Starting phenix.real_space_refine on Mon Jul 28 20:26:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7a5r_11648/07_2025/7a5r_11648.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a5r_11648/07_2025/7a5r_11648.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7a5r_11648/07_2025/7a5r_11648.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a5r_11648/07_2025/7a5r_11648.map" model { file = "/net/cci-nas-00/data/ceres_data/7a5r_11648/07_2025/7a5r_11648.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a5r_11648/07_2025/7a5r_11648.cif" } resolution = 3.7 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: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 6760 2.51 5 N 1748 2.21 5 O 2060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 114 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10608 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2113 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 17, 'TRANS': 246} Chain breaks: 4 Chain: "M" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1568 Classifications: {'peptide': 202} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 190} Chain breaks: 2 Chain: "I" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1595 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 198} Chain breaks: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: L, B, H, D Time building chain proxies: 7.19, per 1000 atoms: 0.68 Number of scatterers: 10608 At special positions: 0 Unit cell: (138.049, 166.311, 71.742, 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 40 16.00 O 2060 8.00 N 1748 7.00 C 6760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG C 1 " - " ASN A 343 " " NAG D 1 " - " ASN B 343 " Time building additional restraints: 2.51 Conformation dependent library (CDL) restraints added in 1.1 seconds 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 30 sheets defined 6.8% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'H' and resid 160 through 162 No H-bonds generated for 'chain 'H' and resid 160 through 162' Processing helix chain 'L' and resid 127 through 134 removed outlier: 3.689A pdb=" N LEU L 131 " --> pdb=" O SER L 127 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS L 132 " --> pdb=" O ASP L 128 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER L 133 " --> pdb=" O GLU L 129 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY L 134 " --> pdb=" O GLN L 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 127 through 134' Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 369 removed outlier: 3.964A pdb=" N LEU A 368 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 369' Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.237A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.759A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.783A pdb=" N ASP A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 369 removed outlier: 3.964A pdb=" N LEU B 368 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 369' Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.238A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.758A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.783A pdb=" N ASP B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 134 removed outlier: 3.690A pdb=" N LEU M 131 " --> pdb=" O SER M 127 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS M 132 " --> pdb=" O ASP M 128 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER M 133 " --> pdb=" O GLU M 129 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY M 134 " --> pdb=" O GLN M 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 127 through 134' Processing helix chain 'I' and resid 160 through 162 No H-bonds generated for 'chain 'I' and resid 160 through 162' Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.749A pdb=" N GLU H 10 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR H 116 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.749A pdb=" N GLU H 10 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR H 116 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL H 108 " --> pdb=" O GLY H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 124 through 128 removed outlier: 4.342A pdb=" N GLY H 143 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS H 144 " --> pdb=" O SER H 184 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER H 184 " --> pdb=" O CYS H 144 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP H 148 " --> pdb=" O TYR H 180 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR H 180 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 155 through 158 removed outlier: 4.747A pdb=" N TYR H 198 " --> pdb=" O VAL H 215 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.247A pdb=" N LEU L 11 " --> pdb=" O GLU L 111 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 30 through 31 removed outlier: 3.772A pdb=" N LYS L 36 " --> pdb=" O TYR L 31 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 120 through 124 removed outlier: 3.879A pdb=" N SER L 120 " --> pdb=" O ASN L 143 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN L 143 " --> pdb=" O SER L 120 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 150 through 156 removed outlier: 3.637A pdb=" N TYR L 198 " --> pdb=" O PHE L 215 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.512A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 277 " --> pdb=" O HIS A 49 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AB4, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.912A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB6, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB7, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.512A pdb=" N HIS B 49 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 277 " --> pdb=" O HIS B 49 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AB9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.912A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC3, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.247A pdb=" N LEU M 11 " --> pdb=" O GLU M 111 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TRP M 41 " --> pdb=" O LEU M 53 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 30 through 31 removed outlier: 3.773A pdb=" N LYS M 36 " --> pdb=" O TYR M 31 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 120 through 124 removed outlier: 3.879A pdb=" N SER M 120 " --> pdb=" O ASN M 143 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN M 143 " --> pdb=" O SER M 120 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 150 through 156 removed outlier: 3.637A pdb=" N TYR M 198 " --> pdb=" O PHE M 215 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AC9, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.749A pdb=" N GLU I 10 " --> pdb=" O THR I 114 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR I 116 " --> pdb=" O GLU I 10 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.749A pdb=" N GLU I 10 " --> pdb=" O THR I 114 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR I 116 " --> pdb=" O GLU I 10 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL I 108 " --> pdb=" O GLY I 98 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 124 through 128 removed outlier: 4.343A pdb=" N GLY I 143 " --> pdb=" O LEU I 128 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS I 144 " --> pdb=" O SER I 184 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER I 184 " --> pdb=" O CYS I 144 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP I 148 " --> pdb=" O TYR I 180 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR I 180 " --> pdb=" O ASP I 148 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 155 through 158 removed outlier: 4.747A pdb=" N TYR I 198 " --> pdb=" O VAL I 215 " (cutoff:3.500A) 322 hydrogen bonds defined for protein. 792 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: 2.94 Time building geometry restraints manager: 2.98 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: 3324 1.34 - 1.46: 2768 1.46 - 1.58: 4730 1.58 - 1.70: 0 1.70 - 1.82: 48 Bond restraints: 10870 Sorted by residual: bond pdb=" N LEU H 174 " pdb=" CA LEU H 174 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.24e-02 6.50e+03 5.14e+00 bond pdb=" N LEU I 174 " pdb=" CA LEU I 174 " ideal model delta sigma weight residual 1.458 1.484 -0.027 1.24e-02 6.50e+03 4.60e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.53e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.44e+00 bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.13e+00 ... (remaining 10865 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 14062 1.68 - 3.36: 608 3.36 - 5.05: 92 5.05 - 6.73: 14 6.73 - 8.41: 10 Bond angle restraints: 14786 Sorted by residual: angle pdb=" C ASN B 370 " pdb=" CA ASN B 370 " pdb=" CB ASN B 370 " ideal model delta sigma weight residual 111.91 116.08 -4.17 1.52e+00 4.33e-01 7.53e+00 angle pdb=" CA ILE M 2 " pdb=" CB ILE M 2 " pdb=" CG1 ILE M 2 " ideal model delta sigma weight residual 110.40 115.06 -4.66 1.70e+00 3.46e-01 7.51e+00 angle pdb=" CA ILE L 2 " pdb=" CB ILE L 2 " pdb=" CG1 ILE L 2 " ideal model delta sigma weight residual 110.40 115.04 -4.64 1.70e+00 3.46e-01 7.45e+00 angle pdb=" C ASN A 370 " pdb=" CA ASN A 370 " pdb=" CB ASN A 370 " ideal model delta sigma weight residual 111.91 116.05 -4.14 1.52e+00 4.33e-01 7.42e+00 angle pdb=" C TYR M 146 " pdb=" N PRO M 147 " pdb=" CA PRO M 147 " ideal model delta sigma weight residual 127.00 133.25 -6.25 2.40e+00 1.74e-01 6.78e+00 ... (remaining 14781 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 5873 17.87 - 35.75: 471 35.75 - 53.62: 102 53.62 - 71.49: 22 71.49 - 89.37: 6 Dihedral angle restraints: 6474 sinusoidal: 2536 harmonic: 3938 Sorted by residual: dihedral pdb=" CA LEU L 141 " pdb=" C LEU L 141 " pdb=" N LEU L 142 " pdb=" CA LEU L 142 " ideal model delta harmonic sigma weight residual 180.00 158.75 21.25 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA LEU M 141 " pdb=" C LEU M 141 " pdb=" N LEU M 142 " pdb=" CA LEU M 142 " ideal model delta harmonic sigma weight residual 180.00 158.75 21.25 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA ALA B 363 " pdb=" C ALA B 363 " pdb=" N ASP B 364 " pdb=" CA ASP B 364 " ideal model delta harmonic sigma weight residual 180.00 159.90 20.10 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 6471 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 964 0.035 - 0.069: 406 0.069 - 0.104: 190 0.104 - 0.138: 83 0.138 - 0.173: 9 Chirality restraints: 1652 Sorted by residual: chirality pdb=" CB ILE L 34 " pdb=" CA ILE L 34 " pdb=" CG1 ILE L 34 " pdb=" CG2 ILE L 34 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.44e-01 chirality pdb=" CB ILE M 34 " pdb=" CA ILE M 34 " pdb=" CG1 ILE M 34 " pdb=" CG2 ILE M 34 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 7.08e-01 chirality pdb=" CB THR I 91 " pdb=" CA THR I 91 " pdb=" OG1 THR I 91 " pdb=" CG2 THR I 91 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.31e-01 ... (remaining 1649 not shown) Planarity restraints: 1884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 152 " 0.034 5.00e-02 4.00e+02 5.12e-02 4.19e+00 pdb=" N PRO H 153 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO H 153 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO H 153 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU I 152 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO I 153 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO I 153 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO I 153 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 512 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.07e+00 pdb=" C VAL B 512 " 0.030 2.00e-02 2.50e+03 pdb=" O VAL B 512 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU B 513 " -0.010 2.00e-02 2.50e+03 ... (remaining 1881 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 60 2.60 - 3.18: 8633 3.18 - 3.75: 13894 3.75 - 4.33: 19421 4.33 - 4.90: 34168 Nonbonded interactions: 76176 Sorted by model distance: nonbonded pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " model vdw 2.033 3.760 ... (remaining 76171 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: 0.05 Found NCS groups: ncs_group { reference = chain 'M' selection = chain 'L' } ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'I' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.870 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 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 : 0.004 0.038 10874 Z= 0.187 Angle : 0.811 8.411 14798 Z= 0.437 Chirality : 0.050 0.173 1652 Planarity : 0.005 0.051 1882 Dihedral : 14.013 89.368 3954 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.59 % Favored : 92.26 % Rotamer: Outliers : 0.67 % Allowed : 6.13 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.22), residues: 1318 helix: -2.70 (0.69), residues: 52 sheet: 0.16 (0.24), residues: 482 loop : -2.31 (0.19), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 83 HIS 0.002 0.001 HIS L 204 PHE 0.017 0.002 PHE H 29 TYR 0.019 0.002 TYR B 351 ARG 0.005 0.001 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00025 ( 2) link_NAG-ASN : angle 2.39084 ( 6) link_BETA1-4 : bond 0.00256 ( 2) link_BETA1-4 : angle 1.30712 ( 6) hydrogen bonds : bond 0.14114 ( 314) hydrogen bonds : angle 8.09289 ( 792) covalent geometry : bond 0.00407 (10870) covalent geometry : angle 0.80927 (14786) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 177 time to evaluate : 1.114 Fit side-chains REVERT: H 142 LEU cc_start: 0.7623 (pp) cc_final: 0.7406 (pp) REVERT: L 132 LYS cc_start: 0.8278 (mttt) cc_final: 0.8055 (pttm) REVERT: M 51 LYS cc_start: 0.8025 (mttt) cc_final: 0.7779 (tttm) REVERT: M 132 LYS cc_start: 0.7935 (mttt) cc_final: 0.7720 (pttm) REVERT: I 6 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8179 (mt0) REVERT: I 38 ARG cc_start: 0.8999 (ptm-80) cc_final: 0.8687 (ptm-80) REVERT: I 142 LEU cc_start: 0.7429 (pp) cc_final: 0.7228 (pp) outliers start: 8 outliers final: 4 residues processed: 179 average time/residue: 0.2772 time to fit residues: 66.1824 Evaluate side-chains 121 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 116 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain I residue 6 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 34 optimal weight: 0.0170 chunk 68 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN H 77 ASN L 6 GLN L 44 GLN L 106 GLN A 49 HIS A 271 GLN A 493 GLN B 271 GLN B 493 GLN M 6 GLN M 44 GLN M 106 GLN I 6 GLN I 77 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.135233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.118909 restraints weight = 16566.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.120215 restraints weight = 13384.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.121207 restraints weight = 11407.209| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10874 Z= 0.160 Angle : 0.686 8.262 14798 Z= 0.354 Chirality : 0.046 0.142 1652 Planarity : 0.005 0.041 1882 Dihedral : 5.962 55.782 1553 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.10 % Allowed : 8.74 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.22), residues: 1318 helix: -3.80 (0.60), residues: 40 sheet: 0.44 (0.23), residues: 508 loop : -2.00 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 83 HIS 0.004 0.001 HIS I 204 PHE 0.018 0.002 PHE L 122 TYR 0.015 0.002 TYR I 180 ARG 0.003 0.001 ARG A 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00083 ( 2) link_NAG-ASN : angle 1.68722 ( 6) link_BETA1-4 : bond 0.00222 ( 2) link_BETA1-4 : angle 0.95002 ( 6) hydrogen bonds : bond 0.04170 ( 314) hydrogen bonds : angle 6.58477 ( 792) covalent geometry : bond 0.00386 (10870) covalent geometry : angle 0.68497 (14786) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 1.132 Fit side-chains REVERT: H 142 LEU cc_start: 0.7425 (pp) cc_final: 0.7171 (pp) REVERT: H 201 ASN cc_start: 0.7653 (OUTLIER) cc_final: 0.7301 (m-40) REVERT: A 336 CYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7781 (m) REVERT: A 471 GLU cc_start: 0.4972 (OUTLIER) cc_final: 0.4455 (tp30) REVERT: A 489 TYR cc_start: 0.8825 (m-80) cc_final: 0.8596 (m-80) REVERT: B 471 GLU cc_start: 0.4774 (OUTLIER) cc_final: 0.4348 (tp30) REVERT: M 51 LYS cc_start: 0.8097 (mttt) cc_final: 0.7769 (tttm) REVERT: M 149 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7618 (tm-30) REVERT: I 142 LEU cc_start: 0.7371 (pp) cc_final: 0.7151 (pp) outliers start: 25 outliers final: 14 residues processed: 137 average time/residue: 0.2555 time to fit residues: 48.3024 Evaluate side-chains 123 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 215 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 184 SER Chi-restraints excluded: chain I residue 201 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 124 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 68 optimal weight: 0.3980 chunk 98 optimal weight: 0.9990 chunk 6 optimal weight: 0.0060 chunk 119 optimal weight: 0.0060 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.3612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN A 422 ASN A 493 GLN B 422 ASN B 493 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.136013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.121596 restraints weight = 16863.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.121799 restraints weight = 15521.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.121935 restraints weight = 13994.564| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10874 Z= 0.110 Angle : 0.584 7.565 14798 Z= 0.298 Chirality : 0.044 0.151 1652 Planarity : 0.004 0.041 1882 Dihedral : 5.170 37.953 1546 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.69 % Allowed : 11.18 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.22), residues: 1318 helix: -4.03 (0.56), residues: 40 sheet: 0.59 (0.23), residues: 512 loop : -1.78 (0.20), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 83 HIS 0.002 0.001 HIS H 168 PHE 0.009 0.001 PHE L 122 TYR 0.011 0.001 TYR L 55 ARG 0.003 0.000 ARG A 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00166 ( 2) link_NAG-ASN : angle 1.20963 ( 6) link_BETA1-4 : bond 0.00475 ( 2) link_BETA1-4 : angle 0.94338 ( 6) hydrogen bonds : bond 0.03425 ( 314) hydrogen bonds : angle 5.90630 ( 792) covalent geometry : bond 0.00257 (10870) covalent geometry : angle 0.58388 (14786) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 1.235 Fit side-chains REVERT: H 142 LEU cc_start: 0.7448 (pp) cc_final: 0.7225 (pp) REVERT: H 201 ASN cc_start: 0.7627 (OUTLIER) cc_final: 0.7353 (m-40) REVERT: A 471 GLU cc_start: 0.4929 (OUTLIER) cc_final: 0.4498 (tp30) REVERT: B 471 GLU cc_start: 0.4929 (OUTLIER) cc_final: 0.4491 (tp30) REVERT: M 51 LYS cc_start: 0.8040 (mttt) cc_final: 0.7768 (tttm) REVERT: M 149 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7428 (tm-30) REVERT: M 155 LYS cc_start: 0.7354 (mmmt) cc_final: 0.6963 (mmmt) REVERT: I 67 GLN cc_start: 0.8444 (mm-40) cc_final: 0.7498 (mt0) REVERT: I 142 LEU cc_start: 0.7375 (pp) cc_final: 0.7136 (pp) outliers start: 32 outliers final: 19 residues processed: 147 average time/residue: 0.2470 time to fit residues: 50.3729 Evaluate side-chains 127 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 215 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 184 SER Chi-restraints excluded: chain I residue 201 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 37 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 57 optimal weight: 0.0870 chunk 129 optimal weight: 0.0470 chunk 49 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN M 95 GLN M 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.132745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.118221 restraints weight = 16857.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.118297 restraints weight = 15705.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.118501 restraints weight = 14456.733| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10874 Z= 0.137 Angle : 0.593 7.622 14798 Z= 0.302 Chirality : 0.044 0.150 1652 Planarity : 0.004 0.041 1882 Dihedral : 4.927 39.166 1546 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.28 % Allowed : 13.45 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.22), residues: 1318 helix: -4.18 (0.56), residues: 40 sheet: 0.68 (0.23), residues: 514 loop : -1.81 (0.20), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.003 0.001 HIS H 168 PHE 0.014 0.002 PHE L 122 TYR 0.014 0.001 TYR I 180 ARG 0.003 0.000 ARG L 60 Details of bonding type rmsd link_NAG-ASN : bond 0.00066 ( 2) link_NAG-ASN : angle 1.33596 ( 6) link_BETA1-4 : bond 0.00172 ( 2) link_BETA1-4 : angle 0.74280 ( 6) hydrogen bonds : bond 0.03462 ( 314) hydrogen bonds : angle 5.74016 ( 792) covalent geometry : bond 0.00336 (10870) covalent geometry : angle 0.59280 (14786) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 109 time to evaluate : 1.285 Fit side-chains REVERT: H 2 MET cc_start: 0.7214 (OUTLIER) cc_final: 0.5794 (ppp) REVERT: H 142 LEU cc_start: 0.7401 (pp) cc_final: 0.7179 (pp) REVERT: H 201 ASN cc_start: 0.7693 (OUTLIER) cc_final: 0.7423 (m-40) REVERT: L 149 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7351 (tm-30) REVERT: A 471 GLU cc_start: 0.4915 (OUTLIER) cc_final: 0.4383 (tp30) REVERT: B 471 GLU cc_start: 0.4744 (OUTLIER) cc_final: 0.4330 (tp30) REVERT: M 51 LYS cc_start: 0.8118 (mttt) cc_final: 0.7837 (tttm) REVERT: M 149 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7468 (tm-30) REVERT: M 155 LYS cc_start: 0.7271 (mmmt) cc_final: 0.6920 (mmmt) REVERT: I 2 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.6252 (ppp) REVERT: I 67 GLN cc_start: 0.8539 (mm-40) cc_final: 0.7655 (mt0) outliers start: 39 outliers final: 28 residues processed: 138 average time/residue: 0.2335 time to fit residues: 45.7980 Evaluate side-chains 138 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 105 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 MET Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 215 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 181 LEU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain I residue 2 MET Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 184 SER Chi-restraints excluded: chain I residue 201 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 81 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 14 optimal weight: 0.3980 chunk 109 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 61 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN B 542 ASN ** M 204 HIS ** 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 = 0.3579 r_free = 0.3579 target = 0.131738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.117370 restraints weight = 16774.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.117437 restraints weight = 15510.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.117636 restraints weight = 14500.460| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10874 Z= 0.138 Angle : 0.578 8.014 14798 Z= 0.295 Chirality : 0.044 0.148 1652 Planarity : 0.004 0.042 1882 Dihedral : 4.839 39.150 1546 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.03 % Allowed : 13.78 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.22), residues: 1318 helix: -4.24 (0.57), residues: 40 sheet: 0.70 (0.23), residues: 514 loop : -1.83 (0.20), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.003 0.001 HIS I 204 PHE 0.013 0.001 PHE L 122 TYR 0.013 0.001 TYR H 180 ARG 0.002 0.000 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00139 ( 2) link_NAG-ASN : angle 1.26465 ( 6) link_BETA1-4 : bond 0.00298 ( 2) link_BETA1-4 : angle 0.71941 ( 6) hydrogen bonds : bond 0.03408 ( 314) hydrogen bonds : angle 5.65152 ( 792) covalent geometry : bond 0.00339 (10870) covalent geometry : angle 0.57772 (14786) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 113 time to evaluate : 1.124 Fit side-chains REVERT: H 2 MET cc_start: 0.7393 (OUTLIER) cc_final: 0.6126 (ppp) REVERT: H 67 GLN cc_start: 0.8701 (mm110) cc_final: 0.8464 (mm110) REVERT: H 142 LEU cc_start: 0.7395 (pp) cc_final: 0.7187 (pp) REVERT: H 201 ASN cc_start: 0.7694 (OUTLIER) cc_final: 0.7457 (m-40) REVERT: L 31 TYR cc_start: 0.8407 (OUTLIER) cc_final: 0.7290 (t80) REVERT: L 149 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7416 (tm-30) REVERT: A 471 GLU cc_start: 0.5020 (OUTLIER) cc_final: 0.4452 (tp30) REVERT: B 471 GLU cc_start: 0.4691 (OUTLIER) cc_final: 0.4272 (tp30) REVERT: M 31 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.6512 (t80) REVERT: M 51 LYS cc_start: 0.8090 (mttt) cc_final: 0.7779 (tttm) REVERT: M 149 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7361 (tm-30) REVERT: M 155 LYS cc_start: 0.7166 (mmmt) cc_final: 0.6857 (mmmt) REVERT: I 2 MET cc_start: 0.7630 (OUTLIER) cc_final: 0.6288 (ppp) REVERT: I 67 GLN cc_start: 0.8588 (mm-40) cc_final: 0.7738 (mt0) REVERT: I 142 LEU cc_start: 0.7481 (pp) cc_final: 0.7218 (pp) outliers start: 48 outliers final: 28 residues processed: 151 average time/residue: 0.2247 time to fit residues: 48.0242 Evaluate side-chains 141 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 106 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 MET Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 215 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 31 TYR Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 181 LEU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain I residue 2 MET Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 184 SER Chi-restraints excluded: chain I residue 201 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 7 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 10 optimal weight: 0.0980 chunk 2 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 40 optimal weight: 0.0050 chunk 64 optimal weight: 0.4980 chunk 4 optimal weight: 0.8980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 130 GLN A 493 GLN A 542 ASN ** M 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.132030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.117342 restraints weight = 16854.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.117416 restraints weight = 15841.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.117582 restraints weight = 14691.801| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10874 Z= 0.123 Angle : 0.569 7.712 14798 Z= 0.290 Chirality : 0.044 0.185 1652 Planarity : 0.004 0.042 1882 Dihedral : 4.759 38.767 1546 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.19 % Allowed : 15.71 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.22), residues: 1318 helix: -4.30 (0.54), residues: 40 sheet: 0.73 (0.23), residues: 514 loop : -1.79 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.002 0.001 HIS I 168 PHE 0.011 0.001 PHE H 126 TYR 0.012 0.001 TYR L 55 ARG 0.002 0.000 ARG B 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00150 ( 2) link_NAG-ASN : angle 1.20589 ( 6) link_BETA1-4 : bond 0.00366 ( 2) link_BETA1-4 : angle 0.77917 ( 6) hydrogen bonds : bond 0.03256 ( 314) hydrogen bonds : angle 5.57619 ( 792) covalent geometry : bond 0.00299 (10870) covalent geometry : angle 0.56889 (14786) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 112 time to evaluate : 1.273 Fit side-chains REVERT: H 2 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.6184 (ppp) REVERT: H 22 CYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8873 (t) REVERT: H 67 GLN cc_start: 0.8642 (mm110) cc_final: 0.8434 (mm110) REVERT: L 31 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.7249 (t80) REVERT: L 149 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7419 (tm-30) REVERT: A 471 GLU cc_start: 0.5001 (OUTLIER) cc_final: 0.4498 (tp30) REVERT: B 471 GLU cc_start: 0.4933 (OUTLIER) cc_final: 0.4559 (tp30) REVERT: M 31 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.6476 (t80) REVERT: M 51 LYS cc_start: 0.8093 (mttt) cc_final: 0.7836 (tttm) REVERT: M 149 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7285 (tm-30) REVERT: M 155 LYS cc_start: 0.7152 (mmmt) cc_final: 0.6925 (mmmt) REVERT: I 2 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.6252 (ppp) REVERT: I 16 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7233 (mt-10) REVERT: I 22 CYS cc_start: 0.9260 (OUTLIER) cc_final: 0.8886 (t) REVERT: I 67 GLN cc_start: 0.8526 (mm-40) cc_final: 0.7757 (mt0) REVERT: I 142 LEU cc_start: 0.7496 (pp) cc_final: 0.7282 (pp) outliers start: 38 outliers final: 25 residues processed: 141 average time/residue: 0.2663 time to fit residues: 53.1867 Evaluate side-chains 137 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 104 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 MET Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 215 PHE Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain M residue 31 TYR Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain I residue 2 MET Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 184 SER Chi-restraints excluded: chain I residue 201 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 33 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN M 35 ASN ** M 204 HIS ** 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 = 0.3557 r_free = 0.3557 target = 0.129955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.115222 restraints weight = 17241.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.115407 restraints weight = 16051.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.115455 restraints weight = 15048.290| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10874 Z= 0.178 Angle : 0.613 8.187 14798 Z= 0.313 Chirality : 0.046 0.172 1652 Planarity : 0.004 0.042 1882 Dihedral : 4.960 40.279 1546 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 4.03 % Allowed : 15.21 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.22), residues: 1318 helix: -4.29 (0.58), residues: 40 sheet: 0.63 (0.23), residues: 514 loop : -1.82 (0.20), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.003 0.001 HIS I 168 PHE 0.018 0.002 PHE L 122 TYR 0.017 0.002 TYR H 180 ARG 0.003 0.000 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00051 ( 2) link_NAG-ASN : angle 1.36091 ( 6) link_BETA1-4 : bond 0.00284 ( 2) link_BETA1-4 : angle 0.92568 ( 6) hydrogen bonds : bond 0.03686 ( 314) hydrogen bonds : angle 5.61112 ( 792) covalent geometry : bond 0.00442 (10870) covalent geometry : angle 0.61239 (14786) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 109 time to evaluate : 1.217 Fit side-chains REVERT: H 2 MET cc_start: 0.7468 (OUTLIER) cc_final: 0.6302 (ppp) REVERT: H 22 CYS cc_start: 0.9278 (OUTLIER) cc_final: 0.8913 (t) REVERT: H 67 GLN cc_start: 0.8666 (mm110) cc_final: 0.8441 (mm110) REVERT: L 31 TYR cc_start: 0.8419 (OUTLIER) cc_final: 0.7114 (t80) REVERT: L 149 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7584 (tm-30) REVERT: A 471 GLU cc_start: 0.4995 (OUTLIER) cc_final: 0.4461 (tp30) REVERT: B 471 GLU cc_start: 0.5116 (OUTLIER) cc_final: 0.4597 (tp30) REVERT: M 31 TYR cc_start: 0.8434 (OUTLIER) cc_final: 0.6425 (t80) REVERT: M 51 LYS cc_start: 0.8174 (mttt) cc_final: 0.7833 (tttm) REVERT: M 149 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7428 (tm-30) REVERT: M 155 LYS cc_start: 0.7191 (mmmt) cc_final: 0.6953 (mmmt) REVERT: I 2 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.6316 (ppp) REVERT: I 16 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7418 (mt-10) REVERT: I 22 CYS cc_start: 0.9305 (OUTLIER) cc_final: 0.8924 (t) REVERT: I 67 GLN cc_start: 0.8503 (mm-40) cc_final: 0.7725 (mt0) REVERT: I 142 LEU cc_start: 0.7542 (pp) cc_final: 0.7316 (pp) outliers start: 48 outliers final: 33 residues processed: 147 average time/residue: 0.2255 time to fit residues: 47.0490 Evaluate side-chains 148 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 107 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 MET Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 215 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 31 TYR Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 181 LEU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain I residue 2 MET Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 184 SER Chi-restraints excluded: chain I residue 201 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 46 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 80 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 77 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 196 GLN A 493 GLN B 474 GLN M 35 ASN ** M 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.130483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.116100 restraints weight = 16887.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.116029 restraints weight = 15997.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.116217 restraints weight = 15262.392| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10874 Z= 0.137 Angle : 0.584 8.407 14798 Z= 0.295 Chirality : 0.044 0.158 1652 Planarity : 0.004 0.043 1882 Dihedral : 4.864 39.462 1546 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.61 % Allowed : 15.63 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.22), residues: 1318 helix: -4.41 (0.52), residues: 40 sheet: 0.65 (0.23), residues: 514 loop : -1.76 (0.20), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.002 0.001 HIS H 168 PHE 0.013 0.001 PHE H 126 TYR 0.013 0.001 TYR L 55 ARG 0.002 0.000 ARG B 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00134 ( 2) link_NAG-ASN : angle 1.30317 ( 6) link_BETA1-4 : bond 0.00288 ( 2) link_BETA1-4 : angle 0.83789 ( 6) hydrogen bonds : bond 0.03344 ( 314) hydrogen bonds : angle 5.50831 ( 792) covalent geometry : bond 0.00336 (10870) covalent geometry : angle 0.58335 (14786) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 107 time to evaluate : 1.235 Fit side-chains REVERT: H 2 MET cc_start: 0.7535 (OUTLIER) cc_final: 0.6393 (ppp) REVERT: H 22 CYS cc_start: 0.9266 (OUTLIER) cc_final: 0.8875 (t) REVERT: H 67 GLN cc_start: 0.8630 (mm110) cc_final: 0.8409 (mm110) REVERT: L 31 TYR cc_start: 0.8419 (OUTLIER) cc_final: 0.7050 (t80) REVERT: L 149 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7506 (tm-30) REVERT: L 155 LYS cc_start: 0.7157 (mmmt) cc_final: 0.6897 (mmmt) REVERT: A 471 GLU cc_start: 0.5110 (OUTLIER) cc_final: 0.4578 (tp30) REVERT: B 471 GLU cc_start: 0.5091 (OUTLIER) cc_final: 0.4599 (tp30) REVERT: M 31 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.6379 (t80) REVERT: M 51 LYS cc_start: 0.8176 (mttt) cc_final: 0.7845 (tttm) REVERT: M 149 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7363 (tm-30) REVERT: I 2 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.6453 (ppp) REVERT: I 22 CYS cc_start: 0.9291 (OUTLIER) cc_final: 0.8900 (t) REVERT: I 67 GLN cc_start: 0.8444 (mm-40) cc_final: 0.7673 (mt0) REVERT: I 142 LEU cc_start: 0.7470 (pp) cc_final: 0.7242 (pp) outliers start: 43 outliers final: 29 residues processed: 142 average time/residue: 0.2595 time to fit residues: 52.1531 Evaluate side-chains 139 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 102 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 MET Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 215 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain M residue 31 TYR Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 181 LEU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain I residue 2 MET Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 184 SER Chi-restraints excluded: chain I residue 201 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 25 optimal weight: 0.0070 chunk 118 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 129 optimal weight: 0.7980 chunk 31 optimal weight: 0.3980 chunk 113 optimal weight: 2.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN B 474 GLN M 35 ASN ** M 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.132766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.118391 restraints weight = 16940.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.118604 restraints weight = 15857.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.118657 restraints weight = 14932.664| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10874 Z= 0.131 Angle : 0.582 8.136 14798 Z= 0.294 Chirality : 0.044 0.155 1652 Planarity : 0.004 0.043 1882 Dihedral : 4.811 39.092 1546 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.53 % Allowed : 15.88 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.22), residues: 1318 helix: -4.44 (0.50), residues: 40 sheet: 0.65 (0.23), residues: 514 loop : -1.73 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.002 0.001 HIS I 168 PHE 0.013 0.001 PHE H 126 TYR 0.012 0.001 TYR L 55 ARG 0.003 0.000 ARG A 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00126 ( 2) link_NAG-ASN : angle 1.28650 ( 6) link_BETA1-4 : bond 0.00306 ( 2) link_BETA1-4 : angle 0.85884 ( 6) hydrogen bonds : bond 0.03316 ( 314) hydrogen bonds : angle 5.45022 ( 792) covalent geometry : bond 0.00323 (10870) covalent geometry : angle 0.58169 (14786) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 102 time to evaluate : 1.253 Fit side-chains REVERT: H 2 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.6422 (ppp) REVERT: H 22 CYS cc_start: 0.9270 (OUTLIER) cc_final: 0.8880 (t) REVERT: H 67 GLN cc_start: 0.8605 (mm110) cc_final: 0.8369 (mm110) REVERT: L 31 TYR cc_start: 0.8417 (OUTLIER) cc_final: 0.6956 (t80) REVERT: L 149 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7438 (tm-30) REVERT: L 155 LYS cc_start: 0.7098 (mmmt) cc_final: 0.6861 (mmmt) REVERT: A 471 GLU cc_start: 0.5012 (OUTLIER) cc_final: 0.4498 (tp30) REVERT: B 471 GLU cc_start: 0.4915 (OUTLIER) cc_final: 0.4431 (tp30) REVERT: M 31 TYR cc_start: 0.8438 (OUTLIER) cc_final: 0.6400 (t80) REVERT: M 51 LYS cc_start: 0.8221 (mttt) cc_final: 0.7853 (tttm) REVERT: M 149 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7405 (tm-30) REVERT: I 2 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.6524 (ppp) REVERT: I 22 CYS cc_start: 0.9300 (OUTLIER) cc_final: 0.8926 (t) REVERT: I 67 GLN cc_start: 0.8473 (mm-40) cc_final: 0.7694 (mt0) REVERT: I 142 LEU cc_start: 0.7436 (pp) cc_final: 0.7208 (pp) outliers start: 42 outliers final: 31 residues processed: 134 average time/residue: 0.3369 time to fit residues: 64.2441 Evaluate side-chains 139 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 100 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 MET Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 215 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain M residue 31 TYR Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 181 LEU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain I residue 2 MET Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 184 SER Chi-restraints excluded: chain I residue 201 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 79 optimal weight: 0.1980 chunk 109 optimal weight: 0.0870 chunk 30 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 78 optimal weight: 0.2980 chunk 126 optimal weight: 3.9990 chunk 32 optimal weight: 0.3980 chunk 96 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 0.0170 overall best weight: 0.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN B 474 GLN M 35 ASN ** M 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.138316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.121657 restraints weight = 16433.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.123021 restraints weight = 13178.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.123967 restraints weight = 11248.906| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10874 Z= 0.090 Angle : 0.554 7.589 14798 Z= 0.277 Chirality : 0.043 0.153 1652 Planarity : 0.004 0.043 1882 Dihedral : 4.586 37.145 1546 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.03 % Allowed : 16.64 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.22), residues: 1318 helix: -4.40 (0.49), residues: 40 sheet: 0.75 (0.23), residues: 514 loop : -1.64 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 436 HIS 0.001 0.000 HIS M 204 PHE 0.012 0.001 PHE H 170 TYR 0.014 0.001 TYR A 495 ARG 0.003 0.000 ARG A 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00205 ( 2) link_NAG-ASN : angle 1.14338 ( 6) link_BETA1-4 : bond 0.00394 ( 2) link_BETA1-4 : angle 0.79336 ( 6) hydrogen bonds : bond 0.02845 ( 314) hydrogen bonds : angle 5.26293 ( 792) covalent geometry : bond 0.00211 (10870) covalent geometry : angle 0.55323 (14786) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 101 time to evaluate : 1.900 Fit side-chains REVERT: H 2 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.6415 (ppp) REVERT: H 22 CYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8811 (t) REVERT: L 31 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.6895 (t80) REVERT: L 149 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7349 (tm-30) REVERT: A 471 GLU cc_start: 0.4733 (OUTLIER) cc_final: 0.4295 (tp30) REVERT: A 516 GLU cc_start: 0.7082 (mt-10) cc_final: 0.6862 (mt-10) REVERT: B 471 GLU cc_start: 0.4739 (OUTLIER) cc_final: 0.4295 (tp30) REVERT: M 31 TYR cc_start: 0.8406 (OUTLIER) cc_final: 0.6288 (t80) REVERT: M 51 LYS cc_start: 0.8119 (mttt) cc_final: 0.7704 (tttm) REVERT: I 22 CYS cc_start: 0.9255 (OUTLIER) cc_final: 0.8853 (t) REVERT: I 67 GLN cc_start: 0.8540 (mm-40) cc_final: 0.7712 (mt0) REVERT: I 133 LYS cc_start: 0.6612 (mttt) cc_final: 0.6200 (pttp) REVERT: I 142 LEU cc_start: 0.7444 (pp) cc_final: 0.7217 (pp) outliers start: 36 outliers final: 28 residues processed: 130 average time/residue: 0.3625 time to fit residues: 67.6414 Evaluate side-chains 137 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 102 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 MET Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 215 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain M residue 31 TYR Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 181 LEU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 184 SER Chi-restraints excluded: chain I residue 185 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 64 optimal weight: 0.6980 chunk 121 optimal weight: 0.0670 chunk 38 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 6 optimal weight: 0.0970 chunk 133 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 119 optimal weight: 0.0270 chunk 25 optimal weight: 0.1980 overall best weight: 0.2174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN M 35 ASN M 204 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.133802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.119332 restraints weight = 16592.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.119313 restraints weight = 15964.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.119467 restraints weight = 14716.179| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10874 Z= 0.093 Angle : 0.552 7.653 14798 Z= 0.277 Chirality : 0.043 0.146 1652 Planarity : 0.004 0.044 1882 Dihedral : 4.463 36.315 1546 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.94 % Allowed : 16.64 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: -0.98 (0.22), residues: 1318 helix: -4.39 (0.48), residues: 40 sheet: 0.77 (0.22), residues: 522 loop : -1.56 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 436 HIS 0.002 0.000 HIS M 204 PHE 0.011 0.001 PHE I 170 TYR 0.013 0.001 TYR A 495 ARG 0.003 0.000 ARG B 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00206 ( 2) link_NAG-ASN : angle 1.12403 ( 6) link_BETA1-4 : bond 0.00384 ( 2) link_BETA1-4 : angle 0.85149 ( 6) hydrogen bonds : bond 0.02790 ( 314) hydrogen bonds : angle 5.15018 ( 792) covalent geometry : bond 0.00223 (10870) covalent geometry : angle 0.55122 (14786) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4036.41 seconds wall clock time: 73 minutes 35.85 seconds (4415.85 seconds total)