Starting phenix.real_space_refine on Fri Aug 22 19:53:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fgx_50432/08_2025/9fgx_50432_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fgx_50432/08_2025/9fgx_50432.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fgx_50432/08_2025/9fgx_50432.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fgx_50432/08_2025/9fgx_50432.map" model { file = "/net/cci-nas-00/data/ceres_data/9fgx_50432/08_2025/9fgx_50432_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fgx_50432/08_2025/9fgx_50432_trim.cif" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 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: 5 Type Number sf(0) Gaussians S 34 5.16 5 C 2394 2.51 5 N 712 2.21 5 O 754 1.98 5 H 3644 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7538 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 1856 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 126, 1855 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Conformer: "B" Number of residues, atoms: 126, 1855 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} bond proxies already assigned to first conformer: 1871 Chain: "D" Number of atoms: 1907 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 128, 1906 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 125} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Conformer: "B" Number of residues, atoms: 128, 1906 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 125} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 bond proxies already assigned to first conformer: 1925 Chain: "E" Number of atoms: 1856 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 126, 1855 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Conformer: "B" Number of residues, atoms: 126, 1855 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} bond proxies already assigned to first conformer: 1871 Chain: "F" Number of atoms: 1907 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 128, 1906 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 125} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Conformer: "B" Number of residues, atoms: 128, 1906 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 125} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 bond proxies already assigned to first conformer: 1925 Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 1, 6 Unusual residues: {'GOL': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 6 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 1, 6 Unusual residues: {'GOL': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" C1 AGOL C 201 " occ=0.11 ... (4 atoms not shown) pdb=" O3 AGOL C 201 " occ=0.11 residue: pdb=" C1 AGOL E 201 " occ=0.20 ... (4 atoms not shown) pdb=" O3 AGOL E 201 " occ=0.20 Time building chain proxies: 1.97, per 1000 atoms: 0.26 Number of scatterers: 7538 At special positions: 0 Unit cell: (48.91, 68.62, 144.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 34 16.00 O 754 8.00 N 712 7.00 C 2394 6.00 H 3644 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS C 11 " - pdb=" SG CYS E 11 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 6 " - pdb=" SG CYS D 127 " distance=2.03 Simple disulfide: pdb=" SG CYS D 30 " - pdb=" SG CYS D 115 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 80 " distance=2.03 Simple disulfide: pdb=" SG CYS D 76 " - pdb=" SG CYS D 94 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 6 " - pdb=" SG CYS F 127 " distance=2.03 Simple disulfide: pdb=" SG CYS F 30 " - pdb=" SG CYS F 115 " distance=2.03 Simple disulfide: pdb=" SG CYS F 64 " - pdb=" SG CYS F 80 " distance=2.03 Simple disulfide: pdb=" SG CYS F 76 " - pdb=" SG CYS F 94 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.48 Conformation dependent library (CDL) restraints added in 297.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 916 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 6 sheets defined 33.3% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'C' and resid 28 through 31 Processing helix chain 'D' and resid 4 through 16 Processing helix chain 'D' and resid 19 through 23 removed outlier: 4.149A pdb=" N GLY D 22 " --> pdb=" O ASN D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 37 removed outlier: 3.708A pdb=" N TRP D 28 " --> pdb=" O SER D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 85 removed outlier: 3.545A pdb=" N LEU D 83 " --> pdb=" O PRO D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 101 removed outlier: 3.630A pdb=" N LYS D 97 " --> pdb=" O ASN D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 107 removed outlier: 7.111A pdb=" N MET D 105 " --> pdb=" O GLY D 102 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN D 106 " --> pdb=" O ASN D 103 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 102 through 107' Processing helix chain 'D' and resid 108 through 115 Processing helix chain 'D' and resid 120 through 125 removed outlier: 4.007A pdb=" N ILE D 124 " --> pdb=" O VAL D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 31 removed outlier: 3.546A pdb=" N SER E 30 " --> pdb=" O SER E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 104 through 108 Processing helix chain 'F' and resid 4 through 16 Processing helix chain 'F' and resid 19 through 23 removed outlier: 4.227A pdb=" N GLY F 22 " --> pdb=" O ASN F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 37 removed outlier: 3.694A pdb=" N TRP F 28 " --> pdb=" O SER F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 85 removed outlier: 3.551A pdb=" N LEU F 83 " --> pdb=" O PRO F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 101 removed outlier: 3.638A pdb=" N LYS F 97 " --> pdb=" O ASN F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 107 removed outlier: 7.163A pdb=" N MET F 105 " --> pdb=" O GLY F 102 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN F 106 " --> pdb=" O ASN F 103 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA F 107 " --> pdb=" O GLY F 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 102 through 107' Processing helix chain 'F' and resid 108 through 115 Processing helix chain 'F' and resid 120 through 125 removed outlier: 4.007A pdb=" N ILE F 124 " --> pdb=" O VAL F 120 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 2 through 7 removed outlier: 3.687A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.605A pdb=" N ALA C 92 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE C 93 " --> pdb=" O GLN C 39 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR C 33 " --> pdb=" O THR C 99 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N MET C 34 " --> pdb=" O ALA C 50 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ALA C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU C 46 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 44 through 45 removed outlier: 3.740A pdb=" N ASN D 44 " --> pdb=" O ASP D 52 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 4 through 8 removed outlier: 3.594A pdb=" N MET E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.225A pdb=" N GLY E 10 " --> pdb=" O MET E 124 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR E 99 " --> pdb=" O TYR E 33 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR E 33 " --> pdb=" O THR E 99 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N MET E 34 " --> pdb=" O ALA E 50 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ALA E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU E 46 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 44 through 45 removed outlier: 3.617A pdb=" N ASN F 44 " --> pdb=" O ASP F 52 " (cutoff:3.500A) 143 hydrogen bonds defined for protein. 372 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: 1.34 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3644 1.03 - 1.23: 10 1.23 - 1.43: 1740 1.43 - 1.62: 2170 1.62 - 1.82: 46 Bond restraints: 7610 Sorted by residual: bond pdb=" N ASP C 1 " pdb=" CA ASP C 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 bond pdb=" N ASP E 1 " pdb=" CA ASP E 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 bond pdb=" C1 AGOL C 201 " pdb=" C2 AGOL C 201 " ideal model delta sigma weight residual 1.514 1.547 -0.033 2.00e-02 2.50e+03 2.68e+00 bond pdb=" N ASP E 1 " pdb=" H ASP E 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.26e+00 bond pdb=" N ASP C 1 " pdb=" H ASP C 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.24e+00 ... (remaining 7605 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 12891 1.09 - 2.18: 629 2.18 - 3.27: 23 3.27 - 4.36: 9 4.36 - 5.44: 4 Bond angle restraints: 13556 Sorted by residual: angle pdb=" C1 AGOL E 201 " pdb=" C2 AGOL E 201 " pdb=" C3 AGOL E 201 " ideal model delta sigma weight residual 110.15 104.71 5.44 3.00e+00 1.11e-01 3.29e+00 angle pdb=" C1 AGOL C 201 " pdb=" C2 AGOL C 201 " pdb=" C3 AGOL C 201 " ideal model delta sigma weight residual 110.15 104.79 5.36 3.00e+00 1.11e-01 3.20e+00 angle pdb=" C LYS C 76 " pdb=" N ASN C 77 " pdb=" CA ASN C 77 " ideal model delta sigma weight residual 121.54 124.95 -3.41 1.91e+00 2.74e-01 3.18e+00 angle pdb=" C CYS F 76 " pdb=" N ASN F 77 " pdb=" CA ASN F 77 " ideal model delta sigma weight residual 121.54 124.76 -3.22 1.91e+00 2.74e-01 2.83e+00 angle pdb=" CA GLN E 111 " pdb=" CB GLN E 111 " pdb=" CG GLN E 111 " ideal model delta sigma weight residual 114.10 117.39 -3.29 2.00e+00 2.50e-01 2.71e+00 ... (remaining 13551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.43: 3238 15.43 - 30.87: 279 30.87 - 46.30: 89 46.30 - 61.73: 35 61.73 - 77.17: 4 Dihedral angle restraints: 3645 sinusoidal: 1947 harmonic: 1698 Sorted by residual: dihedral pdb=" CB CYS C 11 " pdb=" SG CYS C 11 " pdb=" SG CYS E 11 " pdb=" CB CYS E 11 " ideal model delta sinusoidal sigma weight residual -86.00 -112.13 26.13 1 1.00e+01 1.00e-02 9.81e+00 dihedral pdb=" CA GLN E 122 " pdb=" CB GLN E 122 " pdb=" CG GLN E 122 " pdb=" CD GLN E 122 " ideal model delta sinusoidal sigma weight residual -60.00 -105.42 45.42 3 1.50e+01 4.44e-03 8.17e+00 dihedral pdb=" CA ARG D 68 " pdb=" CB ARG D 68 " pdb=" CG ARG D 68 " pdb=" CD ARG D 68 " ideal model delta sinusoidal sigma weight residual -60.00 -103.46 43.46 3 1.50e+01 4.44e-03 7.81e+00 ... (remaining 3642 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 394 0.029 - 0.058: 134 0.058 - 0.087: 21 0.087 - 0.116: 17 0.116 - 0.145: 6 Chirality restraints: 572 Sorted by residual: chirality pdb=" CA ILE F 78 " pdb=" N ILE F 78 " pdb=" C ILE F 78 " pdb=" CB ILE F 78 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.24e-01 chirality pdb=" CA ILE D 78 " pdb=" N ILE D 78 " pdb=" C ILE D 78 " pdb=" CB ILE D 78 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA ILE C 93 " pdb=" N ILE C 93 " pdb=" C ILE C 93 " pdb=" CB ILE C 93 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.05e-01 ... (remaining 569 not shown) Planarity restraints: 1198 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 103 " -0.018 5.00e-02 4.00e+02 2.77e-02 1.23e+00 pdb=" N PRO C 104 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO C 104 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 104 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 103 " 0.018 5.00e-02 4.00e+02 2.70e-02 1.17e+00 pdb=" N PRO E 104 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO E 104 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO E 104 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 76 " 0.005 2.00e-02 2.50e+03 9.78e-03 9.56e-01 pdb=" C LYS C 76 " -0.017 2.00e-02 2.50e+03 pdb=" O LYS C 76 " 0.006 2.00e-02 2.50e+03 pdb=" N ASN C 77 " 0.006 2.00e-02 2.50e+03 ... (remaining 1195 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 399 2.18 - 2.78: 15012 2.78 - 3.39: 21362 3.39 - 3.99: 27356 3.99 - 4.60: 42500 Nonbonded interactions: 106629 Sorted by model distance: nonbonded pdb="HH22 ARG C 67 " pdb=" OD2 ASP C 90 " model vdw 1.571 2.450 nonbonded pdb=" OE1 GLN C 3 " pdb=" H GLN C 3 " model vdw 1.644 2.450 nonbonded pdb=" O TRP D 62 " pdb=" H LEU D 75 " model vdw 1.690 2.450 nonbonded pdb=" O ALA C 108 " pdb=" HH TYR C 114 " model vdw 1.706 2.450 nonbonded pdb=" OE2 GLU C 32 " pdb="HH12 ARG D 112 " model vdw 1.718 2.450 ... (remaining 106624 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 1 through 88 or resid 90 through 126)) selection = (chain 'E' and (resid 1 through 88 or resid 90 through 126)) } ncs_group { reference = (chain 'D' and (resid 2 through 97 or resid 99 through 129)) selection = (chain 'F' and (resid 2 through 97 or resid 99 through 129)) } 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=0.00 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: 4.310 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: 0.030 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.240 Find NCS groups from input model: 0.110 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:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4662 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 0.033 3977 Z= 0.110 Angle : 0.434 5.445 5386 Z= 0.233 Chirality : 0.036 0.145 572 Planarity : 0.003 0.033 698 Dihedral : 12.504 66.978 1404 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.41), residues: 500 helix: 1.80 (0.55), residues: 100 sheet: 0.49 (0.45), residues: 142 loop : 1.51 (0.44), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 73 TYR 0.007 0.001 TYR C 59 PHE 0.006 0.001 PHE D 38 TRP 0.009 0.001 TRP F 63 HIS 0.003 0.001 HIS E 54 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 3966) covalent geometry : angle 0.42680 ( 5364) SS BOND : bond 0.00221 ( 11) SS BOND : angle 1.28744 ( 22) hydrogen bonds : bond 0.20352 ( 143) hydrogen bonds : angle 10.13732 ( 372) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 124 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 124 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Evaluate side-chains 72 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0754 time to fit residues: 7.4036 Evaluate side-chains 62 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 0.4980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 ASN F 46 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4880 r_free = 0.4880 target = 0.256634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.225263 restraints weight = 12409.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.233888 restraints weight = 7182.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.239640 restraints weight = 4644.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.243439 restraints weight = 3215.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.246112 restraints weight = 2344.312| |-----------------------------------------------------------------------------| r_work (final): 0.4833 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4833 r_free = 0.4833 target_work(ls_wunit_k1) = 0.249 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4814 r_free = 0.4814 target_work(ls_wunit_k1) = 0.247 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5128 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3977 Z= 0.178 Angle : 0.558 4.429 5386 Z= 0.310 Chirality : 0.039 0.164 572 Planarity : 0.004 0.036 698 Dihedral : 4.457 35.260 568 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.99 % Allowed : 7.67 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.40), residues: 500 helix: 1.20 (0.55), residues: 102 sheet: 0.08 (0.47), residues: 128 loop : 1.20 (0.42), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 68 TYR 0.024 0.002 TYR E 33 PHE 0.011 0.001 PHE F 3 TRP 0.013 0.002 TRP D 108 HIS 0.004 0.002 HIS D 15 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 3966) covalent geometry : angle 0.55402 ( 5364) SS BOND : bond 0.00396 ( 11) SS BOND : angle 1.19982 ( 22) hydrogen bonds : bond 0.03775 ( 143) hydrogen bonds : angle 7.17886 ( 372) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 124 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 124 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Evaluate side-chains 73 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 124 MET cc_start: 0.5130 (mmm) cc_final: 0.4435 (mmm) REVERT: E 101 LYS cc_start: 0.6850 (mmtt) cc_final: 0.6365 (mttp) outliers start: 4 outliers final: 3 residues processed: 72 average time/residue: 0.0814 time to fit residues: 7.8531 Evaluate side-chains 64 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 CYS Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain E residue 81 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 30 optimal weight: 0.2980 chunk 1 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 26 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 ASN D 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4874 r_free = 0.4874 target = 0.255270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.223357 restraints weight = 12603.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.231907 restraints weight = 7235.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.237951 restraints weight = 4681.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.241934 restraints weight = 3225.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.244725 restraints weight = 2343.483| |-----------------------------------------------------------------------------| r_work (final): 0.4795 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4795 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4795 r_free = 0.4795 target_work(ls_wunit_k1) = 0.245 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4795 r_free = 0.4795 target_work(ls_wunit_k1) = 0.245 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4795 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5163 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3977 Z= 0.148 Angle : 0.514 4.045 5386 Z= 0.285 Chirality : 0.038 0.149 572 Planarity : 0.003 0.029 698 Dihedral : 4.731 41.126 568 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.99 % Allowed : 10.15 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.40), residues: 500 helix: 1.02 (0.54), residues: 102 sheet: -0.07 (0.47), residues: 128 loop : 1.22 (0.42), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 112 TYR 0.015 0.002 TYR C 94 PHE 0.006 0.001 PHE D 34 TRP 0.012 0.001 TRP D 28 HIS 0.003 0.001 HIS E 54 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 3966) covalent geometry : angle 0.50745 ( 5364) SS BOND : bond 0.00381 ( 11) SS BOND : angle 1.39616 ( 22) hydrogen bonds : bond 0.03537 ( 143) hydrogen bonds : angle 6.83070 ( 372) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 124 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 124 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Evaluate side-chains 65 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 124 MET cc_start: 0.5132 (mmm) cc_final: 0.4338 (mmm) REVERT: E 101 LYS cc_start: 0.6998 (mmtt) cc_final: 0.6489 (mttp) outliers start: 4 outliers final: 3 residues processed: 64 average time/residue: 0.0759 time to fit residues: 6.5396 Evaluate side-chains 63 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 CYS Chi-restraints excluded: chain D residue 39 ASN Chi-restraints excluded: chain E residue 81 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 7 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 40 optimal weight: 0.0570 chunk 30 optimal weight: 0.0770 chunk 31 optimal weight: 0.3980 chunk 14 optimal weight: 2.9990 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4878 r_free = 0.4878 target = 0.255765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.224375 restraints weight = 12736.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.233131 restraints weight = 7305.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.238971 restraints weight = 4684.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.242888 restraints weight = 3230.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.245512 restraints weight = 2341.939| |-----------------------------------------------------------------------------| r_work (final): 0.4802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4802 r_free = 0.4802 target_work(ls_wunit_k1) = 0.245 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4802 r_free = 0.4802 target_work(ls_wunit_k1) = 0.245 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4802 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5152 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3977 Z= 0.120 Angle : 0.485 4.366 5386 Z= 0.267 Chirality : 0.037 0.160 572 Planarity : 0.003 0.026 698 Dihedral : 4.459 35.351 568 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.74 % Allowed : 9.65 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.40), residues: 500 helix: 1.05 (0.55), residues: 102 sheet: -0.15 (0.44), residues: 142 loop : 1.23 (0.44), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 112 TYR 0.014 0.001 TYR C 94 PHE 0.005 0.001 PHE D 34 TRP 0.007 0.001 TRP D 28 HIS 0.003 0.001 HIS E 54 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 3966) covalent geometry : angle 0.47752 ( 5364) SS BOND : bond 0.00281 ( 11) SS BOND : angle 1.43389 ( 22) hydrogen bonds : bond 0.03053 ( 143) hydrogen bonds : angle 6.65211 ( 372) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 124 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 124 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Evaluate side-chains 61 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 101 LYS cc_start: 0.7037 (mmtt) cc_final: 0.6535 (mttp) outliers start: 3 outliers final: 3 residues processed: 61 average time/residue: 0.0933 time to fit residues: 7.4337 Evaluate side-chains 59 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 CYS Chi-restraints excluded: chain D residue 39 ASN Chi-restraints excluded: chain E residue 81 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 5.9990 chunk 21 optimal weight: 0.2980 chunk 34 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 0.0570 chunk 16 optimal weight: 4.9990 overall best weight: 0.5902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4863 r_free = 0.4863 target = 0.254005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.222749 restraints weight = 12999.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.231222 restraints weight = 7507.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.236963 restraints weight = 4908.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.240835 restraints weight = 3417.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.243382 restraints weight = 2502.308| |-----------------------------------------------------------------------------| r_work (final): 0.4781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4784 r_free = 0.4784 target_work(ls_wunit_k1) = 0.243 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4784 r_free = 0.4784 target_work(ls_wunit_k1) = 0.243 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5223 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3977 Z= 0.143 Angle : 0.509 5.446 5386 Z= 0.279 Chirality : 0.038 0.150 572 Planarity : 0.003 0.027 698 Dihedral : 4.465 33.303 568 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.50 % Allowed : 10.15 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.40), residues: 500 helix: 1.03 (0.56), residues: 102 sheet: -0.32 (0.45), residues: 132 loop : 0.95 (0.41), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 112 TYR 0.014 0.002 TYR C 116 PHE 0.009 0.001 PHE D 38 TRP 0.013 0.001 TRP F 111 HIS 0.002 0.001 HIS E 54 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 3966) covalent geometry : angle 0.50209 ( 5364) SS BOND : bond 0.00347 ( 11) SS BOND : angle 1.44318 ( 22) hydrogen bonds : bond 0.03107 ( 143) hydrogen bonds : angle 6.48763 ( 372) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 124 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 124 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Evaluate side-chains 61 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 0.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 20 LEU cc_start: 0.5740 (mt) cc_final: 0.5408 (mp) REVERT: E 101 LYS cc_start: 0.7111 (mmtt) cc_final: 0.6594 (mttp) outliers start: 2 outliers final: 1 residues processed: 60 average time/residue: 0.0928 time to fit residues: 7.3807 Evaluate side-chains 61 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 47 optimal weight: 0.4980 chunk 29 optimal weight: 0.0980 chunk 19 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.251870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.220917 restraints weight = 12803.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.229416 restraints weight = 7379.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.235049 restraints weight = 4769.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.238914 restraints weight = 3304.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.241549 restraints weight = 2396.195| |-----------------------------------------------------------------------------| r_work (final): 0.4771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4773 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4773 r_free = 0.4773 target_work(ls_wunit_k1) = 0.242 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4773 r_free = 0.4773 target_work(ls_wunit_k1) = 0.242 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4773 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5247 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3977 Z= 0.135 Angle : 0.494 4.075 5386 Z= 0.275 Chirality : 0.038 0.151 572 Planarity : 0.003 0.026 698 Dihedral : 4.227 22.058 568 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.74 % Allowed : 10.89 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.40), residues: 500 helix: 0.97 (0.56), residues: 102 sheet: -0.38 (0.45), residues: 132 loop : 0.84 (0.42), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 112 TYR 0.010 0.001 TYR C 94 PHE 0.006 0.001 PHE F 3 TRP 0.012 0.001 TRP F 111 HIS 0.002 0.001 HIS D 15 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 3966) covalent geometry : angle 0.48811 ( 5364) SS BOND : bond 0.00285 ( 11) SS BOND : angle 1.30991 ( 22) hydrogen bonds : bond 0.03018 ( 143) hydrogen bonds : angle 6.34514 ( 372) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 124 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 124 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Evaluate side-chains 64 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 20 LEU cc_start: 0.5821 (mt) cc_final: 0.5475 (mp) REVERT: E 101 LYS cc_start: 0.7138 (mmtt) cc_final: 0.6604 (mttp) outliers start: 3 outliers final: 3 residues processed: 64 average time/residue: 0.0817 time to fit residues: 7.0461 Evaluate side-chains 61 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 CYS Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain F residue 55 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 0.0870 chunk 2 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 47 optimal weight: 0.0770 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 103 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4833 r_free = 0.4833 target = 0.250244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.218980 restraints weight = 12878.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.227326 restraints weight = 7427.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.233024 restraints weight = 4813.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.236992 restraints weight = 3358.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.239709 restraints weight = 2438.843| |-----------------------------------------------------------------------------| r_work (final): 0.4756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4756 r_free = 0.4756 target_work(ls_wunit_k1) = 0.240 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4756 r_free = 0.4756 target_work(ls_wunit_k1) = 0.240 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5282 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3977 Z= 0.137 Angle : 0.496 3.953 5386 Z= 0.278 Chirality : 0.038 0.147 572 Planarity : 0.003 0.025 698 Dihedral : 4.156 20.893 568 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.99 % Allowed : 12.13 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.40), residues: 500 helix: 1.03 (0.57), residues: 102 sheet: -0.35 (0.49), residues: 118 loop : 0.71 (0.40), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 61 TYR 0.010 0.001 TYR E 114 PHE 0.007 0.001 PHE D 38 TRP 0.011 0.001 TRP F 111 HIS 0.002 0.001 HIS E 54 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 3966) covalent geometry : angle 0.49122 ( 5364) SS BOND : bond 0.00290 ( 11) SS BOND : angle 1.22170 ( 22) hydrogen bonds : bond 0.02957 ( 143) hydrogen bonds : angle 6.22299 ( 372) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 124 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 124 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Evaluate side-chains 66 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 20 LEU cc_start: 0.5830 (mt) cc_final: 0.5461 (mp) REVERT: E 101 LYS cc_start: 0.7141 (mmtt) cc_final: 0.6638 (mttp) outliers start: 4 outliers final: 3 residues processed: 65 average time/residue: 0.0968 time to fit residues: 8.1579 Evaluate side-chains 61 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 CYS Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain E residue 81 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 16 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.245678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.213795 restraints weight = 12883.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.222254 restraints weight = 7482.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.227973 restraints weight = 4903.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.231538 restraints weight = 3457.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.234382 restraints weight = 2610.795| |-----------------------------------------------------------------------------| r_work (final): 0.4711 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4711 r_free = 0.4711 target_work(ls_wunit_k1) = 0.235 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4711 r_free = 0.4711 target_work(ls_wunit_k1) = 0.235 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5401 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3977 Z= 0.177 Angle : 0.541 4.082 5386 Z= 0.304 Chirality : 0.039 0.153 572 Planarity : 0.003 0.027 698 Dihedral : 4.554 20.384 568 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.50 % Allowed : 12.87 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.39), residues: 500 helix: 0.90 (0.56), residues: 102 sheet: -0.20 (0.51), residues: 108 loop : 0.40 (0.39), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 67 TYR 0.015 0.002 TYR E 114 PHE 0.014 0.001 PHE D 38 TRP 0.015 0.002 TRP D 28 HIS 0.002 0.001 HIS E 54 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 3966) covalent geometry : angle 0.53487 ( 5364) SS BOND : bond 0.00370 ( 11) SS BOND : angle 1.42336 ( 22) hydrogen bonds : bond 0.03345 ( 143) hydrogen bonds : angle 6.36240 ( 372) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 124 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 124 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Evaluate side-chains 62 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 101 LYS cc_start: 0.7125 (mmtt) cc_final: 0.6668 (mttp) outliers start: 2 outliers final: 2 residues processed: 62 average time/residue: 0.1117 time to fit residues: 8.6854 Evaluate side-chains 61 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 CYS Chi-restraints excluded: chain E residue 81 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 36 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.248915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.215955 restraints weight = 12603.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.225165 restraints weight = 6997.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.231222 restraints weight = 4460.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.235088 restraints weight = 3081.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.237887 restraints weight = 2278.839| |-----------------------------------------------------------------------------| r_work (final): 0.4693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4693 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4693 r_free = 0.4693 target_work(ls_wunit_k1) = 0.237 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4693 r_free = 0.4693 target_work(ls_wunit_k1) = 0.237 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4693 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5347 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3977 Z= 0.148 Angle : 0.505 3.859 5386 Z= 0.282 Chirality : 0.038 0.144 572 Planarity : 0.003 0.033 698 Dihedral : 4.389 18.948 568 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.50 % Allowed : 13.12 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.40), residues: 500 helix: 1.04 (0.58), residues: 102 sheet: -0.45 (0.49), residues: 112 loop : 0.41 (0.40), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 73 TYR 0.010 0.002 TYR C 94 PHE 0.005 0.001 PHE F 3 TRP 0.012 0.001 TRP F 111 HIS 0.003 0.001 HIS E 54 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 3966) covalent geometry : angle 0.49938 ( 5364) SS BOND : bond 0.00334 ( 11) SS BOND : angle 1.29898 ( 22) hydrogen bonds : bond 0.03191 ( 143) hydrogen bonds : angle 6.20513 ( 372) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 124 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 124 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Evaluate side-chains 60 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 20 LEU cc_start: 0.5920 (mt) cc_final: 0.5395 (mp) REVERT: E 101 LYS cc_start: 0.7198 (mmtt) cc_final: 0.6665 (mttp) outliers start: 2 outliers final: 2 residues processed: 60 average time/residue: 0.0979 time to fit residues: 7.5121 Evaluate side-chains 59 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 CYS Chi-restraints excluded: chain E residue 81 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 8 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 11 optimal weight: 0.0980 chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 31 optimal weight: 0.2980 chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.250557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.217900 restraints weight = 12703.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.227295 restraints weight = 6971.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.233258 restraints weight = 4398.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.237173 restraints weight = 3038.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.239914 restraints weight = 2232.594| |-----------------------------------------------------------------------------| r_work (final): 0.4710 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4710 r_free = 0.4710 target_work(ls_wunit_k1) = 0.239 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4710 r_free = 0.4710 target_work(ls_wunit_k1) = 0.239 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5300 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3977 Z= 0.121 Angle : 0.485 4.503 5386 Z= 0.270 Chirality : 0.037 0.144 572 Planarity : 0.003 0.034 698 Dihedral : 4.197 17.062 568 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.50 % Allowed : 13.37 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.40), residues: 500 helix: 1.11 (0.57), residues: 102 sheet: -0.36 (0.50), residues: 112 loop : 0.44 (0.40), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 73 TYR 0.008 0.001 TYR E 114 PHE 0.005 0.001 PHE D 38 TRP 0.011 0.001 TRP F 111 HIS 0.003 0.001 HIS E 54 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 3966) covalent geometry : angle 0.47964 ( 5364) SS BOND : bond 0.00293 ( 11) SS BOND : angle 1.19826 ( 22) hydrogen bonds : bond 0.02971 ( 143) hydrogen bonds : angle 6.04677 ( 372) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 124 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 124 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Evaluate side-chains 59 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 20 LEU cc_start: 0.5898 (mt) cc_final: 0.5403 (mp) REVERT: C 83 MET cc_start: 0.3032 (mtp) cc_final: 0.2719 (mtt) REVERT: E 60 TYR cc_start: 0.8434 (m-80) cc_final: 0.8134 (m-80) REVERT: E 101 LYS cc_start: 0.7183 (mmtt) cc_final: 0.6634 (mttp) outliers start: 2 outliers final: 2 residues processed: 59 average time/residue: 0.1235 time to fit residues: 9.2255 Evaluate side-chains 59 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 CYS Chi-restraints excluded: chain E residue 81 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 0.4980 chunk 41 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 0.1980 chunk 32 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 40 optimal weight: 0.3980 chunk 15 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.249953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.217084 restraints weight = 12712.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.226561 restraints weight = 6991.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.232526 restraints weight = 4410.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.236521 restraints weight = 3049.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.239198 restraints weight = 2233.108| |-----------------------------------------------------------------------------| r_work (final): 0.4704 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4703 r_free = 0.4703 target_work(ls_wunit_k1) = 0.238 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4703 r_free = 0.4703 target_work(ls_wunit_k1) = 0.238 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5322 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3977 Z= 0.125 Angle : 0.482 4.343 5386 Z= 0.269 Chirality : 0.037 0.142 572 Planarity : 0.003 0.033 698 Dihedral : 4.178 15.927 568 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.50 % Allowed : 13.61 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.40), residues: 500 helix: 1.16 (0.58), residues: 102 sheet: -0.34 (0.50), residues: 112 loop : 0.36 (0.40), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 73 TYR 0.008 0.001 TYR E 114 PHE 0.005 0.001 PHE F 3 TRP 0.010 0.001 TRP F 111 HIS 0.003 0.001 HIS E 54 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 3966) covalent geometry : angle 0.47674 ( 5364) SS BOND : bond 0.00302 ( 11) SS BOND : angle 1.18567 ( 22) hydrogen bonds : bond 0.02982 ( 143) hydrogen bonds : angle 6.00109 ( 372) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1622.69 seconds wall clock time: 28 minutes 14.15 seconds (1694.15 seconds total)