Starting phenix.real_space_refine on Wed Feb 4 09:41:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v80_64827/02_2026/9v80_64827.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v80_64827/02_2026/9v80_64827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9v80_64827/02_2026/9v80_64827.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v80_64827/02_2026/9v80_64827.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9v80_64827/02_2026/9v80_64827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v80_64827/02_2026/9v80_64827.map" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 6156 2.51 5 N 1669 2.21 5 O 1735 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9607 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3670 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 170} Link IDs: {'PTRANS': 32, 'TRANS': 494} Chain breaks: 20 Unresolved non-hydrogen bonds: 644 Unresolved non-hydrogen angles: 823 Unresolved non-hydrogen dihedrals: 536 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'ARG:plan': 20, 'TRP:plan': 4, 'TYR:plan': 3, 'PHE:plan': 7, 'HIS:plan': 10, 'GLU:plan': 17, 'GLN:plan1': 12, 'ASP:plan': 7, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 392 Chain: "B" Number of atoms: 2907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2907 Classifications: {'peptide': 383} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 13, 'TRANS': 369} Chain breaks: 4 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 6, 'ARG:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 64 Chain: "C" Number of atoms: 3030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3030 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 20, 'TRANS': 379} Chain breaks: 2 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 6, 'GLN:plan1': 3, 'ASP:plan': 8, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 95 Time building chain proxies: 1.87, per 1000 atoms: 0.19 Number of scatterers: 9607 At special positions: 0 Unit cell: (98.6, 125.8, 158.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 47 16.00 O 1735 8.00 N 1669 7.00 C 6156 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 371.7 milliseconds 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2454 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 18 sheets defined 23.9% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 2233 through 2245 removed outlier: 3.987A pdb=" N ARG A2242 " --> pdb=" O ALA A2238 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLN A2243 " --> pdb=" O TRP A2239 " (cutoff:3.500A) Processing helix chain 'A' and resid 2366 through 2391 removed outlier: 3.660A pdb=" N GLU A2371 " --> pdb=" O ILE A2367 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N GLU A2372 " --> pdb=" O VAL A2368 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A2377 " --> pdb=" O LYS A2373 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA A2378 " --> pdb=" O LEU A2374 " (cutoff:3.500A) Processing helix chain 'A' and resid 2503 through 2510 Processing helix chain 'A' and resid 2524 through 2533 Processing helix chain 'A' and resid 2554 through 2569 removed outlier: 3.504A pdb=" N SER A2559 " --> pdb=" O PRO A2555 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLU A2560 " --> pdb=" O SER A2556 " (cutoff:3.500A) Processing helix chain 'A' and resid 2667 through 2688 Processing helix chain 'A' and resid 2690 through 2695 Processing helix chain 'A' and resid 2695 through 2700 removed outlier: 3.722A pdb=" N LEU A2700 " --> pdb=" O LEU A2696 " (cutoff:3.500A) Processing helix chain 'A' and resid 2728 through 2733 Processing helix chain 'A' and resid 2763 through 2767 removed outlier: 3.791A pdb=" N GLU A2766 " --> pdb=" O PRO A2763 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A2767 " --> pdb=" O PHE A2764 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2763 through 2767' Processing helix chain 'A' and resid 2789 through 2822 removed outlier: 4.273A pdb=" N GLN A2795 " --> pdb=" O THR A2791 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLN A2796 " --> pdb=" O TYR A2792 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE A2797 " --> pdb=" O HIS A2793 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU A2804 " --> pdb=" O ILE A2800 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG A2805 " --> pdb=" O LYS A2801 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A2807 " --> pdb=" O ALA A2803 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS A2813 " --> pdb=" O GLU A2809 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU A2817 " --> pdb=" O LYS A2813 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE A2818 " --> pdb=" O MET A2814 " (cutoff:3.500A) Processing helix chain 'A' and resid 2833 through 2843 Processing helix chain 'A' and resid 2857 through 2861 Processing helix chain 'A' and resid 2909 through 2927 removed outlier: 3.547A pdb=" N ILE A2927 " --> pdb=" O TYR A2923 " (cutoff:3.500A) Processing helix chain 'A' and resid 3026 through 3038 removed outlier: 3.782A pdb=" N THR A3030 " --> pdb=" O SER A3026 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLU A3032 " --> pdb=" O LEU A3028 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A3036 " --> pdb=" O GLU A3032 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG A3037 " --> pdb=" O CYS A3033 " (cutoff:3.500A) Processing helix chain 'A' and resid 3041 through 3055 Processing helix chain 'A' and resid 3070 through 3082 Processing helix chain 'A' and resid 3249 through 3254 removed outlier: 3.706A pdb=" N GLU A3254 " --> pdb=" O PRO A3250 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 401 removed outlier: 3.577A pdb=" N THR B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 410 removed outlier: 4.107A pdb=" N SER B 406 " --> pdb=" O PRO B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 431 Processing helix chain 'C' and resid 126 through 131 Processing helix chain 'C' and resid 191 through 195 removed outlier: 4.031A pdb=" N THR C 195 " --> pdb=" O PRO C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 294 Processing helix chain 'C' and resid 342 through 346 Processing helix chain 'C' and resid 396 through 419 Processing sheet with id=AA1, first strand: chain 'A' and resid 2578 through 2579 removed outlier: 3.822A pdb=" N GLU A2578 " --> pdb=" O GLY A2589 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2607 through 2612 Processing sheet with id=AA3, first strand: chain 'A' and resid 2845 through 2853 removed outlier: 5.658A pdb=" N LEU A2846 " --> pdb=" O ALA A3009 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ALA A3009 " --> pdb=" O LEU A2846 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N HIS A2848 " --> pdb=" O GLN A3007 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN A2999 " --> pdb=" O TYR A3002 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N CYS A3004 " --> pdb=" O ALA A2997 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A2997 " --> pdb=" O CYS A3004 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A2993 " --> pdb=" O PHE A3008 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A2992 " --> pdb=" O ARG A2985 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 3093 through 3095 removed outlier: 3.843A pdb=" N VAL A3165 " --> pdb=" O TRP A3145 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TRP A3145 " --> pdb=" O VAL A3165 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 2 through 3 removed outlier: 6.689A pdb=" N ARG B 2 " --> pdb=" O ARG B 343 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N GLN B 345 " --> pdb=" O ARG B 2 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 9 through 13 removed outlier: 4.142A pdb=" N LYS B 377 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N SER B 366 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU B 357 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N CYS B 368 " --> pdb=" O ALA B 355 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ALA B 355 " --> pdb=" O CYS B 368 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 370 " --> pdb=" O PHE B 353 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N PHE B 353 " --> pdb=" O VAL B 370 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL B 372 " --> pdb=" O ARG B 351 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 23 through 26 Processing sheet with id=AA8, first strand: chain 'B' and resid 65 through 71 removed outlier: 6.846A pdb=" N VAL B 84 " --> pdb=" O THR B 66 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL B 68 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL B 82 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL B 70 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU B 80 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE B 119 " --> pdb=" O LEU B 92 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 131 through 133 removed outlier: 6.557A pdb=" N VAL B 152 " --> pdb=" O LYS B 176 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LYS B 176 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ALA B 154 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 186 through 187 Processing sheet with id=AB2, first strand: chain 'B' and resid 256 through 260 removed outlier: 3.686A pdb=" N THR B 284 " --> pdb=" O THR B 280 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU B 285 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER B 300 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU B 287 " --> pdb=" O LEU B 298 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 14 through 21 removed outlier: 6.876A pdb=" N ILE C 392 " --> pdb=" O ASP C 17 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N PHE C 19 " --> pdb=" O VAL C 390 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL C 390 " --> pdb=" O PHE C 19 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY C 389 " --> pdb=" O SER C 386 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL C 385 " --> pdb=" O LEU C 367 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 31 through 32 removed outlier: 4.076A pdb=" N VAL C 50 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 79 through 87 removed outlier: 5.585A pdb=" N ILE C 80 " --> pdb=" O ILE C 102 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE C 102 " --> pdb=" O ILE C 80 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 146 through 153 removed outlier: 8.874A pdb=" N THR C 159 " --> pdb=" O GLU C 175 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N GLU C 175 " --> pdb=" O THR C 159 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE C 161 " --> pdb=" O TYR C 173 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR C 173 " --> pdb=" O PHE C 161 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU C 172 " --> pdb=" O GLN C 185 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN C 181 " --> pdb=" O ASN C 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 201 through 208 removed outlier: 4.534A pdb=" N TYR C 225 " --> pdb=" O CYS C 221 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASP C 232 " --> pdb=" O VAL C 238 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N VAL C 238 " --> pdb=" O ASP C 232 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 250 through 256 removed outlier: 4.556A pdb=" N ASP C 297 " --> pdb=" O ARG C 288 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 310 through 316 removed outlier: 3.530A pdb=" N CYS C 312 " --> pdb=" O ALA C 329 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA C 329 " --> pdb=" O CYS C 312 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N CYS C 337 " --> pdb=" O LEU C 357 " (cutoff:3.500A) 396 hydrogen bonds defined for protein. 1092 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.67 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3181 1.34 - 1.46: 2182 1.46 - 1.58: 4369 1.58 - 1.70: 0 1.70 - 1.81: 71 Bond restraints: 9803 Sorted by residual: bond pdb=" CB PRO A2585 " pdb=" CG PRO A2585 " ideal model delta sigma weight residual 1.492 1.560 -0.068 5.00e-02 4.00e+02 1.84e+00 bond pdb=" CA VAL B 7 " pdb=" CB VAL B 7 " ideal model delta sigma weight residual 1.545 1.535 0.010 9.10e-03 1.21e+04 1.29e+00 bond pdb=" CA HIS A2690 " pdb=" C HIS A2690 " ideal model delta sigma weight residual 1.521 1.506 0.015 1.34e-02 5.57e+03 1.26e+00 bond pdb=" CB MET C 369 " pdb=" CG MET C 369 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.25e+00 bond pdb=" CA GLY C 165 " pdb=" C GLY C 165 " ideal model delta sigma weight residual 1.519 1.509 0.010 8.90e-03 1.26e+04 1.21e+00 ... (remaining 9798 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 13095 2.21 - 4.42: 221 4.42 - 6.63: 26 6.63 - 8.84: 8 8.84 - 11.05: 2 Bond angle restraints: 13352 Sorted by residual: angle pdb=" N GLU B 383 " pdb=" CA GLU B 383 " pdb=" C GLU B 383 " ideal model delta sigma weight residual 112.72 105.57 7.15 1.14e+00 7.69e-01 3.94e+01 angle pdb=" N HIS A3057 " pdb=" CA HIS A3057 " pdb=" C HIS A3057 " ideal model delta sigma weight residual 114.31 108.87 5.44 1.29e+00 6.01e-01 1.78e+01 angle pdb=" N ALA A2689 " pdb=" CA ALA A2689 " pdb=" C ALA A2689 " ideal model delta sigma weight residual 108.54 102.78 5.76 1.41e+00 5.03e-01 1.67e+01 angle pdb=" N TYR A2792 " pdb=" CA TYR A2792 " pdb=" C TYR A2792 " ideal model delta sigma weight residual 113.97 109.18 4.79 1.28e+00 6.10e-01 1.40e+01 angle pdb=" CB MET A2812 " pdb=" CG MET A2812 " pdb=" SD MET A2812 " ideal model delta sigma weight residual 112.70 123.75 -11.05 3.00e+00 1.11e-01 1.36e+01 ... (remaining 13347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 4976 17.79 - 35.58: 627 35.58 - 53.38: 138 53.38 - 71.17: 31 71.17 - 88.96: 12 Dihedral angle restraints: 5784 sinusoidal: 2014 harmonic: 3770 Sorted by residual: dihedral pdb=" CA ARG A2688 " pdb=" C ARG A2688 " pdb=" N ALA A2689 " pdb=" CA ALA A2689 " ideal model delta harmonic sigma weight residual 180.00 147.97 32.03 0 5.00e+00 4.00e-02 4.10e+01 dihedral pdb=" CA HIS A2690 " pdb=" C HIS A2690 " pdb=" N LEU A2691 " pdb=" CA LEU A2691 " ideal model delta harmonic sigma weight residual 180.00 153.43 26.57 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA LEU A2392 " pdb=" C LEU A2392 " pdb=" N PRO A2393 " pdb=" CA PRO A2393 " ideal model delta harmonic sigma weight residual 180.00 154.87 25.13 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 5781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 963 0.033 - 0.066: 392 0.066 - 0.100: 138 0.100 - 0.133: 65 0.133 - 0.166: 2 Chirality restraints: 1560 Sorted by residual: chirality pdb=" CG LEU A2609 " pdb=" CB LEU A2609 " pdb=" CD1 LEU A2609 " pdb=" CD2 LEU A2609 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.89e-01 chirality pdb=" CA PRO C 348 " pdb=" N PRO C 348 " pdb=" C PRO C 348 " pdb=" CB PRO C 348 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" CA VAL A3005 " pdb=" N VAL A3005 " pdb=" C VAL A3005 " pdb=" CB VAL A3005 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 1557 not shown) Planarity restraints: 1724 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A2691 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.73e+00 pdb=" C LEU A2691 " -0.041 2.00e-02 2.50e+03 pdb=" O LEU A2691 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE A2692 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A2584 " 0.035 5.00e-02 4.00e+02 5.18e-02 4.29e+00 pdb=" N PRO A2585 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A2585 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A2585 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A2599 " -0.033 5.00e-02 4.00e+02 5.10e-02 4.17e+00 pdb=" N PRO A2600 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A2600 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A2600 " -0.028 5.00e-02 4.00e+02 ... (remaining 1721 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 159 2.64 - 3.21: 8428 3.21 - 3.77: 14355 3.77 - 4.34: 19219 4.34 - 4.90: 32710 Nonbonded interactions: 74871 Sorted by model distance: nonbonded pdb=" OH TYR B 207 " pdb=" OD2 ASP B 295 " model vdw 2.078 3.040 nonbonded pdb=" OG SER A2550 " pdb=" OD1 ASP C 247 " model vdw 2.102 3.040 nonbonded pdb=" OG SER B 391 " pdb=" OD1 ASP C 17 " model vdw 2.112 3.040 nonbonded pdb=" O CYS B 205 " pdb=" OG1 THR B 245 " model vdw 2.149 3.040 nonbonded pdb=" O GLU B 321 " pdb=" NE2 HIS B 337 " model vdw 2.176 3.120 ... (remaining 74866 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 21.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.610 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 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 : 0.005 0.068 9803 Z= 0.208 Angle : 0.716 11.047 13352 Z= 0.389 Chirality : 0.043 0.166 1560 Planarity : 0.005 0.052 1724 Dihedral : 17.090 88.959 3330 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.11 % Favored : 92.57 % Rotamer: Outliers : 4.91 % Allowed : 28.68 % Favored : 66.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.24), residues: 1252 helix: 0.11 (0.32), residues: 299 sheet: -0.85 (0.25), residues: 427 loop : -1.68 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 153 TYR 0.014 0.001 TYR C 225 PHE 0.012 0.001 PHE A2552 TRP 0.013 0.002 TRP B 299 HIS 0.004 0.001 HIS A2690 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 9803) covalent geometry : angle 0.71630 (13352) hydrogen bonds : bond 0.16952 ( 396) hydrogen bonds : angle 7.45731 ( 1092) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 59 time to evaluate : 0.314 Fit side-chains REVERT: A 2814 MET cc_start: 0.5948 (tmm) cc_final: 0.5699 (tmm) REVERT: A 3034 ASP cc_start: 0.9195 (OUTLIER) cc_final: 0.8961 (p0) REVERT: A 3035 LYS cc_start: 0.8854 (mmmt) cc_final: 0.8628 (mmtm) REVERT: A 3123 MET cc_start: 0.8158 (mmp) cc_final: 0.7953 (mpm) REVERT: B 62 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.6519 (pm20) REVERT: B 149 ASP cc_start: 0.8443 (OUTLIER) cc_final: 0.8165 (p0) REVERT: B 268 THR cc_start: 0.6348 (OUTLIER) cc_final: 0.6003 (p) REVERT: C 298 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7734 (tt0) outliers start: 45 outliers final: 27 residues processed: 100 average time/residue: 0.3531 time to fit residues: 39.0667 Evaluate side-chains 86 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 54 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2525 VAL Chi-restraints excluded: chain A residue 2536 ILE Chi-restraints excluded: chain A residue 2572 THR Chi-restraints excluded: chain A residue 2607 HIS Chi-restraints excluded: chain A residue 2678 LEU Chi-restraints excluded: chain A residue 2808 LEU Chi-restraints excluded: chain A residue 2843 SER Chi-restraints excluded: chain A residue 2980 THR Chi-restraints excluded: chain A residue 3034 ASP Chi-restraints excluded: chain A residue 3091 ASN Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 214 TRP Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 298 GLN Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 318 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.2980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.0370 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.2980 chunk 55 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** 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 = 0.3890 r_free = 0.3890 target = 0.080991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.065863 restraints weight = 37136.552| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 3.81 r_work: 0.3392 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9803 Z= 0.125 Angle : 0.583 9.305 13352 Z= 0.293 Chirality : 0.042 0.157 1560 Planarity : 0.005 0.049 1724 Dihedral : 7.369 85.966 1412 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.87 % Favored : 92.81 % Rotamer: Outliers : 4.91 % Allowed : 28.90 % Favored : 66.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.24), residues: 1252 helix: 0.38 (0.31), residues: 302 sheet: -0.47 (0.25), residues: 424 loop : -1.66 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 153 TYR 0.012 0.001 TYR A2923 PHE 0.015 0.001 PHE A2552 TRP 0.013 0.001 TRP B 299 HIS 0.003 0.001 HIS C 391 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9803) covalent geometry : angle 0.58269 (13352) hydrogen bonds : bond 0.03577 ( 396) hydrogen bonds : angle 5.47023 ( 1092) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 64 time to evaluate : 0.259 Fit side-chains REVERT: A 2607 HIS cc_start: 0.8163 (OUTLIER) cc_final: 0.7857 (t70) REVERT: A 3034 ASP cc_start: 0.8825 (OUTLIER) cc_final: 0.8607 (p0) REVERT: B 62 GLN cc_start: 0.7106 (OUTLIER) cc_final: 0.6903 (pm20) REVERT: B 268 THR cc_start: 0.5935 (OUTLIER) cc_final: 0.5643 (p) REVERT: C 359 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.8322 (tt0) outliers start: 45 outliers final: 11 residues processed: 105 average time/residue: 0.3653 time to fit residues: 42.4759 Evaluate side-chains 69 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2536 ILE Chi-restraints excluded: chain A residue 2553 LEU Chi-restraints excluded: chain A residue 2607 HIS Chi-restraints excluded: chain A residue 3034 ASP Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 214 TRP Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 359 GLN Chi-restraints excluded: chain C residue 372 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 129 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 80 optimal weight: 0.0470 chunk 53 optimal weight: 0.0010 chunk 67 optimal weight: 0.5980 chunk 88 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.5084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.080901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.065805 restraints weight = 37289.799| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 3.79 r_work: 0.3387 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9803 Z= 0.124 Angle : 0.583 7.591 13352 Z= 0.289 Chirality : 0.042 0.154 1560 Planarity : 0.004 0.049 1724 Dihedral : 6.278 88.372 1381 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.99 % Favored : 93.69 % Rotamer: Outliers : 4.47 % Allowed : 30.64 % Favored : 64.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.24), residues: 1252 helix: 0.63 (0.31), residues: 300 sheet: -0.49 (0.25), residues: 423 loop : -1.53 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 153 TYR 0.010 0.001 TYR C 225 PHE 0.016 0.001 PHE A2552 TRP 0.011 0.001 TRP B 299 HIS 0.003 0.001 HIS C 391 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9803) covalent geometry : angle 0.58338 (13352) hydrogen bonds : bond 0.03293 ( 396) hydrogen bonds : angle 5.17571 ( 1092) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 63 time to evaluate : 0.348 Fit side-chains REVERT: A 2530 MET cc_start: 0.7845 (mtt) cc_final: 0.7644 (ttt) REVERT: A 2607 HIS cc_start: 0.8065 (OUTLIER) cc_final: 0.7786 (t70) REVERT: A 3035 LYS cc_start: 0.8580 (mppt) cc_final: 0.8239 (mmtm) REVERT: B 268 THR cc_start: 0.5946 (OUTLIER) cc_final: 0.5663 (p) REVERT: C 56 GLN cc_start: 0.8496 (tt0) cc_final: 0.8215 (tt0) REVERT: C 359 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8359 (tt0) REVERT: C 409 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.7194 (ptp-170) outliers start: 41 outliers final: 17 residues processed: 98 average time/residue: 0.3618 time to fit residues: 39.1237 Evaluate side-chains 78 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2525 VAL Chi-restraints excluded: chain A residue 2536 ILE Chi-restraints excluded: chain A residue 2572 THR Chi-restraints excluded: chain A residue 2607 HIS Chi-restraints excluded: chain A residue 2808 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 214 TRP Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 359 GLN Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 409 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 60 optimal weight: 0.6980 chunk 128 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 31 optimal weight: 0.2980 chunk 95 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 88 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** 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 = 0.3871 r_free = 0.3871 target = 0.080414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.065083 restraints weight = 37712.320| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 3.93 r_work: 0.3357 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9803 Z= 0.145 Angle : 0.595 9.296 13352 Z= 0.292 Chirality : 0.043 0.153 1560 Planarity : 0.004 0.048 1724 Dihedral : 5.455 57.256 1376 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.23 % Favored : 93.45 % Rotamer: Outliers : 4.80 % Allowed : 31.19 % Favored : 64.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.24), residues: 1252 helix: 0.79 (0.31), residues: 300 sheet: -0.40 (0.25), residues: 421 loop : -1.48 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A2528 TYR 0.012 0.001 TYR A3047 PHE 0.016 0.001 PHE A2552 TRP 0.010 0.001 TRP B 299 HIS 0.003 0.001 HIS A2690 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 9803) covalent geometry : angle 0.59534 (13352) hydrogen bonds : bond 0.03242 ( 396) hydrogen bonds : angle 5.09746 ( 1092) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 64 time to evaluate : 0.269 Fit side-chains REVERT: A 2607 HIS cc_start: 0.8076 (OUTLIER) cc_final: 0.7770 (t70) REVERT: A 2795 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.6929 (mp10) REVERT: A 3035 LYS cc_start: 0.8586 (mppt) cc_final: 0.8275 (mmtm) REVERT: B 268 THR cc_start: 0.6016 (OUTLIER) cc_final: 0.5726 (p) REVERT: C 31 LEU cc_start: 0.8867 (tp) cc_final: 0.8638 (tt) REVERT: C 56 GLN cc_start: 0.8533 (tt0) cc_final: 0.8240 (tt0) REVERT: C 359 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8329 (tt0) outliers start: 44 outliers final: 21 residues processed: 105 average time/residue: 0.3087 time to fit residues: 36.2015 Evaluate side-chains 82 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 57 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2525 VAL Chi-restraints excluded: chain A residue 2536 ILE Chi-restraints excluded: chain A residue 2553 LEU Chi-restraints excluded: chain A residue 2572 THR Chi-restraints excluded: chain A residue 2607 HIS Chi-restraints excluded: chain A residue 2795 GLN Chi-restraints excluded: chain A residue 2808 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 214 TRP Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 359 GLN Chi-restraints excluded: chain C residue 372 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 1 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** 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 = 0.3858 r_free = 0.3858 target = 0.079927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.064654 restraints weight = 38086.702| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 3.83 r_work: 0.3354 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9803 Z= 0.166 Angle : 0.605 8.097 13352 Z= 0.299 Chirality : 0.043 0.148 1560 Planarity : 0.004 0.048 1724 Dihedral : 5.515 57.866 1376 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.23 % Favored : 93.45 % Rotamer: Outliers : 4.80 % Allowed : 31.73 % Favored : 63.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.24), residues: 1252 helix: 0.82 (0.31), residues: 301 sheet: -0.38 (0.25), residues: 416 loop : -1.48 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2528 TYR 0.013 0.001 TYR A3047 PHE 0.016 0.001 PHE A2552 TRP 0.010 0.001 TRP B 299 HIS 0.003 0.001 HIS A2690 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 9803) covalent geometry : angle 0.60537 (13352) hydrogen bonds : bond 0.03333 ( 396) hydrogen bonds : angle 5.11605 ( 1092) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 59 time to evaluate : 0.265 Fit side-chains REVERT: A 2607 HIS cc_start: 0.8068 (OUTLIER) cc_final: 0.7775 (t70) REVERT: A 2795 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.6921 (mp10) REVERT: A 2987 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7679 (mp) REVERT: A 3035 LYS cc_start: 0.8586 (mppt) cc_final: 0.8222 (mmtt) REVERT: B 268 THR cc_start: 0.5909 (OUTLIER) cc_final: 0.5620 (p) REVERT: B 383 GLU cc_start: 0.8117 (pm20) cc_final: 0.7878 (pm20) REVERT: C 31 LEU cc_start: 0.8927 (tp) cc_final: 0.8699 (tt) REVERT: C 56 GLN cc_start: 0.8523 (tt0) cc_final: 0.8206 (tt0) REVERT: C 409 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7233 (ptp-170) outliers start: 44 outliers final: 22 residues processed: 100 average time/residue: 0.3446 time to fit residues: 37.9116 Evaluate side-chains 87 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 60 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2525 VAL Chi-restraints excluded: chain A residue 2536 ILE Chi-restraints excluded: chain A residue 2572 THR Chi-restraints excluded: chain A residue 2607 HIS Chi-restraints excluded: chain A residue 2678 LEU Chi-restraints excluded: chain A residue 2795 GLN Chi-restraints excluded: chain A residue 2808 LEU Chi-restraints excluded: chain A residue 2987 LEU Chi-restraints excluded: chain A residue 3053 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 214 TRP Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 409 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 93 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 59 optimal weight: 0.0020 chunk 53 optimal weight: 0.6980 chunk 116 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2243 GLN A3081 HIS ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.080543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.065354 restraints weight = 37695.050| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 3.80 r_work: 0.3378 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9803 Z= 0.132 Angle : 0.581 9.408 13352 Z= 0.285 Chirality : 0.042 0.156 1560 Planarity : 0.004 0.048 1724 Dihedral : 5.409 57.866 1376 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.91 % Favored : 93.85 % Rotamer: Outliers : 4.58 % Allowed : 31.52 % Favored : 63.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.24), residues: 1252 helix: 0.86 (0.30), residues: 307 sheet: -0.33 (0.25), residues: 416 loop : -1.50 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2528 TYR 0.011 0.001 TYR A3047 PHE 0.016 0.001 PHE A2552 TRP 0.011 0.001 TRP B 299 HIS 0.003 0.001 HIS C 391 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 9803) covalent geometry : angle 0.58088 (13352) hydrogen bonds : bond 0.03102 ( 396) hydrogen bonds : angle 5.01524 ( 1092) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 64 time to evaluate : 0.272 Fit side-chains REVERT: A 2579 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7933 (tm-30) REVERT: A 2607 HIS cc_start: 0.8063 (OUTLIER) cc_final: 0.7807 (t70) REVERT: A 2795 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.6984 (mp10) REVERT: A 2987 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7721 (mp) REVERT: A 3035 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8237 (mmtt) REVERT: B 268 THR cc_start: 0.6017 (OUTLIER) cc_final: 0.5733 (p) REVERT: C 56 GLN cc_start: 0.8553 (tt0) cc_final: 0.8230 (tt0) REVERT: C 150 GLU cc_start: 0.8068 (tt0) cc_final: 0.7523 (tp30) REVERT: C 156 GLN cc_start: 0.8596 (pt0) cc_final: 0.8330 (pm20) REVERT: C 409 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7260 (ptp-170) outliers start: 42 outliers final: 19 residues processed: 101 average time/residue: 0.4029 time to fit residues: 44.6413 Evaluate side-chains 86 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 60 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2525 VAL Chi-restraints excluded: chain A residue 2536 ILE Chi-restraints excluded: chain A residue 2553 LEU Chi-restraints excluded: chain A residue 2572 THR Chi-restraints excluded: chain A residue 2579 GLN Chi-restraints excluded: chain A residue 2607 HIS Chi-restraints excluded: chain A residue 2795 GLN Chi-restraints excluded: chain A residue 2808 LEU Chi-restraints excluded: chain A residue 2987 LEU Chi-restraints excluded: chain A residue 3035 LYS Chi-restraints excluded: chain A residue 3053 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 214 TRP Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 409 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 74 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 28 optimal weight: 0.0470 chunk 21 optimal weight: 0.3980 chunk 16 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 11 optimal weight: 0.0670 chunk 15 optimal weight: 0.0270 chunk 129 optimal weight: 3.9990 overall best weight: 0.3074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2243 GLN ** B 75 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 = 0.3901 r_free = 0.3901 target = 0.081616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.066577 restraints weight = 37028.597| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 3.93 r_work: 0.3406 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 9803 Z= 0.102 Angle : 0.580 11.228 13352 Z= 0.278 Chirality : 0.042 0.149 1560 Planarity : 0.004 0.049 1724 Dihedral : 5.214 57.266 1376 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.75 % Favored : 94.01 % Rotamer: Outliers : 4.36 % Allowed : 31.30 % Favored : 64.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.24), residues: 1252 helix: 0.99 (0.31), residues: 308 sheet: -0.18 (0.25), residues: 407 loop : -1.51 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2528 TYR 0.009 0.001 TYR C 225 PHE 0.014 0.001 PHE A2552 TRP 0.013 0.001 TRP B 299 HIS 0.003 0.000 HIS C 391 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 9803) covalent geometry : angle 0.57976 (13352) hydrogen bonds : bond 0.02818 ( 396) hydrogen bonds : angle 4.88568 ( 1092) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 70 time to evaluate : 0.300 Fit side-chains REVERT: A 2530 MET cc_start: 0.7794 (mmm) cc_final: 0.7311 (ttt) REVERT: A 2607 HIS cc_start: 0.8010 (OUTLIER) cc_final: 0.7709 (t70) REVERT: A 2795 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7009 (mp10) REVERT: A 3035 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8208 (mmtt) REVERT: B 268 THR cc_start: 0.5880 (OUTLIER) cc_final: 0.5606 (p) REVERT: C 45 THR cc_start: 0.9122 (OUTLIER) cc_final: 0.8747 (t) REVERT: C 56 GLN cc_start: 0.8574 (tt0) cc_final: 0.8255 (tt0) REVERT: C 150 GLU cc_start: 0.7999 (tt0) cc_final: 0.7470 (tp30) REVERT: C 156 GLN cc_start: 0.8556 (pt0) cc_final: 0.8311 (pm20) REVERT: C 409 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7221 (ptp-170) outliers start: 40 outliers final: 18 residues processed: 105 average time/residue: 0.3518 time to fit residues: 40.6698 Evaluate side-chains 84 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 60 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2521 VAL Chi-restraints excluded: chain A residue 2525 VAL Chi-restraints excluded: chain A residue 2536 ILE Chi-restraints excluded: chain A residue 2553 LEU Chi-restraints excluded: chain A residue 2572 THR Chi-restraints excluded: chain A residue 2607 HIS Chi-restraints excluded: chain A residue 2795 GLN Chi-restraints excluded: chain A residue 2808 LEU Chi-restraints excluded: chain A residue 3035 LYS Chi-restraints excluded: chain A residue 3053 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 409 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 111 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 3 optimal weight: 7.9990 chunk 86 optimal weight: 0.6980 chunk 129 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2243 GLN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** 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 = 0.3819 r_free = 0.3819 target = 0.077990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.062844 restraints weight = 38522.680| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 3.70 r_work: 0.3309 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 9803 Z= 0.331 Angle : 0.748 10.315 13352 Z= 0.372 Chirality : 0.047 0.156 1560 Planarity : 0.005 0.066 1724 Dihedral : 5.835 59.221 1374 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.83 % Favored : 91.93 % Rotamer: Outliers : 4.69 % Allowed : 31.52 % Favored : 63.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.24), residues: 1252 helix: 0.87 (0.31), residues: 297 sheet: -0.68 (0.25), residues: 418 loop : -1.44 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A2528 TYR 0.025 0.002 TYR A3047 PHE 0.023 0.002 PHE A2561 TRP 0.013 0.002 TRP B 214 HIS 0.006 0.001 HIS A2793 Details of bonding type rmsd covalent geometry : bond 0.00750 ( 9803) covalent geometry : angle 0.74808 (13352) hydrogen bonds : bond 0.04226 ( 396) hydrogen bonds : angle 5.48836 ( 1092) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 57 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 2579 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.8026 (tm-30) REVERT: A 2795 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.6918 (mp10) REVERT: B 268 THR cc_start: 0.5876 (OUTLIER) cc_final: 0.5546 (p) REVERT: C 56 GLN cc_start: 0.8435 (tt0) cc_final: 0.8165 (tt0) REVERT: C 156 GLN cc_start: 0.8672 (pt0) cc_final: 0.8391 (pm20) outliers start: 43 outliers final: 24 residues processed: 94 average time/residue: 0.3721 time to fit residues: 38.6265 Evaluate side-chains 85 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 58 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2521 VAL Chi-restraints excluded: chain A residue 2525 VAL Chi-restraints excluded: chain A residue 2536 ILE Chi-restraints excluded: chain A residue 2572 THR Chi-restraints excluded: chain A residue 2579 GLN Chi-restraints excluded: chain A residue 2678 LEU Chi-restraints excluded: chain A residue 2795 GLN Chi-restraints excluded: chain A residue 2808 LEU Chi-restraints excluded: chain A residue 2846 LEU Chi-restraints excluded: chain A residue 3035 LYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 214 TRP Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 409 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 23 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 96 optimal weight: 0.0020 chunk 22 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.080386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.065411 restraints weight = 37611.502| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 3.69 r_work: 0.3379 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9803 Z= 0.135 Angle : 0.633 11.374 13352 Z= 0.303 Chirality : 0.043 0.166 1560 Planarity : 0.004 0.060 1724 Dihedral : 5.093 50.455 1371 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.39 % Favored : 93.37 % Rotamer: Outliers : 3.49 % Allowed : 32.72 % Favored : 63.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.24), residues: 1252 helix: 0.99 (0.31), residues: 304 sheet: -0.43 (0.25), residues: 408 loop : -1.48 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2379 TYR 0.010 0.001 TYR A3047 PHE 0.017 0.001 PHE A2561 TRP 0.015 0.001 TRP B 299 HIS 0.003 0.001 HIS C 391 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9803) covalent geometry : angle 0.63268 (13352) hydrogen bonds : bond 0.03189 ( 396) hydrogen bonds : angle 5.13646 ( 1092) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 60 time to evaluate : 0.404 Fit side-chains REVERT: A 2795 GLN cc_start: 0.7456 (OUTLIER) cc_final: 0.6782 (mp10) REVERT: A 3035 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8200 (mmtt) REVERT: B 268 THR cc_start: 0.5881 (OUTLIER) cc_final: 0.5595 (p) REVERT: C 56 GLN cc_start: 0.8547 (tt0) cc_final: 0.8197 (tt0) REVERT: C 156 GLN cc_start: 0.8609 (pt0) cc_final: 0.8361 (pm20) REVERT: C 409 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7283 (ptp-170) outliers start: 32 outliers final: 19 residues processed: 86 average time/residue: 0.3699 time to fit residues: 35.0867 Evaluate side-chains 79 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 56 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2521 VAL Chi-restraints excluded: chain A residue 2525 VAL Chi-restraints excluded: chain A residue 2536 ILE Chi-restraints excluded: chain A residue 2572 THR Chi-restraints excluded: chain A residue 2795 GLN Chi-restraints excluded: chain A residue 2808 LEU Chi-restraints excluded: chain A residue 3035 LYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 409 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 86 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 46 optimal weight: 0.0370 chunk 70 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 96 optimal weight: 0.0270 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 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 = 0.3886 r_free = 0.3886 target = 0.080922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.065977 restraints weight = 37351.008| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 3.71 r_work: 0.3394 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9803 Z= 0.127 Angle : 0.636 13.134 13352 Z= 0.301 Chirality : 0.043 0.202 1560 Planarity : 0.004 0.059 1724 Dihedral : 4.920 49.890 1371 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.47 % Favored : 93.29 % Rotamer: Outliers : 2.29 % Allowed : 33.81 % Favored : 63.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.24), residues: 1252 helix: 1.04 (0.31), residues: 304 sheet: -0.37 (0.25), residues: 412 loop : -1.42 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 153 TYR 0.010 0.001 TYR A3047 PHE 0.018 0.001 PHE A2561 TRP 0.016 0.001 TRP B 214 HIS 0.003 0.001 HIS C 391 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9803) covalent geometry : angle 0.63573 (13352) hydrogen bonds : bond 0.03020 ( 396) hydrogen bonds : angle 4.99983 ( 1092) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 0.326 Fit side-chains REVERT: A 2795 GLN cc_start: 0.7463 (OUTLIER) cc_final: 0.6828 (mp10) REVERT: A 3035 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8206 (mmtt) REVERT: B 268 THR cc_start: 0.5848 (OUTLIER) cc_final: 0.5584 (p) REVERT: C 56 GLN cc_start: 0.8553 (tt0) cc_final: 0.8222 (tt0) REVERT: C 156 GLN cc_start: 0.8575 (pt0) cc_final: 0.8361 (pm20) REVERT: C 409 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7252 (ptp-170) outliers start: 21 outliers final: 16 residues processed: 80 average time/residue: 0.3954 time to fit residues: 34.8827 Evaluate side-chains 79 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2525 VAL Chi-restraints excluded: chain A residue 2536 ILE Chi-restraints excluded: chain A residue 2572 THR Chi-restraints excluded: chain A residue 2795 GLN Chi-restraints excluded: chain A residue 2808 LEU Chi-restraints excluded: chain A residue 3035 LYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 409 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 110 optimal weight: 0.5980 chunk 50 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 117 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 0.0470 chunk 123 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 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 = 0.3882 r_free = 0.3882 target = 0.080964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.065829 restraints weight = 37566.912| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 3.80 r_work: 0.3385 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9803 Z= 0.136 Angle : 0.641 13.899 13352 Z= 0.304 Chirality : 0.043 0.212 1560 Planarity : 0.004 0.057 1724 Dihedral : 4.884 49.971 1371 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.39 % Favored : 93.37 % Rotamer: Outliers : 3.16 % Allowed : 32.93 % Favored : 63.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.24), residues: 1252 helix: 0.99 (0.31), residues: 308 sheet: -0.38 (0.25), residues: 418 loop : -1.48 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2379 TYR 0.011 0.001 TYR A3047 PHE 0.013 0.001 PHE A2552 TRP 0.022 0.001 TRP A2529 HIS 0.003 0.001 HIS C 391 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9803) covalent geometry : angle 0.64083 (13352) hydrogen bonds : bond 0.03095 ( 396) hydrogen bonds : angle 4.98792 ( 1092) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3455.98 seconds wall clock time: 59 minutes 24.44 seconds (3564.44 seconds total)