Starting phenix.real_space_refine on Fri Oct 23 05:36:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9seh_54810/10_2026/9seh_54810.cif Found real_map, /net/cci-nas-00/data/ceres_data/9seh_54810/10_2026/9seh_54810.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9seh_54810/10_2026/9seh_54810.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9seh_54810/10_2026/9seh_54810.map" model { file = "/net/cci-nas-00/data/ceres_data/9seh_54810/10_2026/9seh_54810.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9seh_54810/10_2026/9seh_54810.cif" } resolution = 2.7 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= 0.119 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 P 7 5.49 5 S 21 5.16 5 C 5719 2.51 5 N 1239 2.21 5 O 1526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8512 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1161 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 3, 'TRANS': 150} Chain: "B" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1161 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 3, 'TRANS': 150} Chain: "C" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1161 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 3, 'TRANS': 150} Chain: "D" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1161 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 3, 'TRANS': 150} Chain: "E" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1161 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 3, 'TRANS': 150} Chain: "F" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1161 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 3, 'TRANS': 150} Chain: "G" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1161 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 3, 'TRANS': 150} Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Unusual residues: {'D12': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "B" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 55 Unusual residues: {'D12': 1, 'OCT': 1, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "C" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 55 Unusual residues: {'D12': 1, 'OCT': 1, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "D" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 63 Unusual residues: {'D12': 1, 'OCT': 2, 'PEE': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "E" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Unusual residues: {'D12': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "F" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 63 Unusual residues: {'D12': 1, 'OCT': 2, 'PEE': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "G" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 55 Unusual residues: {'D12': 1, 'OCT': 1, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Time building chain proxies: 2.00, per 1000 atoms: 0.23 Number of scatterers: 8512 At special positions: 0 Unit cell: (86.1435, 87.207, 92.5245, 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 21 16.00 P 7 15.00 O 1526 8.00 N 1239 7.00 C 5719 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 435.2 milliseconds 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1974 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 7 sheets defined 65.7% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 8 through 40 Processing helix chain 'A' and resid 44 through 72 removed outlier: 3.670A pdb=" N SER A 48 " --> pdb=" O ASP A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 92 Processing helix chain 'A' and resid 93 through 108 removed outlier: 4.111A pdb=" N TYR A 97 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 106 " --> pdb=" O CYS A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 154 Processing helix chain 'B' and resid 9 through 40 Processing helix chain 'B' and resid 44 through 72 removed outlier: 3.669A pdb=" N SER B 48 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 92 Processing helix chain 'B' and resid 93 through 108 removed outlier: 4.112A pdb=" N TYR B 97 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 106 " --> pdb=" O CYS B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 154 Processing helix chain 'C' and resid 9 through 40 Processing helix chain 'C' and resid 44 through 72 removed outlier: 3.669A pdb=" N SER C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 92 Processing helix chain 'C' and resid 93 through 108 removed outlier: 4.111A pdb=" N TYR C 97 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU C 106 " --> pdb=" O CYS C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 154 Processing helix chain 'D' and resid 9 through 40 Processing helix chain 'D' and resid 44 through 72 removed outlier: 3.669A pdb=" N SER D 48 " --> pdb=" O ASP D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 92 Processing helix chain 'D' and resid 93 through 108 removed outlier: 4.112A pdb=" N TYR D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU D 106 " --> pdb=" O CYS D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 154 Processing helix chain 'E' and resid 9 through 40 Processing helix chain 'E' and resid 44 through 72 removed outlier: 3.669A pdb=" N SER E 48 " --> pdb=" O ASP E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 92 Processing helix chain 'E' and resid 93 through 108 removed outlier: 4.112A pdb=" N TYR E 97 " --> pdb=" O LEU E 93 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU E 106 " --> pdb=" O CYS E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 154 Processing helix chain 'F' and resid 9 through 40 Processing helix chain 'F' and resid 44 through 72 removed outlier: 3.669A pdb=" N SER F 48 " --> pdb=" O ASP F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 92 Processing helix chain 'F' and resid 93 through 108 removed outlier: 4.112A pdb=" N TYR F 97 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU F 106 " --> pdb=" O CYS F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 154 Processing helix chain 'G' and resid 9 through 40 Processing helix chain 'G' and resid 44 through 72 removed outlier: 3.669A pdb=" N SER G 48 " --> pdb=" O ASP G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 92 Processing helix chain 'G' and resid 93 through 108 removed outlier: 4.112A pdb=" N TYR G 97 " --> pdb=" O LEU G 93 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU G 106 " --> pdb=" O CYS G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 154 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 120 removed outlier: 3.849A pdb=" N SER B 129 " --> pdb=" O LYS B 136 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 130 removed outlier: 3.849A pdb=" N SER A 129 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 118 through 120 removed outlier: 3.849A pdb=" N SER C 129 " --> pdb=" O LYS C 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 118 through 120 removed outlier: 3.849A pdb=" N SER D 129 " --> pdb=" O LYS D 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 118 through 120 removed outlier: 3.849A pdb=" N SER E 129 " --> pdb=" O LYS E 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 120 removed outlier: 3.849A pdb=" N SER F 129 " --> pdb=" O LYS F 136 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 118 through 120 removed outlier: 3.850A pdb=" N SER G 129 " --> pdb=" O LYS G 136 " (cutoff:3.500A) 610 hydrogen bonds defined for protein. 1791 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: 1.30 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1288 1.32 - 1.44: 2051 1.44 - 1.56: 5236 1.56 - 1.68: 14 1.68 - 1.80: 35 Bond restraints: 8624 Sorted by residual: bond pdb=" C38 PEE F 201 " pdb=" C39 PEE F 201 " ideal model delta sigma weight residual 1.523 1.316 0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C38 PEE B 200 " pdb=" C39 PEE B 200 " ideal model delta sigma weight residual 1.523 1.316 0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C38 PEE A 201 " pdb=" C39 PEE A 201 " ideal model delta sigma weight residual 1.523 1.316 0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C38 PEE G 202 " pdb=" C39 PEE G 202 " ideal model delta sigma weight residual 1.523 1.316 0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C38 PEE C 200 " pdb=" C39 PEE C 200 " ideal model delta sigma weight residual 1.523 1.316 0.207 2.00e-02 2.50e+03 1.07e+02 ... (remaining 8619 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 11459 2.83 - 5.65: 119 5.65 - 8.48: 7 8.48 - 11.30: 7 11.30 - 14.13: 14 Bond angle restraints: 11606 Sorted by residual: angle pdb=" C38 PEE B 200 " pdb=" C39 PEE B 200 " pdb=" C40 PEE B 200 " ideal model delta sigma weight residual 112.47 126.60 -14.13 3.00e+00 1.11e-01 2.22e+01 angle pdb=" C38 PEE A 201 " pdb=" C39 PEE A 201 " pdb=" C40 PEE A 201 " ideal model delta sigma weight residual 112.47 126.60 -14.13 3.00e+00 1.11e-01 2.22e+01 angle pdb=" C38 PEE D 201 " pdb=" C39 PEE D 201 " pdb=" C40 PEE D 201 " ideal model delta sigma weight residual 112.47 126.60 -14.13 3.00e+00 1.11e-01 2.22e+01 angle pdb=" C38 PEE F 201 " pdb=" C39 PEE F 201 " pdb=" C40 PEE F 201 " ideal model delta sigma weight residual 112.47 126.59 -14.12 3.00e+00 1.11e-01 2.22e+01 angle pdb=" C38 PEE C 200 " pdb=" C39 PEE C 200 " pdb=" C40 PEE C 200 " ideal model delta sigma weight residual 112.47 126.59 -14.12 3.00e+00 1.11e-01 2.22e+01 ... (remaining 11601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.59: 5033 33.59 - 67.18: 70 67.18 - 100.77: 21 100.77 - 134.36: 14 134.36 - 167.95: 14 Dihedral angle restraints: 5152 sinusoidal: 2065 harmonic: 3087 Sorted by residual: dihedral pdb=" C3 PEE F 201 " pdb=" C1 PEE F 201 " pdb=" C2 PEE F 201 " pdb=" O3P PEE F 201 " ideal model delta sinusoidal sigma weight residual 62.73 -105.22 167.95 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C3 PEE G 202 " pdb=" C1 PEE G 202 " pdb=" C2 PEE G 202 " pdb=" O3P PEE G 202 " ideal model delta sinusoidal sigma weight residual 62.73 -105.20 167.93 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C3 PEE B 200 " pdb=" C1 PEE B 200 " pdb=" C2 PEE B 200 " pdb=" O3P PEE B 200 " ideal model delta sinusoidal sigma weight residual 62.73 -105.18 167.91 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 5149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1057 0.047 - 0.094: 321 0.094 - 0.142: 71 0.142 - 0.189: 0 0.189 - 0.236: 7 Chirality restraints: 1456 Sorted by residual: chirality pdb=" C2 PEE F 201 " pdb=" C1 PEE F 201 " pdb=" C3 PEE F 201 " pdb=" O2 PEE F 201 " both_signs ideal model delta sigma weight residual False -2.33 -2.56 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" C2 PEE G 202 " pdb=" C1 PEE G 202 " pdb=" C3 PEE G 202 " pdb=" O2 PEE G 202 " both_signs ideal model delta sigma weight residual False -2.33 -2.56 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" C2 PEE E 201 " pdb=" C1 PEE E 201 " pdb=" C3 PEE E 201 " pdb=" O2 PEE E 201 " both_signs ideal model delta sigma weight residual False -2.33 -2.56 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 1453 not shown) Planarity restraints: 1337 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 110 " 0.018 5.00e-02 4.00e+02 2.80e-02 1.25e+00 pdb=" N PRO D 111 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO D 111 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 111 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 27 " -0.012 2.00e-02 2.50e+03 7.05e-03 1.24e+00 pdb=" CG TRP F 27 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP F 27 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP F 27 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP F 27 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP F 27 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 27 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 27 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 27 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP F 27 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 110 " 0.018 5.00e-02 4.00e+02 2.78e-02 1.24e+00 pdb=" N PRO C 111 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO C 111 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 111 " 0.016 5.00e-02 4.00e+02 ... (remaining 1334 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 3292 2.88 - 3.39: 9026 3.39 - 3.89: 13900 3.89 - 4.40: 15551 4.40 - 4.90: 27148 Nonbonded interactions: 68917 Sorted by model distance: nonbonded pdb=" OD1 ASP A 119 " pdb=" N GLY A 122 " model vdw 2.379 3.120 nonbonded pdb=" OD1 ASP E 119 " pdb=" N GLY E 122 " model vdw 2.379 3.120 nonbonded pdb=" OD1 ASP B 119 " pdb=" N GLY B 122 " model vdw 2.379 3.120 nonbonded pdb=" OD1 ASP F 119 " pdb=" N GLY F 122 " model vdw 2.379 3.120 nonbonded pdb=" OD1 ASP D 119 " pdb=" N GLY D 122 " model vdw 2.380 3.120 ... (remaining 68912 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 8 through 161) selection = (chain 'B' and resid 8 through 161) selection = (chain 'C' and resid 8 through 161) selection = (chain 'D' and resid 8 through 161) selection = (chain 'E' and resid 8 through 161) selection = (chain 'F' and resid 8 through 161) selection = (chain 'G' and resid 8 through 161) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.970 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 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 : 0.009 0.207 8624 Z= 0.415 Angle : 0.811 14.131 11606 Z= 0.356 Chirality : 0.045 0.236 1456 Planarity : 0.003 0.028 1337 Dihedral : 19.491 167.953 3178 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 are not related in a simple way. whole: 2.38 (0.27), residues: 1064 helix: 2.57 (0.20), residues: 700 sheet: -0.80 (0.59), residues: 70 loop : -0.26 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 159 TYR 0.012 0.001 TYR C 56 PHE 0.007 0.001 PHE A 87 TRP 0.018 0.004 TRP D 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00907 / 0.42 ( 8624) covalent geometry : angle 0.81073 / 0.36 (11606) hydrogen bonds : bond 0.10584 / 7.57 ( 610) hydrogen bonds : angle 4.60289 / 3.36 ( 1791) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.290 Fit side-chains REVERT: A 128 LYS cc_start: 0.8268 (ptpt) cc_final: 0.7886 (ptpt) REVERT: A 155 LYS cc_start: 0.8648 (mttm) cc_final: 0.8405 (mttm) REVERT: B 117 LYS cc_start: 0.8434 (mttp) cc_final: 0.8223 (mmtp) REVERT: C 110 LYS cc_start: 0.8528 (mttp) cc_final: 0.8035 (mmtt) REVERT: D 113 GLU cc_start: 0.7572 (pt0) cc_final: 0.7351 (pt0) REVERT: E 110 LYS cc_start: 0.8576 (mttp) cc_final: 0.8318 (mttm) REVERT: F 128 LYS cc_start: 0.8154 (ptpt) cc_final: 0.7937 (ptmt) REVERT: F 132 PHE cc_start: 0.8699 (t80) cc_final: 0.8361 (t80) REVERT: G 119 ASP cc_start: 0.7443 (t0) cc_final: 0.7230 (t0) REVERT: G 132 PHE cc_start: 0.8764 (t80) cc_final: 0.8367 (t80) REVERT: G 155 LYS cc_start: 0.8514 (mttm) cc_final: 0.8298 (mttm) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.7731 time to fit residues: 81.6145 Evaluate side-chains 85 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [49, 97, 53, 5, 33, 65, 62, 51, 100, 38, 61] chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 143 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.153812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.120992 restraints weight = 8682.884| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.48 r_work: 0.3232 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8624 Z= 0.171 Angle : 0.619 13.513 11606 Z= 0.302 Chirality : 0.043 0.168 1456 Planarity : 0.003 0.029 1337 Dihedral : 21.361 155.139 1428 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.20 % Allowed : 8.94 % Favored : 89.86 % 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 are not related in a simple way. whole: 2.22 (0.27), residues: 1064 helix: 2.44 (0.19), residues: 707 sheet: -1.70 (0.51), residues: 105 loop : 0.17 (0.44), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 159 TYR 0.015 0.001 TYR C 56 PHE 0.010 0.001 PHE G 120 TRP 0.020 0.004 TRP C 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 ( 8624) covalent geometry : angle 0.61886 / 0.30 (11606) hydrogen bonds : bond 0.04378 / 3.04 ( 610) hydrogen bonds : angle 3.47670 / 2.56 ( 1791) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.300 Fit side-chains REVERT: A 94 LYS cc_start: 0.7064 (ttpp) cc_final: 0.6831 (ttpp) REVERT: A 128 LYS cc_start: 0.8300 (ptpt) cc_final: 0.8051 (ptmt) REVERT: B 94 LYS cc_start: 0.7479 (ttmm) cc_final: 0.6956 (ttpp) REVERT: B 117 LYS cc_start: 0.8164 (mttp) cc_final: 0.7851 (mmmm) REVERT: C 45 LYS cc_start: 0.7753 (mmmm) cc_final: 0.7531 (mptt) REVERT: C 91 MET cc_start: 0.5997 (OUTLIER) cc_final: 0.5768 (tmm) REVERT: C 116 GLU cc_start: 0.8303 (pt0) cc_final: 0.8033 (pt0) REVERT: D 30 LYS cc_start: 0.7509 (mptt) cc_final: 0.7151 (mmtt) REVERT: D 45 LYS cc_start: 0.7630 (mmmm) cc_final: 0.7345 (mptt) REVERT: D 94 LYS cc_start: 0.7385 (ttpp) cc_final: 0.7044 (ttpp) REVERT: D 128 LYS cc_start: 0.8447 (ptpt) cc_final: 0.8175 (ptpt) REVERT: E 45 LYS cc_start: 0.7268 (mmmm) cc_final: 0.6955 (mptt) REVERT: E 91 MET cc_start: 0.6304 (tmm) cc_final: 0.5858 (tmm) REVERT: F 91 MET cc_start: 0.6681 (ttp) cc_final: 0.5837 (tmm) REVERT: F 128 LYS cc_start: 0.8096 (ptpt) cc_final: 0.7856 (ptmt) REVERT: F 132 PHE cc_start: 0.8714 (t80) cc_final: 0.8156 (t80) REVERT: G 91 MET cc_start: 0.6065 (OUTLIER) cc_final: 0.5345 (tmm) REVERT: G 94 LYS cc_start: 0.7244 (ttpp) cc_final: 0.6970 (ttpp) REVERT: G 155 LYS cc_start: 0.8490 (mttm) cc_final: 0.8279 (mttm) outliers start: 11 outliers final: 5 residues processed: 127 average time/residue: 0.6965 time to fit residues: 92.8972 Evaluate side-chains 106 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain C residue 91 MET Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain G residue 91 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [88, 18, 28, 29, 82, 103, 79, 53, 76, 64, 97] chunk 88 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 0.0770 chunk 29 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.151731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.119099 restraints weight = 8712.635| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.47 r_work: 0.3214 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8624 Z= 0.145 Angle : 0.502 9.323 11606 Z= 0.253 Chirality : 0.041 0.131 1456 Planarity : 0.003 0.026 1337 Dihedral : 21.059 172.621 1428 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.53 % Allowed : 13.41 % Favored : 85.06 % 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 are not related in a simple way. whole: 2.24 (0.27), residues: 1064 helix: 2.41 (0.18), residues: 707 sheet: -1.21 (0.55), residues: 105 loop : 0.07 (0.44), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG G 159 TYR 0.012 0.001 TYR E 56 PHE 0.010 0.001 PHE E 87 TRP 0.014 0.003 TRP E 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 8624) covalent geometry : angle 0.50237 / 0.25 (11606) hydrogen bonds : bond 0.04121 / 2.85 ( 610) hydrogen bonds : angle 3.26118 / 2.40 ( 1791) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.310 Fit side-chains REVERT: A 45 LYS cc_start: 0.7723 (mmmm) cc_final: 0.7513 (mptt) REVERT: A 91 MET cc_start: 0.6225 (tmm) cc_final: 0.5706 (tmm) REVERT: A 94 LYS cc_start: 0.7365 (ttpp) cc_final: 0.7017 (ttpp) REVERT: A 128 LYS cc_start: 0.8266 (ptpt) cc_final: 0.7963 (ptmt) REVERT: B 132 PHE cc_start: 0.8702 (t80) cc_final: 0.8392 (t80) REVERT: C 45 LYS cc_start: 0.7759 (mmmm) cc_final: 0.7544 (mptt) REVERT: C 91 MET cc_start: 0.6112 (tmm) cc_final: 0.5702 (tmm) REVERT: D 94 LYS cc_start: 0.7504 (ttpp) cc_final: 0.7003 (ttpp) REVERT: D 128 LYS cc_start: 0.8449 (ptpt) cc_final: 0.8217 (ptpt) REVERT: E 29 SER cc_start: 0.8213 (m) cc_final: 0.7938 (p) REVERT: E 45 LYS cc_start: 0.7371 (mmmm) cc_final: 0.7062 (mptt) REVERT: F 91 MET cc_start: 0.6653 (ttp) cc_final: 0.5866 (tmm) REVERT: F 128 LYS cc_start: 0.8037 (ptpt) cc_final: 0.7766 (ptmt) REVERT: F 132 PHE cc_start: 0.8644 (t80) cc_final: 0.7963 (t80) REVERT: G 45 LYS cc_start: 0.7517 (mptm) cc_final: 0.7315 (mptt) REVERT: G 105 MET cc_start: 0.7267 (OUTLIER) cc_final: 0.6964 (mtp) outliers start: 14 outliers final: 10 residues processed: 112 average time/residue: 0.7291 time to fit residues: 85.8076 Evaluate side-chains 102 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain G residue 105 MET Chi-restraints excluded: chain G residue 161 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [2, 45, 48, 70, 19, 83, 27, 68, 81, 51, 24] chunk 2 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.145979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.112835 restraints weight = 9064.777| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.49 r_work: 0.3136 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 8624 Z= 0.249 Angle : 0.635 10.436 11606 Z= 0.311 Chirality : 0.044 0.131 1456 Planarity : 0.003 0.024 1337 Dihedral : 20.644 178.769 1428 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.74 % Allowed : 16.68 % Favored : 81.57 % 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 are not related in a simple way. whole: 1.58 (0.26), residues: 1064 helix: 2.00 (0.18), residues: 707 sheet: -1.47 (0.55), residues: 105 loop : -0.45 (0.44), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 159 TYR 0.012 0.001 TYR C 56 PHE 0.010 0.002 PHE D 120 TRP 0.010 0.002 TRP E 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.25 ( 8624) covalent geometry : angle 0.63469 / 0.31 (11606) hydrogen bonds : bond 0.04625 / 3.21 ( 610) hydrogen bonds : angle 3.38517 / 2.49 ( 1791) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.291 Fit side-chains REVERT: A 45 LYS cc_start: 0.7728 (mmmm) cc_final: 0.7505 (mptt) REVERT: A 94 LYS cc_start: 0.7698 (ttpp) cc_final: 0.7317 (ttpp) REVERT: A 128 LYS cc_start: 0.8293 (ptpt) cc_final: 0.7984 (ptpt) REVERT: A 132 PHE cc_start: 0.8755 (t80) cc_final: 0.8526 (t80) REVERT: B 94 LYS cc_start: 0.7672 (ttmm) cc_final: 0.7055 (ttpp) REVERT: B 132 PHE cc_start: 0.8745 (t80) cc_final: 0.7827 (t80) REVERT: C 29 SER cc_start: 0.8159 (m) cc_final: 0.7915 (p) REVERT: C 45 LYS cc_start: 0.7858 (mmmm) cc_final: 0.7654 (mptt) REVERT: C 91 MET cc_start: 0.6464 (OUTLIER) cc_final: 0.6086 (tmm) REVERT: D 45 LYS cc_start: 0.7697 (mmmm) cc_final: 0.7389 (mptt) REVERT: D 91 MET cc_start: 0.6702 (ttp) cc_final: 0.6077 (ttm) REVERT: E 45 LYS cc_start: 0.7661 (mmmm) cc_final: 0.7368 (mptt) REVERT: E 91 MET cc_start: 0.6926 (tmm) cc_final: 0.6432 (tmm) REVERT: F 45 LYS cc_start: 0.7755 (mmmm) cc_final: 0.7486 (mptt) REVERT: F 91 MET cc_start: 0.6561 (ttp) cc_final: 0.6090 (tmm) REVERT: F 128 LYS cc_start: 0.8019 (ptpt) cc_final: 0.7710 (ptmt) REVERT: F 132 PHE cc_start: 0.8657 (t80) cc_final: 0.8008 (t80) REVERT: G 91 MET cc_start: 0.6867 (tmm) cc_final: 0.5893 (ttm) outliers start: 16 outliers final: 7 residues processed: 114 average time/residue: 0.6687 time to fit residues: 80.2431 Evaluate side-chains 88 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain C residue 91 MET Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 161 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [84, 10, 25, 52, 19, 95, 99, 30, 49, 38, 31] chunk 84 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 95 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 49 optimal weight: 0.3980 chunk 38 optimal weight: 0.0050 chunk 31 optimal weight: 0.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.150552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.118203 restraints weight = 8824.967| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.43 r_work: 0.3202 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8624 Z= 0.117 Angle : 0.519 10.599 11606 Z= 0.247 Chirality : 0.041 0.238 1456 Planarity : 0.002 0.024 1337 Dihedral : 18.744 171.616 1428 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.42 % Allowed : 17.45 % Favored : 81.13 % 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 are not related in a simple way. whole: 2.22 (0.27), residues: 1064 helix: 2.52 (0.18), residues: 707 sheet: -1.15 (0.56), residues: 105 loop : -0.36 (0.45), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 159 TYR 0.011 0.001 TYR E 56 PHE 0.011 0.001 PHE G 87 TRP 0.011 0.002 TRP C 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 8624) covalent geometry : angle 0.51921 / 0.25 (11606) hydrogen bonds : bond 0.03872 / 2.67 ( 610) hydrogen bonds : angle 3.13199 / 2.30 ( 1791) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.238 Fit side-chains REVERT: A 132 PHE cc_start: 0.8730 (t80) cc_final: 0.8496 (t80) REVERT: B 117 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7733 (mtpp) REVERT: B 132 PHE cc_start: 0.8640 (t80) cc_final: 0.7795 (t80) REVERT: C 45 LYS cc_start: 0.7834 (mmmm) cc_final: 0.7628 (mptt) REVERT: C 91 MET cc_start: 0.6445 (OUTLIER) cc_final: 0.6111 (tmm) REVERT: D 91 MET cc_start: 0.6624 (ttp) cc_final: 0.6064 (ttm) REVERT: E 91 MET cc_start: 0.6558 (tmm) cc_final: 0.6283 (tmm) REVERT: F 45 LYS cc_start: 0.7760 (mmmm) cc_final: 0.7488 (mptt) REVERT: F 91 MET cc_start: 0.6465 (ttp) cc_final: 0.5934 (ttm) REVERT: F 132 PHE cc_start: 0.8618 (t80) cc_final: 0.7913 (t80) outliers start: 13 outliers final: 5 residues processed: 78 average time/residue: 0.5956 time to fit residues: 49.4179 Evaluate side-chains 78 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain B residue 117 LYS Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain C residue 91 MET Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 161 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [44, 35, 99, 38, 102, 47, 31, 70, 19, 97, 50] chunk 44 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 102 optimal weight: 0.2980 chunk 47 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.148904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.116312 restraints weight = 8811.693| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.43 r_work: 0.3181 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8624 Z= 0.148 Angle : 0.535 11.994 11606 Z= 0.258 Chirality : 0.041 0.186 1456 Planarity : 0.002 0.023 1337 Dihedral : 16.405 166.145 1428 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.42 % Allowed : 17.67 % Favored : 80.92 % 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 are not related in a simple way. whole: 2.19 (0.26), residues: 1064 helix: 2.49 (0.18), residues: 707 sheet: -1.17 (0.56), residues: 105 loop : -0.36 (0.45), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 159 TYR 0.010 0.001 TYR B 56 PHE 0.011 0.002 PHE E 87 TRP 0.009 0.002 TRP F 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 8624) covalent geometry : angle 0.53497 / 0.26 (11606) hydrogen bonds : bond 0.03989 / 2.76 ( 610) hydrogen bonds : angle 3.14387 / 2.31 ( 1791) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.259 Fit side-chains REVERT: A 91 MET cc_start: 0.6574 (tmm) cc_final: 0.5976 (ttm) REVERT: A 132 PHE cc_start: 0.8697 (t80) cc_final: 0.8470 (t80) REVERT: B 132 PHE cc_start: 0.8632 (t80) cc_final: 0.7802 (t80) REVERT: C 45 LYS cc_start: 0.7852 (mmmm) cc_final: 0.7649 (mptt) REVERT: D 91 MET cc_start: 0.6679 (ttp) cc_final: 0.6124 (ttm) REVERT: E 91 MET cc_start: 0.6703 (tmm) cc_final: 0.6357 (tmm) REVERT: F 91 MET cc_start: 0.6522 (ttp) cc_final: 0.5997 (ttm) REVERT: F 132 PHE cc_start: 0.8641 (t80) cc_final: 0.7989 (t80) outliers start: 13 outliers final: 8 residues processed: 80 average time/residue: 0.5887 time to fit residues: 49.8347 Evaluate side-chains 81 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain G residue 16 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [86, 22, 11, 16, 79, 89, 35, 71, 33, 70, 75] chunk 86 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 11 optimal weight: 0.0470 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 35 optimal weight: 0.1980 chunk 71 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 overall best weight: 0.5682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.149928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.117273 restraints weight = 8929.509| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.45 r_work: 0.3188 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8624 Z= 0.133 Angle : 0.510 12.125 11606 Z= 0.247 Chirality : 0.040 0.196 1456 Planarity : 0.002 0.023 1337 Dihedral : 16.147 176.875 1428 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.53 % Allowed : 18.21 % Favored : 80.26 % 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 are not related in a simple way. whole: 2.34 (0.27), residues: 1064 helix: 2.60 (0.18), residues: 707 sheet: -1.11 (0.56), residues: 105 loop : -0.31 (0.46), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 159 TYR 0.010 0.001 TYR B 56 PHE 0.012 0.001 PHE C 87 TRP 0.009 0.002 TRP F 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 8624) covalent geometry : angle 0.51007 / 0.25 (11606) hydrogen bonds : bond 0.03843 / 2.66 ( 610) hydrogen bonds : angle 3.09569 / 2.28 ( 1791) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.325 Fit side-chains REVERT: A 91 MET cc_start: 0.6427 (tmm) cc_final: 0.5918 (ttm) REVERT: A 132 PHE cc_start: 0.8632 (t80) cc_final: 0.8392 (t80) REVERT: B 132 PHE cc_start: 0.8603 (t80) cc_final: 0.7824 (t80) REVERT: B 155 LYS cc_start: 0.8461 (mttt) cc_final: 0.8239 (mttp) REVERT: C 45 LYS cc_start: 0.7801 (mmmm) cc_final: 0.7600 (mptt) REVERT: D 91 MET cc_start: 0.6710 (ttp) cc_final: 0.6176 (ttm) REVERT: E 91 MET cc_start: 0.6639 (OUTLIER) cc_final: 0.6328 (tmm) REVERT: F 45 LYS cc_start: 0.7717 (mmmm) cc_final: 0.7477 (mptt) REVERT: F 91 MET cc_start: 0.6651 (ttp) cc_final: 0.6191 (ttm) REVERT: F 132 PHE cc_start: 0.8630 (t80) cc_final: 0.7942 (t80) outliers start: 14 outliers final: 10 residues processed: 85 average time/residue: 0.5803 time to fit residues: 52.4891 Evaluate side-chains 85 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain E residue 91 MET Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain G residue 16 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [100, 7, 32, 61, 58, 98, 19, 76, 53, 54, 56] chunk 100 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.147867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.114537 restraints weight = 9008.292| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.51 r_work: 0.3156 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 8624 Z= 0.165 Angle : 0.533 13.081 11606 Z= 0.262 Chirality : 0.042 0.209 1456 Planarity : 0.002 0.023 1337 Dihedral : 16.139 175.783 1428 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.64 % Allowed : 18.65 % Favored : 79.72 % 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 are not related in a simple way. whole: 2.21 (0.27), residues: 1064 helix: 2.50 (0.18), residues: 707 sheet: -1.37 (0.47), residues: 147 loop : 0.11 (0.51), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 159 TYR 0.011 0.001 TYR B 56 PHE 0.011 0.002 PHE C 87 TRP 0.006 0.001 TRP C 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 ( 8624) covalent geometry : angle 0.53300 / 0.26 (11606) hydrogen bonds : bond 0.04031 / 2.79 ( 610) hydrogen bonds : angle 3.14895 / 2.31 ( 1791) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.307 Fit side-chains REVERT: A 91 MET cc_start: 0.6375 (tmm) cc_final: 0.5854 (ttm) REVERT: A 132 PHE cc_start: 0.8614 (t80) cc_final: 0.8375 (t80) REVERT: B 132 PHE cc_start: 0.8628 (t80) cc_final: 0.7797 (t80) REVERT: C 45 LYS cc_start: 0.7797 (mmmm) cc_final: 0.7592 (mptt) REVERT: D 91 MET cc_start: 0.6679 (ttp) cc_final: 0.6270 (ttm) REVERT: F 45 LYS cc_start: 0.7729 (mmmm) cc_final: 0.7486 (mptt) REVERT: F 91 MET cc_start: 0.6712 (ttp) cc_final: 0.6200 (ttm) REVERT: F 132 PHE cc_start: 0.8673 (t80) cc_final: 0.7975 (t80) outliers start: 15 outliers final: 10 residues processed: 81 average time/residue: 0.5618 time to fit residues: 48.5083 Evaluate side-chains 84 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain G residue 16 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [102, 15, 78, 88, 47, 57, 59, 49, 27, 13, 17] chunk 102 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 59 optimal weight: 0.0980 chunk 49 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.148382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.115144 restraints weight = 8947.070| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.51 r_work: 0.3168 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8624 Z= 0.157 Angle : 0.529 13.117 11606 Z= 0.258 Chirality : 0.041 0.212 1456 Planarity : 0.002 0.023 1337 Dihedral : 15.800 175.715 1428 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.42 % Allowed : 19.08 % Favored : 79.50 % 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 are not related in a simple way. whole: 2.25 (0.27), residues: 1064 helix: 2.54 (0.18), residues: 707 sheet: -1.37 (0.47), residues: 147 loop : 0.10 (0.52), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 159 TYR 0.011 0.001 TYR B 56 PHE 0.011 0.002 PHE C 87 TRP 0.007 0.001 TRP C 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 ( 8624) covalent geometry : angle 0.52905 / 0.26 (11606) hydrogen bonds : bond 0.03985 / 2.76 ( 610) hydrogen bonds : angle 3.13005 / 2.30 ( 1791) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.297 Fit side-chains REVERT: A 91 MET cc_start: 0.6382 (tmm) cc_final: 0.5902 (ttm) REVERT: A 132 PHE cc_start: 0.8621 (t80) cc_final: 0.8383 (t80) REVERT: B 132 PHE cc_start: 0.8618 (t80) cc_final: 0.7765 (t80) REVERT: D 91 MET cc_start: 0.6640 (ttp) cc_final: 0.6146 (ttt) REVERT: E 113 GLU cc_start: 0.8307 (pt0) cc_final: 0.8042 (pt0) REVERT: F 45 LYS cc_start: 0.7731 (mmmm) cc_final: 0.7484 (mptt) REVERT: F 91 MET cc_start: 0.6625 (ttp) cc_final: 0.6045 (ttm) REVERT: F 132 PHE cc_start: 0.8646 (t80) cc_final: 0.7934 (t80) outliers start: 13 outliers final: 12 residues processed: 81 average time/residue: 0.5304 time to fit residues: 45.8195 Evaluate side-chains 81 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain C residue 91 MET Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain G residue 16 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [104, 89, 38, 83, 94, 10, 46, 81, 70, 74, 2] chunk 104 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.148789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.116169 restraints weight = 8954.926| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.48 r_work: 0.3170 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8624 Z= 0.147 Angle : 0.521 13.871 11606 Z= 0.256 Chirality : 0.042 0.266 1456 Planarity : 0.002 0.023 1337 Dihedral : 15.391 167.640 1428 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.20 % Allowed : 19.63 % Favored : 79.17 % 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 are not related in a simple way. whole: 2.30 (0.27), residues: 1064 helix: 2.58 (0.18), residues: 707 sheet: -1.34 (0.47), residues: 147 loop : 0.10 (0.52), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 159 TYR 0.011 0.001 TYR B 56 PHE 0.013 0.001 PHE E 87 TRP 0.007 0.001 TRP C 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 8624) covalent geometry : angle 0.52122 / 0.26 (11606) hydrogen bonds : bond 0.03959 / 2.74 ( 610) hydrogen bonds : angle 3.11462 / 2.29 ( 1791) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.233 Fit side-chains REVERT: A 91 MET cc_start: 0.6466 (tmm) cc_final: 0.5908 (ttm) REVERT: A 132 PHE cc_start: 0.8657 (t80) cc_final: 0.8417 (t80) REVERT: D 91 MET cc_start: 0.6545 (ttp) cc_final: 0.6020 (ttm) REVERT: E 113 GLU cc_start: 0.8323 (pt0) cc_final: 0.8048 (pt0) REVERT: F 45 LYS cc_start: 0.7744 (mmmm) cc_final: 0.7457 (mmpt) REVERT: F 91 MET cc_start: 0.6640 (ttp) cc_final: 0.6104 (ttm) REVERT: F 132 PHE cc_start: 0.8637 (t80) cc_final: 0.7922 (t80) REVERT: G 139 ASP cc_start: 0.7972 (m-30) cc_final: 0.7746 (m-30) outliers start: 11 outliers final: 12 residues processed: 79 average time/residue: 0.4823 time to fit residues: 41.0458 Evaluate side-chains 85 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain G residue 16 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [70, 27, 0, 17, 4, 94, 63, 59, 6, 46, 77] chunk 70 optimal weight: 0.0980 chunk 27 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 63 optimal weight: 0.0030 chunk 59 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.150151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.117683 restraints weight = 8944.279| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.48 r_work: 0.3187 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8624 Z= 0.120 Angle : 0.507 13.589 11606 Z= 0.248 Chirality : 0.041 0.254 1456 Planarity : 0.002 0.023 1337 Dihedral : 15.034 162.874 1428 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.98 % Allowed : 20.50 % Favored : 78.52 % 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 are not related in a simple way. whole: 2.52 (0.27), residues: 1064 helix: 2.75 (0.18), residues: 707 sheet: -1.23 (0.48), residues: 147 loop : 0.14 (0.52), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG G 159 TYR 0.011 0.001 TYR B 56 PHE 0.013 0.001 PHE E 87 TRP 0.009 0.002 TRP F 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 8624) covalent geometry : angle 0.50708 / 0.25 (11606) hydrogen bonds : bond 0.03821 / 2.64 ( 610) hydrogen bonds : angle 3.05644 / 2.25 ( 1791) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2283.39 seconds wall clock time: 39 minutes 50.80 seconds (2390.80 seconds total)