Starting phenix.real_space_refine on Fri Jul 25 10:36:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fgx_50432/07_2025/9fgx_50432_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fgx_50432/07_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_50432/07_2025/9fgx_50432.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fgx_50432/07_2025/9fgx_50432.map" model { file = "/net/cci-nas-00/data/ceres_data/9fgx_50432/07_2025/9fgx_50432_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fgx_50432/07_2025/9fgx_50432_trim.cif" } resolution = 3.53 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= 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.16, per 1000 atoms: 1.08 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: 2.12 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.71 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: 2.72 Time building geometry restraints manager: 2.57 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 1 through 88 or resid 90 through 126 or resid 201)) selection = (chain 'E' and (resid 1 through 88 or resid 90 through 126 or resid 201)) } 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: 4.270 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: 0.170 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 25.960 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.840 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (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 TRP 0.009 0.001 TRP F 63 HIS 0.003 0.001 HIS E 54 PHE 0.006 0.001 PHE D 38 TYR 0.007 0.001 TYR C 59 ARG 0.006 0.000 ARG F 73 Details of bonding type rmsd hydrogen bonds : bond 0.20352 ( 143) hydrogen bonds : angle 10.13732 ( 372) SS BOND : bond 0.00221 ( 11) SS BOND : angle 1.28744 ( 22) covalent geometry : bond 0.00226 ( 3966) covalent geometry : angle 0.42680 ( 5364) *********************** 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 : 0.546 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: 0.2488 time to fit residues: 23.6274 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 : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 ASN F 41 GLN F 46 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4856 r_free = 0.4856 target = 0.253081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.221176 restraints weight = 12556.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.229655 restraints weight = 7389.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.235486 restraints weight = 4856.286| |-----------------------------------------------------------------------------| r_work (final): 0.4705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4705 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4705 r_free = 0.4705 target_work(ls_wunit_k1) = 0.234 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4684 r_free = 0.4684 target_work(ls_wunit_k1) = 0.232 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4684 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5438 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 3977 Z= 0.283 Angle : 0.684 5.077 5386 Z= 0.384 Chirality : 0.042 0.151 572 Planarity : 0.006 0.042 698 Dihedral : 5.332 44.923 568 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.24 % Allowed : 8.91 % Favored : 89.85 % 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: 0.69 (0.39), residues: 500 helix: 0.79 (0.53), residues: 102 sheet: -0.31 (0.49), residues: 118 loop : 0.90 (0.40), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP D 28 HIS 0.006 0.002 HIS D 15 PHE 0.015 0.002 PHE F 3 TYR 0.031 0.003 TYR E 33 ARG 0.006 0.001 ARG D 68 Details of bonding type rmsd hydrogen bonds : bond 0.04495 ( 143) hydrogen bonds : angle 7.47891 ( 372) SS BOND : bond 0.00627 ( 11) SS BOND : angle 1.40008 ( 22) covalent geometry : bond 0.00623 ( 3966) covalent geometry : angle 0.67914 ( 5364) *********************** 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 : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 101 LYS cc_start: 0.7179 (mmtt) cc_final: 0.6727 (mttp) outliers start: 4 outliers final: 3 residues processed: 72 average time/residue: 0.2886 time to fit residues: 26.6871 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 : 0.597 ------------------------------------------------------------------------------- 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 38 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 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 = 0.4838 r_free = 0.4838 target = 0.251283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.219382 restraints weight = 12932.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.227785 restraints weight = 7517.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.233613 restraints weight = 4930.019| |-----------------------------------------------------------------------------| r_work (final): 0.4705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4705 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4705 r_free = 0.4705 target_work(ls_wunit_k1) = 0.234 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4705 r_free = 0.4705 target_work(ls_wunit_k1) = 0.234 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4705 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5423 moved from start: 0.2928 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= 0.175 Angle : 0.551 4.762 5386 Z= 0.305 Chirality : 0.038 0.145 572 Planarity : 0.004 0.033 698 Dihedral : 4.919 42.242 568 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.24 % Allowed : 11.39 % Favored : 87.38 % 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 (0.39), residues: 500 helix: 0.91 (0.54), residues: 102 sheet: -0.48 (0.49), residues: 118 loop : 0.73 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 28 HIS 0.003 0.001 HIS E 54 PHE 0.005 0.001 PHE F 3 TYR 0.014 0.002 TYR E 114 ARG 0.003 0.001 ARG F 73 Details of bonding type rmsd hydrogen bonds : bond 0.03794 ( 143) hydrogen bonds : angle 7.00210 ( 372) SS BOND : bond 0.00285 ( 11) SS BOND : angle 1.48506 ( 22) covalent geometry : bond 0.00384 ( 3966) covalent geometry : angle 0.54398 ( 5364) *********************** 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 68 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.587 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: D 61 ARG cc_start: 0.4910 (OUTLIER) cc_final: 0.4626 (ttp-170) REVERT: E 101 LYS cc_start: 0.7201 (mmtt) cc_final: 0.6753 (mttp) outliers start: 5 outliers final: 3 residues processed: 66 average time/residue: 0.2614 time to fit residues: 22.5686 Evaluate side-chains 61 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 CYS Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain D residue 61 ARG 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 37 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 7 optimal weight: 0.4980 chunk 3 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4808 r_free = 0.4808 target = 0.251441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.218076 restraints weight = 12525.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.227256 restraints weight = 7031.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.233268 restraints weight = 4507.882| |-----------------------------------------------------------------------------| r_work (final): 0.4660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4658 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4658 r_free = 0.4658 target_work(ls_wunit_k1) = 0.232 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4658 r_free = 0.4658 target_work(ls_wunit_k1) = 0.232 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4658 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5428 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3977 Z= 0.165 Angle : 0.542 5.561 5386 Z= 0.296 Chirality : 0.038 0.144 572 Planarity : 0.003 0.027 698 Dihedral : 5.504 53.877 568 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.49 % Allowed : 10.64 % Favored : 87.87 % 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 (0.39), residues: 500 helix: 0.96 (0.56), residues: 102 sheet: -0.50 (0.49), residues: 118 loop : 0.48 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 111 HIS 0.003 0.001 HIS E 54 PHE 0.007 0.001 PHE F 3 TYR 0.013 0.002 TYR C 94 ARG 0.002 0.000 ARG F 112 Details of bonding type rmsd hydrogen bonds : bond 0.03460 ( 143) hydrogen bonds : angle 6.67334 ( 372) SS BOND : bond 0.00479 ( 11) SS BOND : angle 1.49639 ( 22) covalent geometry : bond 0.00367 ( 3966) covalent geometry : angle 0.53417 ( 5364) *********************** 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 65 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 101 LYS cc_start: 0.7296 (mmtt) cc_final: 0.6768 (mttp) outliers start: 6 outliers final: 4 residues processed: 63 average time/residue: 0.2411 time to fit residues: 20.3142 Evaluate side-chains 59 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 CYS Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain F residue 55 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 ASN F 103 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.247957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.214564 restraints weight = 12514.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.223692 restraints weight = 7026.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.229610 restraints weight = 4494.810| |-----------------------------------------------------------------------------| r_work (final): 0.4627 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4628 r_free = 0.4628 target_work(ls_wunit_k1) = 0.228 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4628 r_free = 0.4628 target_work(ls_wunit_k1) = 0.228 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5486 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3977 Z= 0.190 Angle : 0.556 4.190 5386 Z= 0.308 Chirality : 0.039 0.143 572 Planarity : 0.003 0.025 698 Dihedral : 5.229 41.208 568 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.73 % Allowed : 11.39 % 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 (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: 0.30 (0.39), residues: 500 helix: 0.81 (0.56), residues: 102 sheet: -0.22 (0.51), residues: 108 loop : 0.28 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 28 HIS 0.003 0.001 HIS E 54 PHE 0.008 0.001 PHE F 3 TYR 0.015 0.002 TYR E 114 ARG 0.002 0.000 ARG F 73 Details of bonding type rmsd hydrogen bonds : bond 0.03550 ( 143) hydrogen bonds : angle 6.62399 ( 372) SS BOND : bond 0.00380 ( 11) SS BOND : angle 1.48670 ( 22) covalent geometry : bond 0.00420 ( 3966) covalent geometry : angle 0.54867 ( 5364) *********************** 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 65 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 61 ARG cc_start: 0.5036 (OUTLIER) cc_final: 0.4734 (ttp-170) REVERT: E 101 LYS cc_start: 0.7317 (mmtt) cc_final: 0.6782 (mttp) outliers start: 7 outliers final: 5 residues processed: 64 average time/residue: 0.2662 time to fit residues: 22.3283 Evaluate side-chains 61 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 CYS Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain F residue 55 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 25 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 21 optimal weight: 0.0980 chunk 12 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 32 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 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 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.248231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.214939 restraints weight = 12482.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.224190 restraints weight = 6977.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.230124 restraints weight = 4461.138| |-----------------------------------------------------------------------------| r_work (final): 0.4643 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4641 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4641 r_free = 0.4641 target_work(ls_wunit_k1) = 0.230 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4641 r_free = 0.4641 target_work(ls_wunit_k1) = 0.230 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4641 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5467 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3977 Z= 0.145 Angle : 0.507 3.738 5386 Z= 0.280 Chirality : 0.038 0.141 572 Planarity : 0.003 0.023 698 Dihedral : 4.573 25.062 568 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.98 % Allowed : 12.38 % Favored : 85.64 % 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 (0.39), residues: 500 helix: 0.97 (0.57), residues: 102 sheet: -0.35 (0.53), residues: 98 loop : 0.34 (0.38), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 111 HIS 0.003 0.001 HIS E 54 PHE 0.006 0.001 PHE D 38 TYR 0.009 0.001 TYR E 114 ARG 0.003 0.000 ARG F 73 Details of bonding type rmsd hydrogen bonds : bond 0.03212 ( 143) hydrogen bonds : angle 6.34837 ( 372) SS BOND : bond 0.00294 ( 11) SS BOND : angle 1.30688 ( 22) covalent geometry : bond 0.00321 ( 3966) covalent geometry : angle 0.50143 ( 5364) *********************** 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 66 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.625 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: D 61 ARG cc_start: 0.5045 (OUTLIER) cc_final: 0.4708 (ttp-170) REVERT: E 101 LYS cc_start: 0.7291 (mmtt) cc_final: 0.6770 (mttp) outliers start: 8 outliers final: 5 residues processed: 65 average time/residue: 0.2965 time to fit residues: 24.6977 Evaluate side-chains 62 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 CYS Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain F residue 99 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 46 optimal weight: 1.9990 chunk 6 optimal weight: 0.2980 chunk 10 optimal weight: 0.3980 chunk 29 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 7 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 37 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.251209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.218863 restraints weight = 12541.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.228080 restraints weight = 6927.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.234029 restraints weight = 4378.735| |-----------------------------------------------------------------------------| r_work (final): 0.4661 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4660 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4660 r_free = 0.4660 target_work(ls_wunit_k1) = 0.232 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4660 r_free = 0.4660 target_work(ls_wunit_k1) = 0.232 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4660 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5426 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3977 Z= 0.117 Angle : 0.479 3.818 5386 Z= 0.264 Chirality : 0.037 0.144 572 Planarity : 0.003 0.023 698 Dihedral : 4.191 19.331 568 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.49 % Allowed : 13.12 % Favored : 85.40 % 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: 0.38 (0.40), residues: 500 helix: 1.03 (0.57), residues: 102 sheet: -0.62 (0.52), residues: 108 loop : 0.49 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 111 HIS 0.003 0.001 HIS E 54 PHE 0.006 0.001 PHE D 38 TYR 0.007 0.001 TYR E 114 ARG 0.002 0.000 ARG F 73 Details of bonding type rmsd hydrogen bonds : bond 0.02986 ( 143) hydrogen bonds : angle 6.14327 ( 372) SS BOND : bond 0.00300 ( 11) SS BOND : angle 1.15015 ( 22) covalent geometry : bond 0.00260 ( 3966) covalent geometry : angle 0.47404 ( 5364) *********************** 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 62 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.558 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: 0.6162 (mt) cc_final: 0.5416 (mp) REVERT: D 61 ARG cc_start: 0.5000 (OUTLIER) cc_final: 0.4668 (ttp-170) REVERT: E 101 LYS cc_start: 0.7302 (mmtt) cc_final: 0.6750 (mttp) outliers start: 6 outliers final: 4 residues processed: 61 average time/residue: 0.2900 time to fit residues: 22.6253 Evaluate side-chains 60 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 CYS Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain D residue 106 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.246442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.212743 restraints weight = 12777.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.222004 restraints weight = 7091.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.228063 restraints weight = 4523.092| |-----------------------------------------------------------------------------| r_work (final): 0.4612 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4612 r_free = 0.4612 target_work(ls_wunit_k1) = 0.227 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4612 r_free = 0.4612 target_work(ls_wunit_k1) = 0.227 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5509 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3977 Z= 0.167 Angle : 0.522 4.136 5386 Z= 0.290 Chirality : 0.038 0.142 572 Planarity : 0.003 0.022 698 Dihedral : 4.498 17.033 568 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.23 % Allowed : 12.87 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.27 (0.39), residues: 500 helix: 0.88 (0.57), residues: 102 sheet: -0.36 (0.54), residues: 98 loop : 0.25 (0.38), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 28 HIS 0.002 0.001 HIS E 54 PHE 0.008 0.001 PHE F 3 TYR 0.013 0.002 TYR E 114 ARG 0.002 0.000 ARG F 73 Details of bonding type rmsd hydrogen bonds : bond 0.03361 ( 143) hydrogen bonds : angle 6.27710 ( 372) SS BOND : bond 0.00334 ( 11) SS BOND : angle 1.28659 ( 22) covalent geometry : bond 0.00370 ( 3966) covalent geometry : angle 0.51675 ( 5364) *********************** 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 63 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.524 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 REVERT: D 61 ARG cc_start: 0.5115 (OUTLIER) cc_final: 0.4796 (ttp-170) REVERT: E 101 LYS cc_start: 0.7313 (mmtt) cc_final: 0.6764 (mttp) REVERT: F 8 LEU cc_start: 0.6786 (tp) cc_final: 0.6484 (tt) outliers start: 9 outliers final: 6 residues processed: 63 average time/residue: 0.3825 time to fit residues: 30.1460 Evaluate side-chains 61 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 CYS Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain D residue 106 ASN 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 28 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.245748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.211979 restraints weight = 12784.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.221293 restraints weight = 7135.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.227471 restraints weight = 4549.943| |-----------------------------------------------------------------------------| r_work (final): 0.4610 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4608 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4608 r_free = 0.4608 target_work(ls_wunit_k1) = 0.226 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4608 r_free = 0.4608 target_work(ls_wunit_k1) = 0.226 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4608 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5540 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3977 Z= 0.161 Angle : 0.522 4.136 5386 Z= 0.290 Chirality : 0.038 0.140 572 Planarity : 0.003 0.024 698 Dihedral : 4.531 15.944 568 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.23 % Allowed : 12.62 % Favored : 85.15 % 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: 0.17 (0.39), residues: 500 helix: 0.87 (0.57), residues: 102 sheet: -0.42 (0.54), residues: 98 loop : 0.15 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 28 HIS 0.002 0.001 HIS E 54 PHE 0.012 0.001 PHE D 38 TYR 0.010 0.002 TYR C 60 ARG 0.003 0.000 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.03296 ( 143) hydrogen bonds : angle 6.28247 ( 372) SS BOND : bond 0.00324 ( 11) SS BOND : angle 1.23738 ( 22) covalent geometry : bond 0.00354 ( 3966) covalent geometry : angle 0.51697 ( 5364) *********************** 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 63 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.591 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 REVERT: D 61 ARG cc_start: 0.5060 (OUTLIER) cc_final: 0.4811 (mtp180) REVERT: E 101 LYS cc_start: 0.7310 (mmtt) cc_final: 0.6776 (mttp) REVERT: F 8 LEU cc_start: 0.6822 (tp) cc_final: 0.6525 (tt) outliers start: 9 outliers final: 7 residues processed: 63 average time/residue: 0.3345 time to fit residues: 26.2787 Evaluate side-chains 64 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 CYS Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain F residue 99 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 13 optimal weight: 5.9990 chunk 30 optimal weight: 0.3980 chunk 11 optimal weight: 0.2980 chunk 21 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.247304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.214204 restraints weight = 12808.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.223515 restraints weight = 7078.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.229604 restraints weight = 4485.216| |-----------------------------------------------------------------------------| r_work (final): 0.4627 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4627 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4627 r_free = 0.4627 target_work(ls_wunit_k1) = 0.229 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4627 r_free = 0.4627 target_work(ls_wunit_k1) = 0.229 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4627 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5483 moved from start: 0.4948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3977 Z= 0.128 Angle : 0.491 3.848 5386 Z= 0.271 Chirality : 0.037 0.142 572 Planarity : 0.003 0.026 698 Dihedral : 4.283 13.576 568 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.23 % Allowed : 12.62 % Favored : 85.15 % 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 (0.39), residues: 500 helix: 0.94 (0.57), residues: 102 sheet: -0.28 (0.54), residues: 98 loop : 0.16 (0.38), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 111 HIS 0.003 0.001 HIS E 54 PHE 0.007 0.001 PHE D 38 TYR 0.008 0.001 TYR E 114 ARG 0.002 0.000 ARG F 73 Details of bonding type rmsd hydrogen bonds : bond 0.03102 ( 143) hydrogen bonds : angle 6.10836 ( 372) SS BOND : bond 0.00297 ( 11) SS BOND : angle 1.15646 ( 22) covalent geometry : bond 0.00283 ( 3966) covalent geometry : angle 0.48618 ( 5364) ********************** 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 66 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.555 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: D 61 ARG cc_start: 0.5004 (OUTLIER) cc_final: 0.4757 (mtp180) REVERT: E 101 LYS cc_start: 0.7303 (mmtt) cc_final: 0.6748 (mttp) REVERT: F 8 LEU cc_start: 0.6849 (tp) cc_final: 0.6518 (tt) outliers start: 9 outliers final: 7 residues processed: 66 average time/residue: 0.3238 time to fit residues: 26.7266 Evaluate side-chains 62 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 CYS Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain F residue 99 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 43 optimal weight: 0.2980 chunk 16 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 28 optimal weight: 0.3980 chunk 32 optimal weight: 0.1980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.247542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.214799 restraints weight = 12629.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.224165 restraints weight = 6960.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.230292 restraints weight = 4407.706| |-----------------------------------------------------------------------------| r_work (final): 0.4636 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4633 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4633 r_free = 0.4633 target_work(ls_wunit_k1) = 0.229 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4633 r_free = 0.4633 target_work(ls_wunit_k1) = 0.229 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4633 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5455 moved from start: 0.4975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3977 Z= 0.116 Angle : 0.494 7.660 5386 Z= 0.272 Chirality : 0.037 0.141 572 Planarity : 0.003 0.025 698 Dihedral : 4.141 13.718 568 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.23 % Allowed : 12.87 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.39), residues: 500 helix: 1.04 (0.57), residues: 102 sheet: -0.54 (0.52), residues: 108 loop : 0.26 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 111 HIS 0.002 0.001 HIS E 54 PHE 0.008 0.001 PHE D 38 TYR 0.007 0.001 TYR C 60 ARG 0.002 0.000 ARG F 128 Details of bonding type rmsd hydrogen bonds : bond 0.03028 ( 143) hydrogen bonds : angle 6.00912 ( 372) SS BOND : bond 0.00287 ( 11) SS BOND : angle 1.10155 ( 22) covalent geometry : bond 0.00259 ( 3966) covalent geometry : angle 0.49041 ( 5364) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3843.79 seconds wall clock time: 67 minutes 27.08 seconds (4047.08 seconds total)