Starting phenix.real_space_refine on Fri Feb 14 21:26:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7a5r_11648/02_2025/7a5r_11648.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a5r_11648/02_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_11648/02_2025/7a5r_11648.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a5r_11648/02_2025/7a5r_11648.map" model { file = "/net/cci-nas-00/data/ceres_data/7a5r_11648/02_2025/7a5r_11648.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a5r_11648/02_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-5592/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: 7.85, per 1000 atoms: 0.74 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 1.2 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: 1.41 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: 3.24 Time building geometry restraints manager: 2.92 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: 0.06 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: 3.900 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.350 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.050 ------------------------------------------------------------------------------- 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 10870 Z= 0.262 Angle : 0.809 8.411 14786 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 *********************** 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 : 1.203 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: 0.2918 time to fit residues: 69.3824 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 : 1.139 ------------------------------------------------------------------------------- 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 = 54)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.118949 restraints weight = 16566.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.120237 restraints weight = 13312.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.121094 restraints weight = 11405.387| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 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 10870 Z= 0.251 Angle : 0.685 8.262 14786 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 *********************** 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 : 1.225 Fit side-chains REVERT: H 142 LEU cc_start: 0.7476 (pp) cc_final: 0.7216 (pp) REVERT: H 201 ASN cc_start: 0.7636 (OUTLIER) cc_final: 0.7288 (m-40) REVERT: A 336 CYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7805 (m) REVERT: A 471 GLU cc_start: 0.4904 (OUTLIER) cc_final: 0.4363 (tp30) REVERT: A 489 TYR cc_start: 0.8840 (m-80) cc_final: 0.8602 (m-80) REVERT: B 336 CYS cc_start: 0.8266 (OUTLIER) cc_final: 0.8043 (m) REVERT: B 471 GLU cc_start: 0.4708 (OUTLIER) cc_final: 0.4264 (tp30) REVERT: M 51 LYS cc_start: 0.8090 (mttt) cc_final: 0.7732 (tttm) REVERT: M 149 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7637 (tm-30) REVERT: I 142 LEU cc_start: 0.7418 (pp) cc_final: 0.7198 (pp) outliers start: 25 outliers final: 14 residues processed: 137 average time/residue: 0.2621 time to fit residues: 49.4162 Evaluate side-chains 124 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 1.197 ------------------------------------------------------------------------------- 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 336 CYS 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: 0.9980 chunk 68 optimal weight: 0.0470 chunk 98 optimal weight: 0.9980 chunk 6 optimal weight: 0.0050 chunk 119 optimal weight: 0.0170 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 64 optimal weight: 0.1980 overall best weight: 0.2330 ------------------------------------------------------------------------------- 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 = 0.3646 r_free = 0.3646 target = 0.137009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.123251 restraints weight = 16856.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.123083 restraints weight = 16413.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.123302 restraints weight = 15084.272| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10870 Z= 0.149 Angle : 0.578 7.440 14786 Z= 0.295 Chirality : 0.043 0.149 1652 Planarity : 0.004 0.040 1882 Dihedral : 5.122 37.260 1546 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.69 % Allowed : 10.76 % Favored : 86.55 % 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: -1.26 (0.22), residues: 1318 helix: -4.04 (0.54), residues: 40 sheet: 0.61 (0.23), residues: 512 loop : -1.78 (0.20), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 83 HIS 0.002 0.001 HIS H 168 PHE 0.008 0.001 PHE I 170 TYR 0.011 0.001 TYR L 55 ARG 0.003 0.000 ARG A 403 *********************** 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 : 1.245 Fit side-chains REVERT: H 201 ASN cc_start: 0.7636 (OUTLIER) cc_final: 0.7349 (m-40) REVERT: A 471 GLU cc_start: 0.5125 (OUTLIER) cc_final: 0.4776 (tp30) REVERT: B 336 CYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7818 (m) REVERT: B 471 GLU cc_start: 0.5111 (OUTLIER) cc_final: 0.4886 (tp30) REVERT: I 67 GLN cc_start: 0.8296 (mm-40) cc_final: 0.7417 (mt0) REVERT: I 142 LEU cc_start: 0.7240 (pp) cc_final: 0.7016 (pp) outliers start: 32 outliers final: 17 residues processed: 147 average time/residue: 0.2551 time to fit residues: 52.1575 Evaluate side-chains 125 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 1.127 ------------------------------------------------------------------------------- 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 440 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain B residue 336 CYS 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 132 LYS Chi-restraints excluded: chain M residue 215 PHE 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 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: 3.9990 chunk 20 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 106 optimal weight: 0.4980 chunk 94 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN M 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.129858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.114983 restraints weight = 16967.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.115140 restraints weight = 15986.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.115247 restraints weight = 14596.121| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10870 Z= 0.335 Angle : 0.672 8.691 14786 Z= 0.345 Chirality : 0.047 0.154 1652 Planarity : 0.005 0.043 1882 Dihedral : 5.275 42.162 1546 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.61 % Allowed : 13.28 % Favored : 83.11 % 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: -1.38 (0.22), residues: 1318 helix: -4.14 (0.76), residues: 28 sheet: 0.63 (0.23), residues: 514 loop : -2.00 (0.20), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 47 HIS 0.005 0.002 HIS H 204 PHE 0.023 0.002 PHE L 122 TYR 0.024 0.002 TYR I 180 ARG 0.004 0.001 ARG A 457 *********************** 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 150 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 107 time to evaluate : 1.229 Fit side-chains REVERT: H 2 MET cc_start: 0.7379 (OUTLIER) cc_final: 0.6176 (ppp) REVERT: H 201 ASN cc_start: 0.7747 (OUTLIER) cc_final: 0.7499 (m-40) REVERT: L 31 TYR cc_start: 0.8449 (OUTLIER) cc_final: 0.7368 (t80) REVERT: L 149 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7741 (tm-30) REVERT: A 471 GLU cc_start: 0.5218 (OUTLIER) cc_final: 0.4649 (tp30) REVERT: A 489 TYR cc_start: 0.8880 (m-80) cc_final: 0.8506 (m-80) REVERT: B 336 CYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7924 (m) REVERT: B 471 GLU cc_start: 0.5075 (OUTLIER) cc_final: 0.4604 (tp30) REVERT: M 31 TYR cc_start: 0.8366 (OUTLIER) cc_final: 0.6668 (t80) REVERT: M 149 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7852 (tm-30) REVERT: M 155 LYS cc_start: 0.7365 (mmmt) cc_final: 0.6851 (mmmt) REVERT: I 2 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.6305 (ppp) REVERT: I 67 GLN cc_start: 0.8525 (mm-40) cc_final: 0.7660 (mt0) REVERT: I 142 LEU cc_start: 0.7553 (pp) cc_final: 0.7302 (pp) outliers start: 43 outliers final: 28 residues processed: 138 average time/residue: 0.2547 time to fit residues: 49.2380 Evaluate side-chains 134 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 98 time to evaluate : 1.260 ------------------------------------------------------------------------------- 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 31 TYR 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 336 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 361 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 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 173 VAL 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: 0.5980 chunk 120 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 0.0870 chunk 109 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.131222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.116387 restraints weight = 16810.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.116600 restraints weight = 15584.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.116813 restraints weight = 14171.116| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10870 Z= 0.230 Angle : 0.597 8.257 14786 Z= 0.303 Chirality : 0.044 0.153 1652 Planarity : 0.004 0.042 1882 Dihedral : 5.017 39.717 1546 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.12 % Allowed : 13.87 % Favored : 82.02 % 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: -1.34 (0.22), residues: 1318 helix: -4.22 (0.61), residues: 40 sheet: 0.66 (0.23), residues: 514 loop : -1.92 (0.20), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 436 HIS 0.003 0.001 HIS I 204 PHE 0.012 0.001 PHE L 122 TYR 0.014 0.001 TYR H 180 ARG 0.002 0.000 ARG A 457 *********************** 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 159 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 110 time to evaluate : 1.160 Fit side-chains REVERT: H 2 MET cc_start: 0.7419 (OUTLIER) cc_final: 0.6232 (ppp) REVERT: H 22 CYS cc_start: 0.9285 (OUTLIER) cc_final: 0.8873 (t) REVERT: H 67 GLN cc_start: 0.8644 (mm110) cc_final: 0.8417 (mm110) REVERT: H 201 ASN cc_start: 0.7688 (OUTLIER) cc_final: 0.7425 (m-40) REVERT: L 31 TYR cc_start: 0.8419 (OUTLIER) cc_final: 0.7273 (t80) REVERT: L 114 ARG cc_start: 0.7246 (ptm-80) cc_final: 0.6967 (ptm160) REVERT: L 149 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7603 (tm-30) REVERT: A 471 GLU cc_start: 0.5148 (OUTLIER) cc_final: 0.4650 (tp30) REVERT: B 336 CYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7939 (m) REVERT: B 471 GLU cc_start: 0.5019 (OUTLIER) cc_final: 0.4598 (tp30) REVERT: M 31 TYR cc_start: 0.8365 (OUTLIER) cc_final: 0.6610 (t80) REVERT: M 149 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7692 (tm-30) REVERT: M 155 LYS cc_start: 0.7269 (mmmt) cc_final: 0.6873 (mmmt) REVERT: I 2 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.6286 (ppp) REVERT: I 16 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7230 (mt-10) REVERT: I 22 CYS cc_start: 0.9276 (OUTLIER) cc_final: 0.8900 (t) REVERT: I 67 GLN cc_start: 0.8553 (mm-40) cc_final: 0.7691 (mt0) outliers start: 49 outliers final: 29 residues processed: 146 average time/residue: 0.2184 time to fit residues: 45.6684 Evaluate side-chains 142 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 103 time to evaluate : 1.182 ------------------------------------------------------------------------------- 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 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 H residue 201 ASN 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 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 336 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 361 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 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 179 LEU 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: 0.9980 chunk 33 optimal weight: 0.0170 chunk 133 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 chunk 100 optimal weight: 2.9990 chunk 40 optimal weight: 0.0010 chunk 64 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 overall best weight: 0.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN A 542 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.132275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.117735 restraints weight = 16771.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.117986 restraints weight = 15648.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.117998 restraints weight = 14645.641| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10870 Z= 0.168 Angle : 0.559 7.814 14786 Z= 0.283 Chirality : 0.043 0.147 1652 Planarity : 0.004 0.042 1882 Dihedral : 4.803 38.267 1546 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.53 % Allowed : 14.87 % Favored : 81.60 % 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: -4.27 (0.57), residues: 40 sheet: 0.74 (0.23), residues: 514 loop : -1.84 (0.20), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 436 HIS 0.002 0.001 HIS H 168 PHE 0.009 0.001 PHE H 170 TYR 0.012 0.001 TYR L 55 ARG 0.002 0.000 ARG B 408 *********************** 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 153 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 111 time to evaluate : 1.211 Fit side-chains REVERT: H 2 MET cc_start: 0.7412 (OUTLIER) cc_final: 0.6216 (ppp) REVERT: H 22 CYS cc_start: 0.9287 (OUTLIER) cc_final: 0.8859 (t) REVERT: H 67 GLN cc_start: 0.8646 (mm110) cc_final: 0.8417 (mm110) REVERT: H 201 ASN cc_start: 0.7669 (OUTLIER) cc_final: 0.7431 (m-40) REVERT: L 149 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7490 (tm-30) REVERT: A 471 GLU cc_start: 0.5146 (OUTLIER) cc_final: 0.4685 (tp30) REVERT: B 336 CYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7943 (m) REVERT: B 471 GLU cc_start: 0.5113 (OUTLIER) cc_final: 0.4692 (tp30) REVERT: M 149 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7533 (tm-30) REVERT: M 155 LYS cc_start: 0.7207 (mmmt) cc_final: 0.6868 (mmmt) REVERT: I 67 GLN cc_start: 0.8520 (mm-40) cc_final: 0.7737 (mt0) outliers start: 42 outliers final: 30 residues processed: 143 average time/residue: 0.2267 time to fit residues: 46.3209 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 : 1.204 ------------------------------------------------------------------------------- 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 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 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 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 336 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 361 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 181 LEU Chi-restraints excluded: chain M residue 215 PHE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 33 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 92 optimal weight: 0.0370 chunk 71 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 103 optimal weight: 0.0770 chunk 27 optimal weight: 0.7980 overall best weight: 0.5416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3578 r_free = 0.3578 target = 0.131646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.116908 restraints weight = 17108.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.117152 restraints weight = 15881.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.117334 restraints weight = 14356.934| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10870 Z= 0.204 Angle : 0.576 7.674 14786 Z= 0.293 Chirality : 0.044 0.187 1652 Planarity : 0.004 0.042 1882 Dihedral : 4.790 38.555 1546 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.95 % Allowed : 15.38 % Favored : 80.67 % 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: -1.19 (0.22), residues: 1318 helix: -4.28 (0.56), residues: 40 sheet: 0.75 (0.23), residues: 514 loop : -1.80 (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 I 168 PHE 0.012 0.001 PHE L 122 TYR 0.012 0.001 TYR H 180 ARG 0.002 0.000 ARG A 408 *********************** 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 150 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 103 time to evaluate : 1.185 Fit side-chains REVERT: H 2 MET cc_start: 0.7523 (OUTLIER) cc_final: 0.6310 (ppp) REVERT: H 22 CYS cc_start: 0.9279 (OUTLIER) cc_final: 0.8873 (t) REVERT: H 67 GLN cc_start: 0.8701 (mm110) cc_final: 0.8445 (mm110) REVERT: L 31 TYR cc_start: 0.8417 (OUTLIER) cc_final: 0.7236 (t80) REVERT: L 149 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7555 (tm-30) REVERT: A 471 GLU cc_start: 0.4903 (OUTLIER) cc_final: 0.4369 (tp30) REVERT: B 336 CYS cc_start: 0.8322 (OUTLIER) cc_final: 0.8014 (m) REVERT: B 471 GLU cc_start: 0.4841 (OUTLIER) cc_final: 0.4391 (tp30) REVERT: M 31 TYR cc_start: 0.8389 (OUTLIER) cc_final: 0.6504 (t80) REVERT: M 149 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7525 (tm-30) REVERT: M 155 LYS cc_start: 0.7212 (mmmt) cc_final: 0.6880 (mmmt) REVERT: I 2 MET cc_start: 0.7652 (OUTLIER) cc_final: 0.6378 (ppp) REVERT: I 22 CYS cc_start: 0.9281 (OUTLIER) cc_final: 0.8876 (t) REVERT: I 67 GLN cc_start: 0.8594 (mm-40) cc_final: 0.7741 (mt0) REVERT: I 142 LEU cc_start: 0.7517 (pp) cc_final: 0.7279 (pp) outliers start: 47 outliers final: 32 residues processed: 139 average time/residue: 0.2155 time to fit residues: 43.4908 Evaluate side-chains 143 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 102 time to evaluate : 1.143 ------------------------------------------------------------------------------- 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 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 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 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 336 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 361 CYS 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: 0.4980 chunk 18 optimal weight: 0.9990 chunk 116 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 80 optimal weight: 0.0020 chunk 70 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 14 optimal weight: 0.2980 chunk 5 optimal weight: 0.0030 chunk 84 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 196 GLN L 204 HIS A 493 GLN B 474 GLN M 35 ASN M 204 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.132689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.118366 restraints weight = 16761.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.118238 restraints weight = 16469.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.118552 restraints weight = 15611.869| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10870 Z= 0.150 Angle : 0.549 7.372 14786 Z= 0.278 Chirality : 0.043 0.176 1652 Planarity : 0.004 0.042 1882 Dihedral : 4.625 37.444 1546 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.36 % Allowed : 16.39 % Favored : 80.25 % 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: -1.10 (0.22), residues: 1318 helix: -4.34 (0.51), residues: 40 sheet: 0.80 (0.23), residues: 514 loop : -1.71 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 436 HIS 0.001 0.001 HIS I 168 PHE 0.010 0.001 PHE H 170 TYR 0.012 0.001 TYR L 55 ARG 0.003 0.000 ARG A 454 *********************** 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 140 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 100 time to evaluate : 1.199 Fit side-chains REVERT: H 2 MET cc_start: 0.7433 (OUTLIER) cc_final: 0.6265 (ppp) REVERT: H 67 GLN cc_start: 0.8635 (mm110) cc_final: 0.8409 (mm110) REVERT: L 31 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.7169 (t80) REVERT: L 149 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7387 (tm-30) REVERT: A 471 GLU cc_start: 0.4918 (OUTLIER) cc_final: 0.4618 (tp30) REVERT: B 471 GLU cc_start: 0.4942 (OUTLIER) cc_final: 0.4545 (tp30) REVERT: M 31 TYR cc_start: 0.8340 (OUTLIER) cc_final: 0.6411 (t80) REVERT: M 149 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7362 (tm-30) REVERT: M 155 LYS cc_start: 0.7176 (mmmt) cc_final: 0.6920 (mmmt) REVERT: I 2 MET cc_start: 0.7603 (OUTLIER) cc_final: 0.6438 (ppp) REVERT: I 22 CYS cc_start: 0.9273 (OUTLIER) cc_final: 0.8871 (t) REVERT: I 67 GLN cc_start: 0.8479 (mm-40) cc_final: 0.7687 (mt0) REVERT: I 142 LEU cc_start: 0.7390 (pp) cc_final: 0.7175 (pp) outliers start: 40 outliers final: 27 residues processed: 131 average time/residue: 0.2304 time to fit residues: 43.6214 Evaluate side-chains 133 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 99 time to evaluate : 1.175 ------------------------------------------------------------------------------- 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 31 THR 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 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 361 CYS 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 25 optimal weight: 0.4980 chunk 118 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 chunk 130 optimal weight: 0.2980 chunk 100 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 129 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN B 474 GLN M 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.135192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.118336 restraints weight = 16764.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.119724 restraints weight = 13387.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.120711 restraints weight = 11383.185| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10870 Z= 0.236 Angle : 0.577 7.598 14786 Z= 0.294 Chirality : 0.044 0.172 1652 Planarity : 0.004 0.042 1882 Dihedral : 4.736 39.004 1546 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.70 % Allowed : 16.05 % Favored : 80.25 % 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: -1.13 (0.22), residues: 1318 helix: -4.34 (0.53), residues: 40 sheet: 0.77 (0.23), residues: 514 loop : -1.73 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.002 0.001 HIS I 168 PHE 0.014 0.002 PHE L 122 TYR 0.013 0.001 TYR H 180 ARG 0.003 0.000 ARG A 408 *********************** 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 149 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 105 time to evaluate : 1.258 Fit side-chains REVERT: H 2 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.6399 (ppp) REVERT: H 67 GLN cc_start: 0.8743 (mm110) cc_final: 0.8470 (mm110) REVERT: L 31 TYR cc_start: 0.8418 (OUTLIER) cc_final: 0.6785 (t80) REVERT: L 149 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7517 (tm-30) REVERT: A 41 LYS cc_start: 0.7824 (tppt) cc_final: 0.6886 (mtmm) REVERT: A 471 GLU cc_start: 0.4881 (OUTLIER) cc_final: 0.4306 (tp30) REVERT: B 41 LYS cc_start: 0.7735 (tppt) cc_final: 0.6780 (mtmm) REVERT: B 471 GLU cc_start: 0.4848 (OUTLIER) cc_final: 0.4348 (tp30) REVERT: M 31 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.6329 (t80) REVERT: M 149 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7504 (tm-30) REVERT: M 155 LYS cc_start: 0.7253 (mmmt) cc_final: 0.6969 (mmmt) REVERT: I 2 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.6538 (ppp) REVERT: I 22 CYS cc_start: 0.9281 (OUTLIER) cc_final: 0.8871 (t) REVERT: I 67 GLN cc_start: 0.8552 (mm-40) cc_final: 0.7683 (mt0) REVERT: I 142 LEU cc_start: 0.7524 (pp) cc_final: 0.7288 (pp) outliers start: 44 outliers final: 33 residues processed: 141 average time/residue: 0.2320 time to fit residues: 46.7685 Evaluate side-chains 142 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 102 time to evaluate : 1.141 ------------------------------------------------------------------------------- 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 31 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 H residue 201 ASN 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 361 CYS 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 53 LEU 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 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: 0.0870 chunk 109 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 122 optimal weight: 0.9980 chunk 78 optimal weight: 0.3980 chunk 126 optimal weight: 0.2980 chunk 32 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 24 optimal weight: 0.4980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN B 474 GLN M 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.137333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.122488 restraints weight = 16447.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.122687 restraints weight = 15241.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.122862 restraints weight = 13808.753| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10870 Z= 0.169 Angle : 0.555 7.604 14786 Z= 0.281 Chirality : 0.043 0.163 1652 Planarity : 0.004 0.043 1882 Dihedral : 4.629 38.076 1546 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.45 % Allowed : 16.13 % 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: -1.05 (0.22), residues: 1318 helix: -4.32 (0.53), residues: 40 sheet: 0.81 (0.23), residues: 514 loop : -1.67 (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 170 TYR 0.012 0.001 TYR L 55 ARG 0.003 0.000 ARG A 408 ********************** 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 141 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 100 time to evaluate : 1.152 Fit side-chains REVERT: H 2 MET cc_start: 0.7629 (OUTLIER) cc_final: 0.6404 (ppp) REVERT: H 67 GLN cc_start: 0.8720 (mm110) cc_final: 0.8459 (mm110) REVERT: L 31 TYR cc_start: 0.8417 (OUTLIER) cc_final: 0.6815 (t80) REVERT: L 149 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7460 (tm-30) REVERT: A 471 GLU cc_start: 0.4815 (OUTLIER) cc_final: 0.4316 (tp30) REVERT: B 471 GLU cc_start: 0.4793 (OUTLIER) cc_final: 0.4317 (tp30) REVERT: M 31 TYR cc_start: 0.8408 (OUTLIER) cc_final: 0.6334 (t80) REVERT: M 149 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7426 (tm-30) REVERT: M 155 LYS cc_start: 0.7251 (mmmt) cc_final: 0.6986 (mmmt) REVERT: I 2 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.6528 (ppp) REVERT: I 22 CYS cc_start: 0.9268 (OUTLIER) cc_final: 0.8849 (t) REVERT: I 67 GLN cc_start: 0.8545 (mm-40) cc_final: 0.7685 (mt0) REVERT: I 142 LEU cc_start: 0.7512 (pp) cc_final: 0.7289 (pp) outliers start: 41 outliers final: 33 residues processed: 133 average time/residue: 0.2212 time to fit residues: 42.0745 Evaluate side-chains 135 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 95 time to evaluate : 1.178 ------------------------------------------------------------------------------- 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 31 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 H residue 201 ASN 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 53 LEU 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 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 185 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 64 optimal weight: 0.5980 chunk 121 optimal weight: 0.0470 chunk 38 optimal weight: 0.7980 chunk 128 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 93 optimal weight: 0.3980 chunk 6 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 208 ASN A 493 GLN B 474 GLN M 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.131661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.117139 restraints weight = 16683.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.117189 restraints weight = 15939.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.117441 restraints weight = 14517.977| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10870 Z= 0.199 Angle : 0.568 7.624 14786 Z= 0.288 Chirality : 0.044 0.163 1652 Planarity : 0.004 0.042 1882 Dihedral : 4.659 38.750 1546 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.53 % Allowed : 16.30 % Favored : 80.17 % 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: -1.06 (0.22), residues: 1318 helix: -4.30 (0.54), residues: 40 sheet: 0.71 (0.22), residues: 526 loop : -1.63 (0.21), residues: 752 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 L 122 TYR 0.012 0.001 TYR L 55 ARG 0.003 0.000 ARG A 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3204.69 seconds wall clock time: 58 minutes 59.81 seconds (3539.81 seconds total)