Starting phenix.real_space_refine on Thu Mar 6 08:21:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xrd_33414/03_2025/7xrd_33414.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xrd_33414/03_2025/7xrd_33414.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xrd_33414/03_2025/7xrd_33414.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xrd_33414/03_2025/7xrd_33414.map" model { file = "/net/cci-nas-00/data/ceres_data/7xrd_33414/03_2025/7xrd_33414.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xrd_33414/03_2025/7xrd_33414.cif" } resolution = 3.9 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= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 24 5.16 5 C 3420 2.51 5 N 964 2.21 5 O 1036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5460 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1332 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 5, 'TRANS': 158} Chain: "B" Number of atoms: 1332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1332 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 5, 'TRANS': 158} Chain: "C" Number of atoms: 1332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1332 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 5, 'TRANS': 158} Chain: "D" Number of atoms: 1332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1332 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 5, 'TRANS': 158} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.18, per 1000 atoms: 0.77 Number of scatterers: 5460 At special positions: 0 Unit cell: (91.3, 104.5, 86.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 24 16.00 P 12 15.00 Mg 4 11.99 O 1036 8.00 N 964 7.00 C 3420 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 560.7 milliseconds 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1216 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 5 sheets defined 43.8% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 25 through 36 Processing helix chain 'A' and resid 67 through 78 Proline residue: A 72 - end of helix removed outlier: 3.862A pdb=" N TYR A 78 " --> pdb=" O ARG A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 95 through 108 Processing helix chain 'A' and resid 110 through 115 removed outlier: 3.934A pdb=" N ARG A 113 " --> pdb=" O ARG A 110 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ASP A 114 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 Processing helix chain 'A' and resid 140 through 144 Processing helix chain 'A' and resid 161 through 172 Processing helix chain 'B' and resid 25 through 35 Processing helix chain 'B' and resid 67 through 78 Proline residue: B 72 - end of helix removed outlier: 4.049A pdb=" N TYR B 78 " --> pdb=" O ARG B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 94 No H-bonds generated for 'chain 'B' and resid 92 through 94' Processing helix chain 'B' and resid 95 through 108 Processing helix chain 'B' and resid 110 through 115 removed outlier: 3.858A pdb=" N ARG B 113 " --> pdb=" O ARG B 110 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ASP B 114 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 140 Processing helix chain 'B' and resid 141 through 144 Processing helix chain 'B' and resid 161 through 172 Processing helix chain 'C' and resid 25 through 35 Processing helix chain 'C' and resid 67 through 78 removed outlier: 3.542A pdb=" N ARG C 71 " --> pdb=" O ASP C 68 " (cutoff:3.500A) Proline residue: C 72 - end of helix removed outlier: 4.060A pdb=" N TYR C 78 " --> pdb=" O ARG C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 94 No H-bonds generated for 'chain 'C' and resid 92 through 94' Processing helix chain 'C' and resid 95 through 108 Processing helix chain 'C' and resid 110 through 115 removed outlier: 3.856A pdb=" N ARG C 113 " --> pdb=" O ARG C 110 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASP C 114 " --> pdb=" O GLU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 139 Processing helix chain 'C' and resid 140 through 144 Processing helix chain 'C' and resid 161 through 172 Processing helix chain 'D' and resid 25 through 36 Processing helix chain 'D' and resid 67 through 78 Proline residue: D 72 - end of helix removed outlier: 3.881A pdb=" N TYR D 78 " --> pdb=" O ARG D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 108 Processing helix chain 'D' and resid 110 through 115 removed outlier: 3.863A pdb=" N ARG D 113 " --> pdb=" O ARG D 110 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASP D 114 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 139 Processing helix chain 'D' and resid 140 through 144 Processing helix chain 'D' and resid 161 through 172 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 53 removed outlier: 6.801A pdb=" N LYS A 12 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ASN A 60 " --> pdb=" O LYS A 12 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N MET A 14 " --> pdb=" O ASN A 60 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N TRP A 62 " --> pdb=" O MET A 14 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ILE A 16 " --> pdb=" O TRP A 62 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N VAL A 64 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N MET A 18 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N GLY A 83 " --> pdb=" O GLU A 13 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG A 15 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ILE A 85 " --> pdb=" O ARG A 15 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU A 17 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL A 87 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU A 19 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N ASP A 89 " --> pdb=" O LEU A 19 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE A 117 " --> pdb=" O TYR A 150 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N GLN A 152 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE A 119 " --> pdb=" O GLN A 152 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39 removed outlier: 4.574A pdb=" N SER A 38 " --> pdb=" O THR C 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 53 removed outlier: 6.826A pdb=" N LYS B 12 " --> pdb=" O LYS B 58 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ASN B 60 " --> pdb=" O LYS B 12 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N MET B 14 " --> pdb=" O ASN B 60 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N TRP B 62 " --> pdb=" O MET B 14 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE B 16 " --> pdb=" O TRP B 62 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL B 64 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N MET B 18 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 8.960A pdb=" N GLY B 83 " --> pdb=" O GLU B 13 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ARG B 15 " --> pdb=" O GLY B 83 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ILE B 85 " --> pdb=" O ARG B 15 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU B 17 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N VAL B 87 " --> pdb=" O LEU B 17 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU B 19 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N ASP B 89 " --> pdb=" O LEU B 19 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 47 through 53 removed outlier: 6.791A pdb=" N LYS C 12 " --> pdb=" O LYS C 58 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ASN C 60 " --> pdb=" O LYS C 12 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N MET C 14 " --> pdb=" O ASN C 60 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N TRP C 62 " --> pdb=" O MET C 14 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE C 16 " --> pdb=" O TRP C 62 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VAL C 64 " --> pdb=" O ILE C 16 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N MET C 18 " --> pdb=" O VAL C 64 " (cutoff:3.500A) removed outlier: 8.939A pdb=" N GLY C 83 " --> pdb=" O GLU C 13 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ARG C 15 " --> pdb=" O GLY C 83 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ILE C 85 " --> pdb=" O ARG C 15 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU C 17 " --> pdb=" O ILE C 85 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL C 87 " --> pdb=" O LEU C 17 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU C 19 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N ASP C 89 " --> pdb=" O LEU C 19 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 47 through 53 removed outlier: 6.757A pdb=" N LYS D 12 " --> pdb=" O LYS D 58 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ASN D 60 " --> pdb=" O LYS D 12 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N MET D 14 " --> pdb=" O ASN D 60 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N TRP D 62 " --> pdb=" O MET D 14 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ILE D 16 " --> pdb=" O TRP D 62 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N VAL D 64 " --> pdb=" O ILE D 16 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N MET D 18 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N GLY D 83 " --> pdb=" O GLU D 13 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG D 15 " --> pdb=" O GLY D 83 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ILE D 85 " --> pdb=" O ARG D 15 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU D 17 " --> pdb=" O ILE D 85 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N VAL D 87 " --> pdb=" O LEU D 17 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU D 19 " --> pdb=" O VAL D 87 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ASP D 89 " --> pdb=" O LEU D 19 " (cutoff:3.500A) 214 hydrogen bonds defined for protein. 552 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.21 Time building geometry restraints manager: 1.45 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: 1771 1.34 - 1.46: 1205 1.46 - 1.58: 2532 1.58 - 1.69: 20 1.69 - 1.81: 40 Bond restraints: 5568 Sorted by residual: bond pdb=" N LYS B 55 " pdb=" CA LYS B 55 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 9.86e-01 bond pdb=" C ARG A 71 " pdb=" N PRO A 72 " ideal model delta sigma weight residual 1.335 1.341 -0.006 1.19e-02 7.06e+03 2.62e-01 bond pdb=" CA GLY A 20 " pdb=" C GLY A 20 " ideal model delta sigma weight residual 1.509 1.515 -0.005 1.04e-02 9.25e+03 2.61e-01 bond pdb=" O3A GTP D 202 " pdb=" PB GTP D 202 " ideal model delta sigma weight residual 1.610 1.620 -0.010 2.00e-02 2.50e+03 2.48e-01 bond pdb=" C ILE B 42 " pdb=" N PRO B 43 " ideal model delta sigma weight residual 1.334 1.345 -0.012 2.34e-02 1.83e+03 2.45e-01 ... (remaining 5563 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 7371 1.42 - 2.84: 149 2.84 - 4.26: 25 4.26 - 5.69: 13 5.69 - 7.11: 6 Bond angle restraints: 7564 Sorted by residual: angle pdb=" O3A GTP D 202 " pdb=" PB GTP D 202 " pdb=" O3B GTP D 202 " ideal model delta sigma weight residual 102.60 109.71 -7.11 3.00e+00 1.11e-01 5.61e+00 angle pdb=" C1' GTP B 202 " pdb=" C2' GTP B 202 " pdb=" C3' GTP B 202 " ideal model delta sigma weight residual 111.00 104.06 6.94 3.00e+00 1.11e-01 5.36e+00 angle pdb=" C1' GTP C 202 " pdb=" C2' GTP C 202 " pdb=" C3' GTP C 202 " ideal model delta sigma weight residual 111.00 104.11 6.89 3.00e+00 1.11e-01 5.28e+00 angle pdb=" C1' GTP D 202 " pdb=" C2' GTP D 202 " pdb=" C3' GTP D 202 " ideal model delta sigma weight residual 111.00 104.18 6.82 3.00e+00 1.11e-01 5.17e+00 angle pdb=" C1' GTP A 202 " pdb=" C2' GTP A 202 " pdb=" C3' GTP A 202 " ideal model delta sigma weight residual 111.00 104.24 6.76 3.00e+00 1.11e-01 5.07e+00 ... (remaining 7559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.18: 3220 24.18 - 48.37: 65 48.37 - 72.55: 13 72.55 - 96.74: 6 96.74 - 120.92: 12 Dihedral angle restraints: 3316 sinusoidal: 1420 harmonic: 1896 Sorted by residual: dihedral pdb=" C8 GTP C 202 " pdb=" C1' GTP C 202 " pdb=" N9 GTP C 202 " pdb=" O4' GTP C 202 " ideal model delta sinusoidal sigma weight residual 104.59 -16.33 120.92 1 2.00e+01 2.50e-03 3.63e+01 dihedral pdb=" C8 GTP A 202 " pdb=" C1' GTP A 202 " pdb=" N9 GTP A 202 " pdb=" O4' GTP A 202 " ideal model delta sinusoidal sigma weight residual 104.59 -15.29 119.88 1 2.00e+01 2.50e-03 3.60e+01 dihedral pdb=" C8 GTP B 202 " pdb=" C1' GTP B 202 " pdb=" N9 GTP B 202 " pdb=" O4' GTP B 202 " ideal model delta sinusoidal sigma weight residual 104.59 -14.75 119.34 1 2.00e+01 2.50e-03 3.58e+01 ... (remaining 3313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 522 0.031 - 0.062: 185 0.062 - 0.093: 53 0.093 - 0.124: 62 0.124 - 0.155: 10 Chirality restraints: 832 Sorted by residual: chirality pdb=" CA ILE C 42 " pdb=" N ILE C 42 " pdb=" C ILE C 42 " pdb=" CB ILE C 42 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.01e-01 chirality pdb=" CA ILE D 42 " pdb=" N ILE D 42 " pdb=" C ILE D 42 " pdb=" CB ILE D 42 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.75e-01 chirality pdb=" CA ILE A 42 " pdb=" N ILE A 42 " pdb=" C ILE A 42 " pdb=" CB ILE A 42 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.65e-01 ... (remaining 829 not shown) Planarity restraints: 940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 131 " -0.021 5.00e-02 4.00e+02 3.13e-02 1.57e+00 pdb=" N PRO C 132 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO C 132 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 132 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 131 " -0.019 5.00e-02 4.00e+02 2.86e-02 1.31e+00 pdb=" N PRO D 132 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO D 132 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 132 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 71 " -0.019 5.00e-02 4.00e+02 2.86e-02 1.30e+00 pdb=" N PRO B 72 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 72 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 72 " -0.016 5.00e-02 4.00e+02 ... (remaining 937 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 30 2.59 - 3.17: 4313 3.17 - 3.74: 7869 3.74 - 4.32: 11731 4.32 - 4.90: 18789 Nonbonded interactions: 42732 Sorted by model distance: nonbonded pdb=" OD2 ASP D 63 " pdb="MG MG D 201 " model vdw 2.012 2.170 nonbonded pdb=" OG1 THR A 27 " pdb="MG MG A 201 " model vdw 2.017 2.170 nonbonded pdb=" OG1 THR D 27 " pdb="MG MG D 201 " model vdw 2.024 2.170 nonbonded pdb=" OD2 ASP A 63 " pdb="MG MG A 201 " model vdw 2.041 2.170 nonbonded pdb=" OD1 ASP B 22 " pdb="MG MG B 201 " model vdw 2.074 2.170 ... (remaining 42727 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = 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: 3.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.850 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 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 : 0.002 0.013 5568 Z= 0.114 Angle : 0.575 7.107 7564 Z= 0.298 Chirality : 0.045 0.155 832 Planarity : 0.003 0.031 940 Dihedral : 14.120 120.919 2100 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.52 % Allowed : 0.69 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.32), residues: 648 helix: -1.41 (0.31), residues: 216 sheet: 0.16 (0.38), residues: 164 loop : 0.24 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 168 HIS 0.002 0.001 HIS D 76 PHE 0.005 0.001 PHE D 120 TYR 0.010 0.001 TYR A 77 ARG 0.002 0.000 ARG C 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 213 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 THR cc_start: 0.7924 (m) cc_final: 0.7711 (m) REVERT: B 130 MET cc_start: 0.7631 (mtm) cc_final: 0.7138 (mtm) REVERT: C 169 LEU cc_start: 0.8897 (mt) cc_final: 0.8614 (tt) REVERT: D 125 ASP cc_start: 0.8467 (p0) cc_final: 0.8013 (m-30) REVERT: D 131 LYS cc_start: 0.7896 (mppt) cc_final: 0.7643 (mmmt) outliers start: 3 outliers final: 0 residues processed: 216 average time/residue: 0.2932 time to fit residues: 73.5373 Evaluate side-chains 183 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 0.0980 chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN C 136 GLN C 148 ASN C 172 ASN D 104 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.126537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.102778 restraints weight = 6891.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.106337 restraints weight = 4376.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.108887 restraints weight = 3159.137| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5568 Z= 0.254 Angle : 0.698 7.276 7564 Z= 0.344 Chirality : 0.050 0.171 832 Planarity : 0.005 0.040 940 Dihedral : 15.617 115.835 784 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.91 % Allowed : 11.28 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.32), residues: 648 helix: -0.38 (0.34), residues: 240 sheet: 0.09 (0.36), residues: 172 loop : -0.22 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 149 HIS 0.003 0.001 HIS D 76 PHE 0.016 0.002 PHE B 59 TYR 0.015 0.002 TYR B 163 ARG 0.008 0.001 ARG A 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 186 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: A 28 THR cc_start: 0.8443 (m) cc_final: 0.8211 (m) REVERT: A 32 LYS cc_start: 0.9013 (tptt) cc_final: 0.8608 (tptt) REVERT: A 37 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7798 (mp10) REVERT: A 39 VAL cc_start: 0.8529 (t) cc_final: 0.8296 (m) REVERT: A 69 LYS cc_start: 0.8904 (mmmt) cc_final: 0.8652 (mmmm) REVERT: A 71 ARG cc_start: 0.6784 (mmt-90) cc_final: 0.5059 (mmt-90) REVERT: B 73 LEU cc_start: 0.7871 (tp) cc_final: 0.7607 (tp) REVERT: B 123 LYS cc_start: 0.8858 (mttt) cc_final: 0.8534 (mttt) REVERT: B 130 MET cc_start: 0.7425 (mtm) cc_final: 0.6333 (mtm) REVERT: C 37 GLN cc_start: 0.8639 (mt0) cc_final: 0.8414 (mt0) REVERT: C 73 LEU cc_start: 0.7969 (tp) cc_final: 0.7611 (tp) REVERT: C 89 ASP cc_start: 0.8536 (t0) cc_final: 0.8247 (t0) REVERT: C 101 GLN cc_start: 0.7871 (mm-40) cc_final: 0.7355 (mt0) REVERT: C 133 HIS cc_start: 0.6851 (p-80) cc_final: 0.6598 (p-80) REVERT: D 32 LYS cc_start: 0.9011 (tppt) cc_final: 0.7831 (tppt) REVERT: D 125 ASP cc_start: 0.8285 (p0) cc_final: 0.7731 (m-30) outliers start: 11 outliers final: 6 residues processed: 191 average time/residue: 0.2641 time to fit residues: 59.5626 Evaluate side-chains 193 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 187 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 70 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 23 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN B 136 GLN C 56 ASN C 172 ASN D 152 GLN D 172 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.120627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.097791 restraints weight = 7065.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.101147 restraints weight = 4557.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.103662 restraints weight = 3329.669| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 5568 Z= 0.306 Angle : 0.686 8.449 7564 Z= 0.340 Chirality : 0.051 0.166 832 Planarity : 0.004 0.033 940 Dihedral : 15.550 123.554 784 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.17 % Allowed : 12.33 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.32), residues: 648 helix: -0.26 (0.34), residues: 240 sheet: -0.03 (0.35), residues: 172 loop : -0.49 (0.38), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 149 HIS 0.003 0.001 HIS A 104 PHE 0.016 0.002 PHE B 59 TYR 0.020 0.002 TYR A 150 ARG 0.004 0.001 ARG A 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.9022 (tptt) cc_final: 0.8696 (tptt) REVERT: B 15 ARG cc_start: 0.7317 (mtp85) cc_final: 0.6929 (mtp85) REVERT: B 73 LEU cc_start: 0.7955 (tp) cc_final: 0.7699 (tp) REVERT: B 130 MET cc_start: 0.7546 (mtm) cc_final: 0.6653 (mtm) REVERT: C 37 GLN cc_start: 0.8758 (mt0) cc_final: 0.8552 (mt0) REVERT: C 73 LEU cc_start: 0.7979 (tp) cc_final: 0.7636 (tp) REVERT: C 133 HIS cc_start: 0.6907 (p-80) cc_final: 0.6583 (p-80) REVERT: C 160 ASP cc_start: 0.7636 (t0) cc_final: 0.7247 (t0) REVERT: D 32 LYS cc_start: 0.9083 (tppt) cc_final: 0.8743 (tppt) REVERT: D 37 GLN cc_start: 0.7798 (mp10) cc_final: 0.7544 (mp10) REVERT: D 54 TYR cc_start: 0.7831 (t80) cc_final: 0.6936 (t80) REVERT: D 70 ILE cc_start: 0.9222 (OUTLIER) cc_final: 0.9014 (mp) REVERT: D 125 ASP cc_start: 0.8417 (p0) cc_final: 0.7669 (m-30) outliers start: 24 outliers final: 13 residues processed: 192 average time/residue: 0.2698 time to fit residues: 61.3158 Evaluate side-chains 191 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 177 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 170 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 28 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 43 optimal weight: 0.0470 chunk 24 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.122068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.097930 restraints weight = 7185.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.101438 restraints weight = 4589.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.104149 restraints weight = 3327.259| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5568 Z= 0.227 Angle : 0.632 6.832 7564 Z= 0.310 Chirality : 0.049 0.168 832 Planarity : 0.004 0.033 940 Dihedral : 14.799 123.793 784 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.99 % Allowed : 14.06 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.32), residues: 648 helix: 0.07 (0.35), residues: 240 sheet: 0.09 (0.36), residues: 172 loop : -0.64 (0.38), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 168 HIS 0.003 0.001 HIS C 104 PHE 0.012 0.002 PHE B 59 TYR 0.013 0.001 TYR A 150 ARG 0.007 0.000 ARG B 93 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASP cc_start: 0.8688 (p0) cc_final: 0.7878 (m-30) REVERT: B 15 ARG cc_start: 0.7368 (mtp85) cc_final: 0.6963 (mtp85) REVERT: B 73 LEU cc_start: 0.8043 (tp) cc_final: 0.7753 (tp) REVERT: C 73 LEU cc_start: 0.7984 (tp) cc_final: 0.7628 (tp) REVERT: C 95 ARG cc_start: 0.7307 (ptp-170) cc_final: 0.7038 (ttm170) REVERT: C 141 LEU cc_start: 0.8664 (mt) cc_final: 0.8432 (mt) REVERT: C 174 LYS cc_start: 0.7110 (pptt) cc_final: 0.6896 (pttp) REVERT: D 14 MET cc_start: 0.8437 (ttt) cc_final: 0.8185 (ttm) REVERT: D 32 LYS cc_start: 0.9057 (tppt) cc_final: 0.8744 (tppt) REVERT: D 37 GLN cc_start: 0.7792 (mp10) cc_final: 0.7549 (mp10) REVERT: D 125 ASP cc_start: 0.8399 (p0) cc_final: 0.7645 (m-30) REVERT: D 138 LYS cc_start: 0.8369 (mmmm) cc_final: 0.8080 (mtpp) outliers start: 23 outliers final: 14 residues processed: 180 average time/residue: 0.2618 time to fit residues: 55.8005 Evaluate side-chains 174 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain D residue 120 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 0.6980 chunk 44 optimal weight: 0.4980 chunk 1 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN C 124 GLN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.124380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.101161 restraints weight = 7010.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.104585 restraints weight = 4556.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.107149 restraints weight = 3328.448| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5568 Z= 0.157 Angle : 0.609 6.585 7564 Z= 0.295 Chirality : 0.048 0.183 832 Planarity : 0.004 0.040 940 Dihedral : 13.878 113.965 784 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.12 % Allowed : 15.28 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.33), residues: 648 helix: 0.46 (0.36), residues: 236 sheet: 0.36 (0.37), residues: 172 loop : -0.55 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 62 HIS 0.003 0.001 HIS C 104 PHE 0.011 0.001 PHE B 59 TYR 0.016 0.001 TYR A 54 ARG 0.006 0.000 ARG C 15 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 0.597 Fit side-chains REVERT: A 32 LYS cc_start: 0.8904 (tptt) cc_final: 0.8636 (tptt) REVERT: A 69 LYS cc_start: 0.9018 (mmmt) cc_final: 0.8716 (mmmt) REVERT: A 125 ASP cc_start: 0.8676 (p0) cc_final: 0.7938 (m-30) REVERT: B 15 ARG cc_start: 0.7290 (mtp85) cc_final: 0.6838 (mtp85) REVERT: B 73 LEU cc_start: 0.8007 (tp) cc_final: 0.7688 (tp) REVERT: C 73 LEU cc_start: 0.7886 (tp) cc_final: 0.7529 (tp) REVERT: C 133 HIS cc_start: 0.6853 (p-80) cc_final: 0.6629 (p-80) REVERT: C 141 LEU cc_start: 0.8716 (mt) cc_final: 0.8484 (mt) REVERT: C 174 LYS cc_start: 0.7180 (pptt) cc_final: 0.6936 (ptmm) REVERT: D 14 MET cc_start: 0.8466 (ttt) cc_final: 0.8205 (ttm) REVERT: D 32 LYS cc_start: 0.9032 (tppt) cc_final: 0.8743 (tppt) REVERT: D 138 LYS cc_start: 0.8331 (mmmm) cc_final: 0.8097 (mtpp) outliers start: 18 outliers final: 9 residues processed: 171 average time/residue: 0.2709 time to fit residues: 54.5379 Evaluate side-chains 170 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 161 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain C residue 17 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 3 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.124441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.101360 restraints weight = 6979.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.104770 restraints weight = 4549.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.107344 restraints weight = 3324.583| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5568 Z= 0.174 Angle : 0.621 6.566 7564 Z= 0.298 Chirality : 0.049 0.188 832 Planarity : 0.004 0.039 940 Dihedral : 13.531 112.475 784 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.82 % Allowed : 16.49 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.33), residues: 648 helix: 0.57 (0.36), residues: 236 sheet: 0.50 (0.38), residues: 172 loop : -0.62 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 168 HIS 0.002 0.001 HIS C 104 PHE 0.012 0.001 PHE B 59 TYR 0.013 0.001 TYR A 54 ARG 0.002 0.000 ARG C 15 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 0.625 Fit side-chains revert: symmetry clash REVERT: A 37 GLN cc_start: 0.8179 (mp10) cc_final: 0.7938 (mp10) REVERT: A 69 LYS cc_start: 0.8988 (mmmt) cc_final: 0.8543 (mmmt) REVERT: A 125 ASP cc_start: 0.8669 (p0) cc_final: 0.7970 (m-30) REVERT: B 15 ARG cc_start: 0.7386 (mtp85) cc_final: 0.6936 (mtp85) REVERT: B 73 LEU cc_start: 0.7996 (tp) cc_final: 0.7684 (tp) REVERT: C 37 GLN cc_start: 0.8661 (mt0) cc_final: 0.8423 (mt0) REVERT: C 73 LEU cc_start: 0.7898 (tp) cc_final: 0.7532 (tp) REVERT: C 133 HIS cc_start: 0.6875 (p-80) cc_final: 0.6632 (p-80) REVERT: C 141 LEU cc_start: 0.8680 (mt) cc_final: 0.8439 (mt) REVERT: C 174 LYS cc_start: 0.7130 (pptt) cc_final: 0.6913 (ptmm) REVERT: D 32 LYS cc_start: 0.9097 (tppt) cc_final: 0.8817 (tppt) REVERT: D 125 ASP cc_start: 0.8284 (p0) cc_final: 0.7389 (m-30) outliers start: 22 outliers final: 13 residues processed: 171 average time/residue: 0.2639 time to fit residues: 53.5346 Evaluate side-chains 172 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 113 ARG Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 154 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 2.9990 chunk 12 optimal weight: 0.1980 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 60 optimal weight: 0.0970 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN C 56 ASN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.122944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.099839 restraints weight = 7207.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.103205 restraints weight = 4705.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.105758 restraints weight = 3452.967| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.5278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5568 Z= 0.194 Angle : 0.623 6.888 7564 Z= 0.300 Chirality : 0.049 0.197 832 Planarity : 0.004 0.040 940 Dihedral : 13.426 111.543 784 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.65 % Allowed : 17.88 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.33), residues: 648 helix: 0.55 (0.36), residues: 236 sheet: 0.32 (0.38), residues: 184 loop : -0.47 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 168 HIS 0.003 0.001 HIS B 104 PHE 0.009 0.001 PHE B 59 TYR 0.012 0.001 TYR A 54 ARG 0.004 0.000 ARG D 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8961 (mmmt) cc_final: 0.8495 (mmmt) REVERT: A 108 ASN cc_start: 0.7349 (m-40) cc_final: 0.6835 (m-40) REVERT: A 125 ASP cc_start: 0.8632 (p0) cc_final: 0.7964 (m-30) REVERT: B 15 ARG cc_start: 0.7324 (mtp85) cc_final: 0.7027 (mtp85) REVERT: B 73 LEU cc_start: 0.7978 (tp) cc_final: 0.7684 (tp) REVERT: B 101 GLN cc_start: 0.8226 (mm-40) cc_final: 0.7792 (mt0) REVERT: C 37 GLN cc_start: 0.8648 (mt0) cc_final: 0.8390 (mt0) REVERT: C 73 LEU cc_start: 0.7872 (tp) cc_final: 0.7522 (tp) REVERT: C 123 LYS cc_start: 0.8921 (mttt) cc_final: 0.8262 (pttt) REVERT: C 133 HIS cc_start: 0.6915 (p-80) cc_final: 0.6587 (p-80) REVERT: C 141 LEU cc_start: 0.8671 (mt) cc_final: 0.8446 (mt) REVERT: C 174 LYS cc_start: 0.7190 (pptt) cc_final: 0.6984 (ptmm) REVERT: D 14 MET cc_start: 0.8550 (ttt) cc_final: 0.8295 (ttm) REVERT: D 32 LYS cc_start: 0.9076 (tppt) cc_final: 0.8769 (tppt) REVERT: D 125 ASP cc_start: 0.8254 (p0) cc_final: 0.7509 (m-30) outliers start: 21 outliers final: 14 residues processed: 163 average time/residue: 0.2761 time to fit residues: 52.9146 Evaluate side-chains 163 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 154 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 50 optimal weight: 0.0020 chunk 54 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN C 56 ASN C 124 GLN ** D 122 ASN ** 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 = 0.3310 r_free = 0.3310 target = 0.124458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.101389 restraints weight = 7156.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.104790 restraints weight = 4657.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.107379 restraints weight = 3409.966| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.5448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5568 Z= 0.178 Angle : 0.627 8.174 7564 Z= 0.300 Chirality : 0.049 0.203 832 Planarity : 0.004 0.042 940 Dihedral : 13.189 107.394 784 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.65 % Allowed : 17.71 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.34), residues: 648 helix: 0.60 (0.36), residues: 236 sheet: 0.38 (0.38), residues: 184 loop : -0.55 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 168 HIS 0.002 0.001 HIS C 104 PHE 0.009 0.001 PHE B 59 TYR 0.013 0.001 TYR A 54 ARG 0.002 0.000 ARG B 93 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.547 Fit side-chains revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8952 (mmmt) cc_final: 0.8460 (mmmt) REVERT: A 108 ASN cc_start: 0.7359 (m-40) cc_final: 0.6831 (m-40) REVERT: A 125 ASP cc_start: 0.8616 (p0) cc_final: 0.7905 (m-30) REVERT: B 15 ARG cc_start: 0.7418 (mtp85) cc_final: 0.6899 (mtp85) REVERT: B 73 LEU cc_start: 0.7916 (tp) cc_final: 0.7604 (tp) REVERT: B 101 GLN cc_start: 0.8266 (mm-40) cc_final: 0.7845 (mt0) REVERT: C 37 GLN cc_start: 0.8680 (mt0) cc_final: 0.8418 (mt0) REVERT: C 73 LEU cc_start: 0.7835 (tp) cc_final: 0.7477 (tp) REVERT: C 133 HIS cc_start: 0.6961 (p-80) cc_final: 0.6587 (p-80) REVERT: C 141 LEU cc_start: 0.8680 (mt) cc_final: 0.8432 (mt) REVERT: C 174 LYS cc_start: 0.7116 (pptt) cc_final: 0.6906 (ptmm) REVERT: D 14 MET cc_start: 0.8563 (ttt) cc_final: 0.8329 (ttm) REVERT: D 32 LYS cc_start: 0.9056 (tppt) cc_final: 0.8752 (tppt) REVERT: D 101 GLN cc_start: 0.8330 (tt0) cc_final: 0.7832 (tm-30) REVERT: D 125 ASP cc_start: 0.8288 (p0) cc_final: 0.7522 (m-30) outliers start: 21 outliers final: 15 residues processed: 161 average time/residue: 0.2709 time to fit residues: 51.5342 Evaluate side-chains 162 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 154 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 16 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN C 56 ASN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.126210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.102684 restraints weight = 7184.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.106179 restraints weight = 4721.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.108643 restraints weight = 3485.752| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.5524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5568 Z= 0.160 Angle : 0.635 7.587 7564 Z= 0.302 Chirality : 0.049 0.205 832 Planarity : 0.004 0.043 940 Dihedral : 12.948 104.674 784 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.43 % Allowed : 19.10 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.34), residues: 648 helix: 0.70 (0.36), residues: 236 sheet: 0.51 (0.39), residues: 184 loop : -0.57 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 168 HIS 0.002 0.000 HIS C 104 PHE 0.008 0.001 PHE B 59 TYR 0.013 0.001 TYR A 54 ARG 0.004 0.000 ARG D 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8930 (mmmt) cc_final: 0.8440 (mmmt) REVERT: A 95 ARG cc_start: 0.7592 (ptm160) cc_final: 0.7201 (ptm160) REVERT: A 108 ASN cc_start: 0.7348 (m-40) cc_final: 0.6820 (m-40) REVERT: A 125 ASP cc_start: 0.8524 (p0) cc_final: 0.8021 (m-30) REVERT: A 168 TRP cc_start: 0.8736 (t60) cc_final: 0.8098 (t60) REVERT: B 15 ARG cc_start: 0.7380 (mtp85) cc_final: 0.6852 (mtp85) REVERT: B 73 LEU cc_start: 0.7908 (tp) cc_final: 0.7625 (tp) REVERT: B 101 GLN cc_start: 0.8241 (mm-40) cc_final: 0.7837 (mt0) REVERT: C 37 GLN cc_start: 0.8666 (mt0) cc_final: 0.8412 (mt0) REVERT: C 73 LEU cc_start: 0.7824 (tp) cc_final: 0.7476 (tp) REVERT: C 123 LYS cc_start: 0.8669 (mttt) cc_final: 0.8394 (pttt) REVERT: C 133 HIS cc_start: 0.6940 (p-80) cc_final: 0.6558 (p-80) REVERT: C 141 LEU cc_start: 0.8731 (mt) cc_final: 0.8485 (mt) REVERT: D 14 MET cc_start: 0.8544 (ttt) cc_final: 0.8288 (ttm) REVERT: D 32 LYS cc_start: 0.9038 (tppt) cc_final: 0.8720 (tppt) REVERT: D 108 ASN cc_start: 0.7154 (m-40) cc_final: 0.6953 (m-40) REVERT: D 125 ASP cc_start: 0.8304 (p0) cc_final: 0.7557 (m-30) outliers start: 14 outliers final: 10 residues processed: 160 average time/residue: 0.2841 time to fit residues: 53.4221 Evaluate side-chains 160 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 150 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 154 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 20 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 chunk 26 optimal weight: 0.0870 chunk 42 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 GLN ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 GLN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.121598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.098109 restraints weight = 7255.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.101382 restraints weight = 4841.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.103817 restraints weight = 3613.548| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.5700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5568 Z= 0.242 Angle : 0.676 7.537 7564 Z= 0.326 Chirality : 0.051 0.203 832 Planarity : 0.004 0.043 940 Dihedral : 13.410 107.523 784 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.43 % Allowed : 19.97 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.33), residues: 648 helix: 0.53 (0.36), residues: 236 sheet: 0.31 (0.38), residues: 184 loop : -0.60 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 168 HIS 0.007 0.001 HIS B 104 PHE 0.010 0.002 PHE D 120 TYR 0.012 0.001 TYR B 163 ARG 0.005 0.000 ARG B 93 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 0.626 Fit side-chains revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8890 (tptt) cc_final: 0.8651 (tptp) REVERT: A 69 LYS cc_start: 0.8884 (mmmt) cc_final: 0.8403 (mmmt) REVERT: A 95 ARG cc_start: 0.7752 (ptm160) cc_final: 0.7305 (ptm160) REVERT: A 108 ASN cc_start: 0.7405 (m-40) cc_final: 0.6873 (m-40) REVERT: A 125 ASP cc_start: 0.8484 (p0) cc_final: 0.8014 (m-30) REVERT: B 15 ARG cc_start: 0.7266 (mtp85) cc_final: 0.6791 (mtp85) REVERT: B 73 LEU cc_start: 0.8028 (tp) cc_final: 0.7722 (tp) REVERT: B 101 GLN cc_start: 0.8284 (mm-40) cc_final: 0.7794 (mt0) REVERT: B 102 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6855 (mm-30) REVERT: C 37 GLN cc_start: 0.8681 (mt0) cc_final: 0.8424 (mt0) REVERT: C 73 LEU cc_start: 0.7913 (tp) cc_final: 0.7559 (tp) REVERT: C 141 LEU cc_start: 0.8668 (mt) cc_final: 0.8424 (mt) REVERT: D 32 LYS cc_start: 0.8978 (tppt) cc_final: 0.8673 (tppt) REVERT: D 125 ASP cc_start: 0.8314 (p0) cc_final: 0.7605 (m-30) outliers start: 14 outliers final: 12 residues processed: 162 average time/residue: 0.2756 time to fit residues: 52.7114 Evaluate side-chains 163 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 154 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 46 optimal weight: 0.4980 chunk 11 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 12 optimal weight: 0.6980 chunk 41 optimal weight: 7.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.124039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.100977 restraints weight = 7196.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.104413 restraints weight = 4731.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.106930 restraints weight = 3477.255| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.5736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5568 Z= 0.182 Angle : 0.658 8.119 7564 Z= 0.313 Chirality : 0.050 0.201 832 Planarity : 0.004 0.043 940 Dihedral : 13.044 106.052 784 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.43 % Allowed : 19.97 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.34), residues: 648 helix: 0.61 (0.36), residues: 236 sheet: 0.38 (0.39), residues: 184 loop : -0.63 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 168 HIS 0.007 0.001 HIS B 104 PHE 0.009 0.001 PHE D 120 TYR 0.017 0.001 TYR D 54 ARG 0.004 0.000 ARG B 93 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3605.64 seconds wall clock time: 62 minutes 24.53 seconds (3744.53 seconds total)