00 8.16e-02 2.34e+01 angle pdb=" CA LEU A 247 " pdb=" CB LEU A 247 " pdb=" CG LEU A 247 " ideal model delta sigma weight residual 116.30 131.87 -15.57 3.50e+00 8.16e-02 1.98e+01 angle pdb=" CA PRO A 830 " pdb=" C PRO A 830 " pdb=" N TYR A 831 " ideal model delta sigma weight residual 114.65 120.20 -5.55 1.27e+00 6.20e-01 1.91e+01 angle pdb=" N PHE A 321 " pdb=" CA PHE A 321 " pdb=" C PHE A 321 " ideal model delta sigma weight residual 110.36 104.55 5.81 1.34e+00 5.57e-01 1.88e+01 ... (remaining 29724 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 6972 17.42 - 34.83: 634 34.83 - 52.25: 177 52.25 - 69.67: 81 69.67 - 87.08: 16 Dihedral angle restraints: 7880 sinusoidal: 4275 harmonic: 3605 Sorted by residual: dihedral pdb=" CA ASP A 465 " pdb=" C ASP A 465 " pdb=" N ILE A 466 " pdb=" CA ILE A 466 " ideal model delta harmonic sigma weight residual -180.00 -136.97 -43.03 0 5.00e+00 4.00e-02 7.41e+01 dihedral pdb=" CA VAL A 234 " pdb=" C VAL A 234 " pdb=" N ASP A 235 " pdb=" CA ASP A 235 " ideal model delta harmonic sigma weight residual -180.00 -139.49 -40.51 0 5.00e+00 4.00e-02 6.56e+01 dihedral pdb=" CA LEU B 180 " pdb=" C LEU B 180 " pdb=" N ALA B 181 " pdb=" CA ALA B 181 " ideal model delta harmonic sigma weight residual 180.00 141.10 38.90 0 5.00e+00 4.00e-02 6.05e+01 ... (remaining 7877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1052 0.076 - 0.152: 253 0.152 - 0.229: 27 0.229 - 0.305: 2 0.305 - 0.381: 1 Chirality restraints: 1335 Sorted by residual: chirality pdb=" CB VAL A 473 " pdb=" CA VAL A 473 " pdb=" CG1 VAL A 473 " pdb=" CG2 VAL A 473 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CA PRO A 296 " pdb=" N PRO A 296 " pdb=" C PRO A 296 " pdb=" CB PRO A 296 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CB VAL A 763 " pdb=" CA VAL A 763 " pdb=" CG1 VAL A 763 " pdb=" CG2 VAL A 763 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 1332 not shown) Planarity restraints: 2410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 166 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.19e+00 pdb=" C VAL A 166 " 0.052 2.00e-02 2.50e+03 pdb=" O VAL A 166 " -0.020 2.00e-02 2.50e+03 pdb=" N GLU A 167 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 134 " 0.015 2.00e-02 2.50e+03 3.02e-02 9.11e+00 pdb=" C ASP B 134 " -0.052 2.00e-02 2.50e+03 pdb=" O ASP B 134 " 0.020 2.00e-02 2.50e+03 pdb=" N TYR B 135 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 238 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.51e+00 pdb=" C TYR A 238 " 0.050 2.00e-02 2.50e+03 pdb=" O TYR A 238 " -0.019 2.00e-02 2.50e+03 pdb=" N SER A 239 " -0.017 2.00e-02 2.50e+03 ... (remaining 2407 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 1295 2.19 - 2.79: 34516 2.79 - 3.39: 46566 3.39 - 4.00: 59821 4.00 - 4.60: 90605 Nonbonded interactions: 232803 Sorted by model distance: nonbonded pdb="HE21 GLN A 210 " pdb=" O GLY A 214 " model vdw 1.583 2.450 nonbonded pdb=" OD1 ASP A 194 " pdb=" HH TYR A 289 " model vdw 1.601 2.450 nonbonded pdb=" O ASP A 454 " pdb=" H ARG A 457 " model vdw 1.648 2.450 nonbonded pdb=" O VAL A 234 " pdb=" H TYR A 237 " model vdw 1.650 2.450 nonbonded pdb=" O PHE A 480 " pdb=" HZ1 LYS A 641 " model vdw 1.655 2.450 ... (remaining 232798 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 Found NCS groups: ncs_group { reference = (chain 'E' and resid 3 through 8) selection = (chain 'F' and resid 3 through 8) } 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: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.270 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 51.730 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5560 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 : 0.014 0.690 8549 Z= 0.588 Angle : 1.334 32.088 11664 Z= 0.717 Chirality : 0.064 0.381 1335 Planarity : 0.008 0.059 1427 Dihedral : 13.837 78.509 3174 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.15 % Favored : 84.85 % Rotamer: Outliers : 0.23 % Allowed : 3.97 % Favored : 95.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.72 % 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: -5.15 (0.20), residues: 990 helix: -3.28 (0.17), residues: 427 sheet: -2.91 (0.47), residues: 86 loop : -3.65 (0.24), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP A 290 HIS 0.022 0.005 HIS A 613 PHE 0.044 0.005 PHE A 326 TYR 0.031 0.005 TYR A 788 ARG 0.020 0.003 ARG A 132 Details of bonding type rmsd hydrogen bonds : bond 0.15727 ( 380) hydrogen bonds : angle 7.65771 ( 1051) metal coordination : bond 0.27511 ( 7) metal coordination : angle 24.15317 ( 3) covalent geometry : bond 0.01185 ( 8542) covalent geometry : angle 1.27679 (11661) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 384 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 172 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 170 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 859 PHE cc_start: 0.7511 (t80) cc_final: 0.6713 (t80) REVERT: A 884 TYR cc_start: 0.8757 (m-10) cc_final: 0.8551 (m-10) REVERT: A 885 LEU cc_start: 0.8528 (mt) cc_final: 0.8304 (tp) REVERT: B 104 ASN cc_start: 0.6760 (t160) cc_final: 0.6326 (m110) REVERT: C 47 GLU cc_start: 0.8062 (mp0) cc_final: 0.7726 (mp0) REVERT: D 87 MET cc_start: 0.6526 (ttm) cc_final: 0.5334 (mmp) outliers start: 2 outliers final: 1 residues processed: 171 average time/residue: 0.4823 time to fit residues: 114.6893 Evaluate side-chains 134 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 463 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 78 optimal weight: 8.9990 chunk 30 optimal weight: 0.0970 chunk 47 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 ASN A 414 ASN A 491 ASN ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 ASN A 705 ASN A 743 ASN B 104 ASN B 118 ASN B 136 ASN C 31 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.154627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.139030 restraints weight = 100949.211| |-----------------------------------------------------------------------------| r_work (start): 0.4506 rms_B_bonded: 5.81 r_work (final): 0.4506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5580 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8549 Z= 0.149 Angle : 0.702 9.276 11664 Z= 0.369 Chirality : 0.040 0.140 1335 Planarity : 0.005 0.051 1427 Dihedral : 13.048 73.968 1340 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 1.36 % Allowed : 8.63 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.23), residues: 990 helix: -2.12 (0.21), residues: 443 sheet: -2.38 (0.53), residues: 80 loop : -2.86 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 598 HIS 0.006 0.002 HIS C 36 PHE 0.018 0.001 PHE A 471 TYR 0.015 0.002 TYR A 289 ARG 0.003 0.001 ARG A 654 Details of bonding type rmsd hydrogen bonds : bond 0.04763 ( 380) hydrogen bonds : angle 5.72698 ( 1051) metal coordination : bond 0.01154 ( 7) metal coordination : angle 5.68779 ( 3) covalent geometry : bond 0.00318 ( 8542) covalent geometry : angle 0.69591 (11661) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 384 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 164 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ASP cc_start: 0.7468 (m-30) cc_final: 0.6992 (p0) REVERT: A 479 TYR cc_start: 0.7314 (OUTLIER) cc_final: 0.6526 (t80) REVERT: A 794 MET cc_start: 0.3337 (ttp) cc_final: 0.2787 (ttp) REVERT: A 859 PHE cc_start: 0.7565 (t80) cc_final: 0.6707 (t80) REVERT: A 884 TYR cc_start: 0.8646 (m-10) cc_final: 0.8306 (m-10) REVERT: A 885 LEU cc_start: 0.8488 (mt) cc_final: 0.8012 (tt) REVERT: A 886 GLN cc_start: 0.9144 (mm110) cc_final: 0.8430 (mm-40) REVERT: A 888 ILE cc_start: 0.7486 (mt) cc_final: 0.7236 (mt) REVERT: B 104 ASN cc_start: 0.7156 (t0) cc_final: 0.6624 (m110) REVERT: D 87 MET cc_start: 0.6899 (ttm) cc_final: 0.5682 (mmt) outliers start: 12 outliers final: 10 residues processed: 158 average time/residue: 0.4172 time to fit residues: 92.6526 Evaluate side-chains 148 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 599 HIS Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain C residue 21 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 23 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 98 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 6 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 ASN ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.150867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.135127 restraints weight = 101465.056| |-----------------------------------------------------------------------------| r_work (start): 0.4450 rms_B_bonded: 5.79 r_work (final): 0.4450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5759 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8549 Z= 0.192 Angle : 0.683 7.765 11664 Z= 0.367 Chirality : 0.040 0.140 1335 Planarity : 0.005 0.051 1427 Dihedral : 12.750 73.744 1340 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 2.04 % Allowed : 10.33 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.24), residues: 990 helix: -1.61 (0.22), residues: 443 sheet: -2.40 (0.48), residues: 91 loop : -2.71 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 598 HIS 0.007 0.002 HIS C 36 PHE 0.022 0.002 PHE A 782 TYR 0.016 0.002 TYR A 674 ARG 0.003 0.000 ARG A 624 Details of bonding type rmsd hydrogen bonds : bond 0.04796 ( 380) hydrogen bonds : angle 5.52772 ( 1051) metal coordination : bond 0.01604 ( 7) metal coordination : angle 4.63757 ( 3) covalent geometry : bond 0.00408 ( 8542) covalent geometry : angle 0.67881 (11661) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 384 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 164 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ASP cc_start: 0.7568 (m-30) cc_final: 0.7041 (p0) REVERT: A 479 TYR cc_start: 0.7405 (OUTLIER) cc_final: 0.6659 (t80) REVERT: A 859 PHE cc_start: 0.7738 (t80) cc_final: 0.6762 (t80) REVERT: A 884 TYR cc_start: 0.8866 (m-10) cc_final: 0.8520 (m-10) REVERT: A 885 LEU cc_start: 0.8571 (mt) cc_final: 0.8136 (tt) REVERT: A 886 GLN cc_start: 0.9215 (mm110) cc_final: 0.8504 (mm-40) REVERT: A 888 ILE cc_start: 0.7537 (mt) cc_final: 0.7169 (mt) REVERT: B 104 ASN cc_start: 0.7066 (t0) cc_final: 0.6469 (m110) REVERT: D 87 MET cc_start: 0.6949 (ttm) cc_final: 0.5689 (mmt) outliers start: 18 outliers final: 15 residues processed: 157 average time/residue: 0.4388 time to fit residues: 94.8054 Evaluate side-chains 148 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 521 TYR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 599 HIS Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 146 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 91 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 94 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN A 489 ASN A 491 ASN ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 773 GLN B 118 ASN D 88 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.144277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.128019 restraints weight = 102710.288| |-----------------------------------------------------------------------------| r_work (start): 0.4336 rms_B_bonded: 5.71 r_work (final): 0.4336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6024 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 8549 Z= 0.303 Angle : 0.833 9.784 11664 Z= 0.455 Chirality : 0.045 0.169 1335 Planarity : 0.006 0.058 1427 Dihedral : 12.943 73.818 1340 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 31.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.55 % Favored : 85.45 % Rotamer: Outliers : 3.29 % Allowed : 11.92 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.63 (0.24), residues: 990 helix: -1.69 (0.22), residues: 430 sheet: -2.55 (0.48), residues: 92 loop : -3.10 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 617 HIS 0.013 0.002 HIS A 309 PHE 0.032 0.003 PHE A 753 TYR 0.026 0.003 TYR A 674 ARG 0.005 0.001 ARG A 624 Details of bonding type rmsd hydrogen bonds : bond 0.05764 ( 380) hydrogen bonds : angle 6.22082 ( 1051) metal coordination : bond 0.01820 ( 7) metal coordination : angle 5.49565 ( 3) covalent geometry : bond 0.00652 ( 8542) covalent geometry : angle 0.82803 (11661) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 384 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 166 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 GLU cc_start: 0.8409 (mp0) cc_final: 0.8006 (mm-30) REVERT: A 499 ASP cc_start: 0.8119 (m-30) cc_final: 0.7915 (m-30) REVERT: A 525 ASP cc_start: 0.8321 (t0) cc_final: 0.7645 (p0) REVERT: A 859 PHE cc_start: 0.7960 (t80) cc_final: 0.6984 (t80) REVERT: A 884 TYR cc_start: 0.8958 (m-10) cc_final: 0.8609 (m-10) REVERT: A 885 LEU cc_start: 0.8654 (mt) cc_final: 0.8202 (tp) REVERT: A 886 GLN cc_start: 0.9369 (mm110) cc_final: 0.8827 (mm-40) REVERT: A 888 ILE cc_start: 0.7824 (mt) cc_final: 0.7456 (mt) REVERT: B 130 VAL cc_start: 0.0855 (OUTLIER) cc_final: 0.0567 (t) outliers start: 29 outliers final: 24 residues processed: 155 average time/residue: 0.5525 time to fit residues: 123.6873 Evaluate side-chains 156 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 2.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 599 HIS Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain D residue 90 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 43 optimal weight: 0.6980 chunk 35 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.147331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.131302 restraints weight = 102708.757| |-----------------------------------------------------------------------------| r_work (start): 0.4379 rms_B_bonded: 5.77 r_work (final): 0.4379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5902 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8549 Z= 0.169 Angle : 0.658 8.495 11664 Z= 0.352 Chirality : 0.040 0.137 1335 Planarity : 0.005 0.053 1427 Dihedral : 12.494 73.765 1340 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.21 % Favored : 88.79 % Rotamer: Outliers : 2.84 % Allowed : 14.07 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.24), residues: 990 helix: -1.16 (0.23), residues: 438 sheet: -2.88 (0.48), residues: 86 loop : -2.84 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 598 HIS 0.009 0.002 HIS A 572 PHE 0.015 0.002 PHE A 753 TYR 0.013 0.002 TYR A 238 ARG 0.004 0.000 ARG A 624 Details of bonding type rmsd hydrogen bonds : bond 0.04528 ( 380) hydrogen bonds : angle 5.44538 ( 1051) metal coordination : bond 0.01519 ( 7) metal coordination : angle 3.89670 ( 3) covalent geometry : bond 0.00357 ( 8542) covalent geometry : angle 0.65467 (11661) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 384 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 163 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.7988 (mtt90) cc_final: 0.7749 (mtt90) REVERT: A 350 GLU cc_start: 0.8247 (mp0) cc_final: 0.7858 (mm-30) REVERT: A 499 ASP cc_start: 0.8100 (m-30) cc_final: 0.7885 (m-30) REVERT: A 525 ASP cc_start: 0.8219 (t0) cc_final: 0.7841 (p0) REVERT: A 859 PHE cc_start: 0.7990 (t80) cc_final: 0.7066 (t80) REVERT: A 884 TYR cc_start: 0.8846 (m-10) cc_final: 0.8582 (m-10) REVERT: A 885 LEU cc_start: 0.8630 (mt) cc_final: 0.8339 (tp) REVERT: A 888 ILE cc_start: 0.7701 (mt) cc_final: 0.7437 (mt) REVERT: C 47 GLU cc_start: 0.7283 (mp0) cc_final: 0.7007 (mp0) outliers start: 25 outliers final: 20 residues processed: 152 average time/residue: 0.5041 time to fit residues: 111.4727 Evaluate side-chains 156 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 599 HIS Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 92 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 21 optimal weight: 0.9990 chunk 50 optimal weight: 0.0870 chunk 22 optimal weight: 0.8980 chunk 11 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 ASN ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.150160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.134561 restraints weight = 100868.815| |-----------------------------------------------------------------------------| r_work (start): 0.4422 rms_B_bonded: 5.72 r_work (final): 0.4422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5789 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8549 Z= 0.120 Angle : 0.590 7.987 11664 Z= 0.309 Chirality : 0.038 0.164 1335 Planarity : 0.004 0.045 1427 Dihedral : 12.161 73.545 1340 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 2.04 % Allowed : 14.76 % Favored : 83.20 % 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: -2.42 (0.25), residues: 990 helix: -0.57 (0.24), residues: 440 sheet: -2.77 (0.54), residues: 71 loop : -2.44 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 598 HIS 0.005 0.001 HIS C 36 PHE 0.013 0.001 PHE A 753 TYR 0.012 0.001 TYR A 516 ARG 0.003 0.000 ARG A 624 Details of bonding type rmsd hydrogen bonds : bond 0.03884 ( 380) hydrogen bonds : angle 4.92641 ( 1051) metal coordination : bond 0.00735 ( 7) metal coordination : angle 2.93918 ( 3) covalent geometry : bond 0.00253 ( 8542) covalent geometry : angle 0.58780 (11661) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 384 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 GLU cc_start: 0.8132 (mp0) cc_final: 0.7745 (mm-30) REVERT: A 499 ASP cc_start: 0.8112 (m-30) cc_final: 0.7860 (m-30) REVERT: B 104 ASN cc_start: 0.6606 (t0) cc_final: 0.5969 (m110) REVERT: C 47 GLU cc_start: 0.7312 (mp0) cc_final: 0.7074 (mp0) outliers start: 18 outliers final: 15 residues processed: 154 average time/residue: 0.3829 time to fit residues: 84.1022 Evaluate side-chains 148 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 599 HIS Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 92 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 77 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 99 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 743 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.144540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.128645 restraints weight = 101332.145| |-----------------------------------------------------------------------------| r_work (start): 0.4330 rms_B_bonded: 5.63 r_work (final): 0.4330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5999 moved from start: 0.5421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 8549 Z= 0.244 Angle : 0.723 8.671 11664 Z= 0.389 Chirality : 0.042 0.139 1335 Planarity : 0.005 0.050 1427 Dihedral : 12.333 73.506 1337 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 22.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 3.52 % Allowed : 14.42 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.93 (0.24), residues: 990 helix: -0.96 (0.23), residues: 432 sheet: -2.54 (0.46), residues: 99 loop : -2.79 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 598 HIS 0.012 0.002 HIS A 309 PHE 0.029 0.002 PHE A 471 TYR 0.019 0.002 TYR A 674 ARG 0.005 0.001 ARG A 624 Details of bonding type rmsd hydrogen bonds : bond 0.04838 ( 380) hydrogen bonds : angle 5.57568 ( 1051) metal coordination : bond 0.01961 ( 7) metal coordination : angle 4.42884 ( 3) covalent geometry : bond 0.00522 ( 8542) covalent geometry : angle 0.71951 (11661) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 384 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 171 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 PHE cc_start: 0.2212 (OUTLIER) cc_final: 0.1850 (m-80) REVERT: A 350 GLU cc_start: 0.8227 (mp0) cc_final: 0.7852 (mm-30) REVERT: A 499 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7831 (m-30) outliers start: 31 outliers final: 28 residues processed: 161 average time/residue: 0.4037 time to fit residues: 92.3128 Evaluate side-chains 162 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 489 ASN Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 599 HIS Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 92 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 ASN ** 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 = 0.4666 r_free = 0.4666 target = 0.146352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.130778 restraints weight = 100484.992| |-----------------------------------------------------------------------------| r_work (start): 0.4362 rms_B_bonded: 5.61 r_work (final): 0.4362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5916 moved from start: 0.5691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8549 Z= 0.160 Angle : 0.636 8.038 11664 Z= 0.335 Chirality : 0.039 0.128 1335 Planarity : 0.004 0.050 1427 Dihedral : 12.146 73.458 1337 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.81 % Favored : 89.19 % Rotamer: Outliers : 2.72 % Allowed : 15.66 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.68 (0.25), residues: 990 helix: -0.70 (0.23), residues: 438 sheet: -2.60 (0.43), residues: 106 loop : -2.68 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 598 HIS 0.007 0.001 HIS A 309 PHE 0.019 0.002 PHE A 471 TYR 0.014 0.002 TYR A 238 ARG 0.004 0.000 ARG A 624 Details of bonding type rmsd hydrogen bonds : bond 0.04157 ( 380) hydrogen bonds : angle 5.18599 ( 1051) metal coordination : bond 0.01362 ( 7) metal coordination : angle 3.48332 ( 3) covalent geometry : bond 0.00337 ( 8542) covalent geometry : angle 0.63349 (11661) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 384 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 161 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.1862 (OUTLIER) cc_final: 0.1312 (t80) REVERT: A 350 GLU cc_start: 0.8224 (mp0) cc_final: 0.7822 (mm-30) outliers start: 24 outliers final: 21 residues processed: 154 average time/residue: 0.4134 time to fit residues: 91.6398 Evaluate side-chains 157 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 599 HIS Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 92 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 93 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 99 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 ASN ** 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 = 0.4662 r_free = 0.4662 target = 0.144434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.128943 restraints weight = 98442.655| |-----------------------------------------------------------------------------| r_work (start): 0.4358 rms_B_bonded: 5.47 r_work (final): 0.4358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6014 moved from start: 0.6133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8549 Z= 0.224 Angle : 0.714 8.200 11664 Z= 0.381 Chirality : 0.042 0.131 1335 Planarity : 0.006 0.095 1427 Dihedral : 12.223 73.281 1337 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 22.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.94 % Favored : 86.06 % Rotamer: Outliers : 3.52 % Allowed : 15.21 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.98 (0.24), residues: 990 helix: -0.92 (0.23), residues: 435 sheet: -2.36 (0.45), residues: 106 loop : -2.97 (0.26), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 598 HIS 0.011 0.002 HIS A 309 PHE 0.024 0.002 PHE A 753 TYR 0.018 0.002 TYR A 238 ARG 0.008 0.001 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.04703 ( 380) hydrogen bonds : angle 5.54008 ( 1051) metal coordination : bond 0.01992 ( 7) metal coordination : angle 4.53488 ( 3) covalent geometry : bond 0.00475 ( 8542) covalent geometry : angle 0.71034 (11661) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 384 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 167 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 GLU cc_start: 0.8318 (mp0) cc_final: 0.7941 (mm-30) REVERT: A 674 TYR cc_start: 0.7748 (m-80) cc_final: 0.7447 (m-80) outliers start: 31 outliers final: 27 residues processed: 158 average time/residue: 0.3847 time to fit residues: 87.3891 Evaluate side-chains 160 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 489 ASN Chi-restraints excluded: chain A residue 521 TYR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 599 HIS Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 92 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 65 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 75 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 97 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 507 ASN ** 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 = 0.4712 r_free = 0.4712 target = 0.148249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.133196 restraints weight = 99452.288| |-----------------------------------------------------------------------------| r_work (start): 0.4417 rms_B_bonded: 5.58 r_work (final): 0.4417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5871 moved from start: 0.6280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8549 Z= 0.129 Angle : 0.626 7.792 11664 Z= 0.324 Chirality : 0.038 0.132 1335 Planarity : 0.004 0.066 1427 Dihedral : 11.986 73.266 1337 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 2.50 % Allowed : 15.55 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.51 (0.25), residues: 990 helix: -0.45 (0.24), residues: 442 sheet: -2.86 (0.42), residues: 105 loop : -2.63 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 598 HIS 0.006 0.001 HIS C 36 PHE 0.017 0.002 PHE A 471 TYR 0.013 0.002 TYR A 828 ARG 0.007 0.001 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.03882 ( 380) hydrogen bonds : angle 4.94621 ( 1051) metal coordination : bond 0.00777 ( 7) metal coordination : angle 3.19954 ( 3) covalent geometry : bond 0.00277 ( 8542) covalent geometry : angle 0.62390 (11661) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 384 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.1762 (OUTLIER) cc_final: 0.1427 (t80) REVERT: A 350 GLU cc_start: 0.8141 (mp0) cc_final: 0.7756 (mm-30) REVERT: A 857 GLU cc_start: 0.8647 (tp30) cc_final: 0.8234 (tp30) REVERT: A 859 PHE cc_start: 0.8038 (t80) cc_final: 0.7145 (t80) REVERT: C 47 GLU cc_start: 0.7196 (mp0) cc_final: 0.6905 (mp0) outliers start: 22 outliers final: 21 residues processed: 151 average time/residue: 0.4186 time to fit residues: 90.4382 Evaluate side-chains 153 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 489 ASN Chi-restraints excluded: chain A residue 521 TYR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 599 HIS Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 92 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 47 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.145770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.130410 restraints weight = 98021.048| |-----------------------------------------------------------------------------| r_work (start): 0.4376 rms_B_bonded: 5.47 r_work (final): 0.4376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5967 moved from start: 0.6486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8549 Z= 0.185 Angle : 0.657 8.049 11664 Z= 0.347 Chirality : 0.040 0.129 1335 Planarity : 0.005 0.063 1427 Dihedral : 11.999 73.229 1337 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.22 % Favored : 87.78 % Rotamer: Outliers : 2.38 % Allowed : 15.89 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.55 (0.25), residues: 990 helix: -0.49 (0.24), residues: 436 sheet: -2.46 (0.43), residues: 111 loop : -2.74 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 598 HIS 0.008 0.002 HIS A 309 PHE 0.017 0.002 PHE A 753 TYR 0.018 0.002 TYR A 238 ARG 0.007 0.001 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.04189 ( 380) hydrogen bonds : angle 5.19730 ( 1051) metal coordination : bond 0.01709 ( 7) metal coordination : angle 3.82420 ( 3) covalent geometry : bond 0.00395 ( 8542) covalent geometry : angle 0.65397 (11661) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6645.47 seconds wall clock time: 116 minutes 24.71 seconds (6984.71 seconds total)