Starting phenix.real_space_refine on Tue Feb 3 23:08:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m7c_63681/02_2026/9m7c_63681.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m7c_63681/02_2026/9m7c_63681.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9m7c_63681/02_2026/9m7c_63681.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m7c_63681/02_2026/9m7c_63681.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m7c_63681/02_2026/9m7c_63681.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m7c_63681/02_2026/9m7c_63681.map" } resolution = 3.65 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 ------------------------------------------------------------------------------- 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= 0.003 sd= 0.101 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 4914 2.51 5 N 1236 2.21 5 O 1644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7806 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1301 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 2, 'TRANS': 163} Chain: "B" Number of atoms: 1301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1301 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 2, 'TRANS': 163} Chain: "C" Number of atoms: 1301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1301 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 2, 'TRANS': 163} Chain: "D" Number of atoms: 1301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1301 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 2, 'TRANS': 163} Chain: "E" Number of atoms: 1301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1301 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 2, 'TRANS': 163} Chain: "F" Number of atoms: 1301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1301 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 2, 'TRANS': 163} Time building chain proxies: 1.69, per 1000 atoms: 0.22 Number of scatterers: 7806 At special positions: 0 Unit cell: (126, 117.6, 91.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 1644 8.00 N 1236 7.00 C 4914 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: 0.71 Conformation dependent library (CDL) restraints added in 303.6 milliseconds 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1884 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 7 sheets defined 13.8% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 6 through 8 No H-bonds generated for 'chain 'A' and resid 6 through 8' Processing helix chain 'A' and resid 18 through 20 No H-bonds generated for 'chain 'A' and resid 18 through 20' Processing helix chain 'A' and resid 73 through 85 Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'B' and resid 6 through 8 No H-bonds generated for 'chain 'B' and resid 6 through 8' Processing helix chain 'B' and resid 18 through 20 No H-bonds generated for 'chain 'B' and resid 18 through 20' Processing helix chain 'B' and resid 73 through 84 removed outlier: 3.528A pdb=" N GLU B 77 " --> pdb=" O LYS B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'C' and resid 18 through 20 No H-bonds generated for 'chain 'C' and resid 18 through 20' Processing helix chain 'C' and resid 73 through 85 removed outlier: 3.552A pdb=" N GLU C 77 " --> pdb=" O LYS C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 Processing helix chain 'D' and resid 6 through 8 No H-bonds generated for 'chain 'D' and resid 6 through 8' Processing helix chain 'D' and resid 18 through 20 No H-bonds generated for 'chain 'D' and resid 18 through 20' Processing helix chain 'D' and resid 73 through 85 Processing helix chain 'D' and resid 100 through 104 Processing helix chain 'E' and resid 6 through 8 No H-bonds generated for 'chain 'E' and resid 6 through 8' Processing helix chain 'E' and resid 18 through 20 No H-bonds generated for 'chain 'E' and resid 18 through 20' Processing helix chain 'E' and resid 73 through 85 removed outlier: 3.542A pdb=" N GLU E 77 " --> pdb=" O LYS E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 104 Processing helix chain 'F' and resid 18 through 20 No H-bonds generated for 'chain 'F' and resid 18 through 20' Processing helix chain 'F' and resid 73 through 85 removed outlier: 3.545A pdb=" N GLU F 77 " --> pdb=" O LYS F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 104 Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 16 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 10 through 16 current: chain 'A' and resid 59 through 67 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 59 through 67 current: chain 'A' and resid 107 through 121 removed outlier: 6.599A pdb=" N GLU A 134 " --> pdb=" O SER A 117 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N PHE A 119 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLU A 132 " --> pdb=" O PHE A 119 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LYS A 121 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N GLU A 130 " --> pdb=" O LYS A 121 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 130 through 137 current: chain 'B' and resid 26 through 27 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 26 through 27 current: chain 'B' and resid 59 through 67 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 59 through 67 current: chain 'B' and resid 107 through 121 removed outlier: 6.592A pdb=" N GLU B 134 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE B 119 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N GLU B 132 " --> pdb=" O PHE B 119 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N LYS B 121 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N GLU B 130 " --> pdb=" O LYS B 121 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 130 through 137 current: chain 'C' and resid 26 through 27 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 26 through 27 current: chain 'C' and resid 59 through 67 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 59 through 67 current: chain 'C' and resid 107 through 121 removed outlier: 6.598A pdb=" N GLU C 134 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE C 119 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N GLU C 132 " --> pdb=" O PHE C 119 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LYS C 121 " --> pdb=" O GLU C 130 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N GLU C 130 " --> pdb=" O LYS C 121 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 130 through 137 current: chain 'D' and resid 59 through 67 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 59 through 67 current: chain 'D' and resid 107 through 121 removed outlier: 6.583A pdb=" N GLU D 134 " --> pdb=" O SER D 117 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE D 119 " --> pdb=" O GLU D 132 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLU D 132 " --> pdb=" O PHE D 119 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LYS D 121 " --> pdb=" O GLU D 130 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N GLU D 130 " --> pdb=" O LYS D 121 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 130 through 137 current: chain 'E' and resid 26 through 27 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 26 through 27 current: chain 'E' and resid 59 through 67 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 59 through 67 current: chain 'E' and resid 107 through 121 removed outlier: 6.599A pdb=" N GLU E 134 " --> pdb=" O SER E 117 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N PHE E 119 " --> pdb=" O GLU E 132 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLU E 132 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LYS E 121 " --> pdb=" O GLU E 130 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N GLU E 130 " --> pdb=" O LYS E 121 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 130 through 137 current: chain 'F' and resid 26 through 27 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 26 through 27 current: chain 'F' and resid 59 through 67 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 59 through 67 current: chain 'F' and resid 107 through 121 removed outlier: 6.602A pdb=" N GLU F 134 " --> pdb=" O SER F 117 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N PHE F 119 " --> pdb=" O GLU F 132 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLU F 132 " --> pdb=" O PHE F 119 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LYS F 121 " --> pdb=" O GLU F 130 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N GLU F 130 " --> pdb=" O LYS F 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 45 removed outlier: 3.579A pdb=" N ASP A 43 " --> pdb=" O ASN A 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 42 through 47 removed outlier: 3.672A pdb=" N ASP B 43 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR B 47 " --> pdb=" O GLY B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 47 removed outlier: 3.801A pdb=" N ASP C 43 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN C 54 " --> pdb=" O ASP C 43 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR C 47 " --> pdb=" O GLY C 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 42 through 45 removed outlier: 3.602A pdb=" N ASP D 43 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN D 54 " --> pdb=" O ASP D 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 42 through 47 removed outlier: 3.670A pdb=" N ASP E 43 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR E 47 " --> pdb=" O GLY E 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 42 through 47 removed outlier: 3.789A pdb=" N ASP F 43 " --> pdb=" O ASN F 54 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN F 54 " --> pdb=" O ASP F 43 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR F 47 " --> pdb=" O GLY F 50 " (cutoff:3.500A) 98 hydrogen bonds defined for protein. 240 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: 0.62 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2586 1.34 - 1.46: 1569 1.46 - 1.57: 3753 1.57 - 1.69: 0 1.69 - 1.80: 24 Bond restraints: 7932 Sorted by residual: bond pdb=" CB ASP C 43 " pdb=" CG ASP C 43 " ideal model delta sigma weight residual 1.516 1.539 -0.023 2.50e-02 1.60e+03 8.65e-01 bond pdb=" CB LYS D 73 " pdb=" CG LYS D 73 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.61e-01 bond pdb=" CB LYS A 73 " pdb=" CG LYS A 73 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.50e-01 bond pdb=" CB ASP D 43 " pdb=" CG ASP D 43 " ideal model delta sigma weight residual 1.516 1.539 -0.023 2.50e-02 1.60e+03 8.40e-01 bond pdb=" CB ASP F 43 " pdb=" CG ASP F 43 " ideal model delta sigma weight residual 1.516 1.539 -0.023 2.50e-02 1.60e+03 8.24e-01 ... (remaining 7927 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 10146 1.19 - 2.37: 480 2.37 - 3.56: 48 3.56 - 4.74: 20 4.74 - 5.93: 16 Bond angle restraints: 10710 Sorted by residual: angle pdb=" C THR E 100 " pdb=" N ASP E 101 " pdb=" CA ASP E 101 " ideal model delta sigma weight residual 121.54 127.41 -5.87 1.91e+00 2.74e-01 9.43e+00 angle pdb=" C THR B 100 " pdb=" N ASP B 101 " pdb=" CA ASP B 101 " ideal model delta sigma weight residual 121.54 127.40 -5.86 1.91e+00 2.74e-01 9.42e+00 angle pdb=" C THR F 100 " pdb=" N ASP F 101 " pdb=" CA ASP F 101 " ideal model delta sigma weight residual 121.54 127.38 -5.84 1.91e+00 2.74e-01 9.35e+00 angle pdb=" C THR A 100 " pdb=" N ASP A 101 " pdb=" CA ASP A 101 " ideal model delta sigma weight residual 121.54 127.36 -5.82 1.91e+00 2.74e-01 9.29e+00 angle pdb=" C THR C 100 " pdb=" N ASP C 101 " pdb=" CA ASP C 101 " ideal model delta sigma weight residual 121.54 127.26 -5.72 1.91e+00 2.74e-01 8.96e+00 ... (remaining 10705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 4299 16.01 - 32.02: 355 32.02 - 48.03: 97 48.03 - 64.04: 19 64.04 - 80.05: 6 Dihedral angle restraints: 4776 sinusoidal: 1860 harmonic: 2916 Sorted by residual: dihedral pdb=" CA MET A 28 " pdb=" C MET A 28 " pdb=" N ALA A 29 " pdb=" CA ALA A 29 " ideal model delta harmonic sigma weight residual -180.00 -160.48 -19.52 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA MET D 28 " pdb=" C MET D 28 " pdb=" N ALA D 29 " pdb=" CA ALA D 29 " ideal model delta harmonic sigma weight residual -180.00 -160.51 -19.49 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA TYR B 14 " pdb=" C TYR B 14 " pdb=" N ARG B 15 " pdb=" CA ARG B 15 " ideal model delta harmonic sigma weight residual 180.00 164.01 15.99 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 4773 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 790 0.031 - 0.061: 252 0.061 - 0.092: 72 0.092 - 0.123: 70 0.123 - 0.153: 10 Chirality restraints: 1194 Sorted by residual: chirality pdb=" CA ASP D 101 " pdb=" N ASP D 101 " pdb=" C ASP D 101 " pdb=" CB ASP D 101 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" CA VAL B 166 " pdb=" N VAL B 166 " pdb=" C VAL B 166 " pdb=" CB VAL B 166 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.86e-01 chirality pdb=" CA VAL E 166 " pdb=" N VAL E 166 " pdb=" C VAL E 166 " pdb=" CB VAL E 166 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.83e-01 ... (remaining 1191 not shown) Planarity restraints: 1392 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 73 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.82e+00 pdb=" C LYS D 73 " 0.023 2.00e-02 2.50e+03 pdb=" O LYS D 73 " -0.009 2.00e-02 2.50e+03 pdb=" N HIS D 74 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 73 " 0.007 2.00e-02 2.50e+03 1.34e-02 1.80e+00 pdb=" C LYS A 73 " -0.023 2.00e-02 2.50e+03 pdb=" O LYS A 73 " 0.009 2.00e-02 2.50e+03 pdb=" N HIS A 74 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 73 " -0.006 2.00e-02 2.50e+03 1.20e-02 1.43e+00 pdb=" C LYS C 73 " 0.021 2.00e-02 2.50e+03 pdb=" O LYS C 73 " -0.008 2.00e-02 2.50e+03 pdb=" N HIS C 74 " -0.007 2.00e-02 2.50e+03 ... (remaining 1389 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2463 2.83 - 3.35: 5695 3.35 - 3.86: 10933 3.86 - 4.38: 11879 4.38 - 4.90: 21141 Nonbonded interactions: 52111 Sorted by model distance: nonbonded pdb=" OH TYR A 111 " pdb=" OE1 GLN A 113 " model vdw 2.310 3.040 nonbonded pdb=" OH TYR D 111 " pdb=" OE1 GLN D 113 " model vdw 2.313 3.040 nonbonded pdb=" OH TYR F 111 " pdb=" OE1 GLN F 113 " model vdw 2.318 3.040 nonbonded pdb=" OH TYR C 111 " pdb=" OE1 GLN C 113 " model vdw 2.320 3.040 nonbonded pdb=" NZ LYS D 143 " pdb=" OD2 ASP E 79 " model vdw 2.388 3.120 ... (remaining 52106 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.240 Find NCS groups from input model: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 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 0.028 7932 Z= 0.127 Angle : 0.612 5.928 10710 Z= 0.381 Chirality : 0.042 0.153 1194 Planarity : 0.002 0.024 1392 Dihedral : 13.208 80.051 2892 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.61 % Allowed : 2.85 % Favored : 96.54 % 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: -1.16 (0.26), residues: 984 helix: 0.98 (0.55), residues: 72 sheet: 0.09 (0.25), residues: 444 loop : -1.97 (0.24), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 40 TYR 0.008 0.001 TYR F 111 PHE 0.010 0.001 PHE B 112 TRP 0.007 0.001 TRP D 91 HIS 0.002 0.001 HIS D 74 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 7932) covalent geometry : angle 0.61246 (10710) hydrogen bonds : bond 0.25128 ( 98) hydrogen bonds : angle 7.15575 ( 240) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.290 Fit side-chains REVERT: B 73 LYS cc_start: 0.8381 (tptp) cc_final: 0.8138 (tptp) REVERT: B 105 ASP cc_start: 0.7721 (m-30) cc_final: 0.7441 (m-30) REVERT: D 126 GLU cc_start: 0.8047 (pm20) cc_final: 0.7664 (pm20) REVERT: E 73 LYS cc_start: 0.8359 (tptp) cc_final: 0.8112 (tptp) REVERT: E 105 ASP cc_start: 0.7737 (m-30) cc_final: 0.7532 (m-30) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.0828 time to fit residues: 12.6528 Evaluate side-chains 102 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN B 113 GLN C 113 GLN D 113 GLN E 113 GLN F 113 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.178064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.152823 restraints weight = 7586.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.153821 restraints weight = 6569.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.154333 restraints weight = 5870.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.155098 restraints weight = 5485.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.155221 restraints weight = 5139.387| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 7932 Z= 0.114 Angle : 0.473 6.025 10710 Z= 0.261 Chirality : 0.043 0.140 1194 Planarity : 0.002 0.022 1392 Dihedral : 4.548 19.892 1044 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.37 % Favored : 95.43 % Rotamer: Outliers : 0.72 % Allowed : 6.59 % Favored : 92.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.28 (0.26), residues: 984 helix: -0.36 (0.48), residues: 114 sheet: 0.03 (0.25), residues: 444 loop : -1.95 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D 40 TYR 0.008 0.001 TYR C 14 PHE 0.012 0.001 PHE E 112 TRP 0.006 0.001 TRP D 91 HIS 0.002 0.001 HIS B 34 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 7932) covalent geometry : angle 0.47317 (10710) hydrogen bonds : bond 0.03226 ( 98) hydrogen bonds : angle 4.79097 ( 240) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.299 Fit side-chains REVERT: B 73 LYS cc_start: 0.8110 (tptp) cc_final: 0.7880 (tptp) REVERT: D 126 GLU cc_start: 0.8049 (pm20) cc_final: 0.7621 (pm20) REVERT: E 73 LYS cc_start: 0.8091 (tptp) cc_final: 0.7843 (tptp) outliers start: 6 outliers final: 4 residues processed: 95 average time/residue: 0.0793 time to fit residues: 10.4290 Evaluate side-chains 94 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain F residue 70 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 26 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN C 84 ASN F 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.157239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.123538 restraints weight = 7938.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.125158 restraints weight = 6703.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.126447 restraints weight = 5905.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.127378 restraints weight = 5398.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.127777 restraints weight = 5052.251| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 7932 Z= 0.084 Angle : 0.427 5.973 10710 Z= 0.236 Chirality : 0.042 0.124 1194 Planarity : 0.002 0.019 1392 Dihedral : 4.043 14.854 1044 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.86 % Favored : 95.93 % Rotamer: Outliers : 0.96 % Allowed : 9.23 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.07 (0.27), residues: 984 helix: 0.00 (0.51), residues: 114 sheet: 0.10 (0.26), residues: 444 loop : -1.80 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 40 TYR 0.006 0.001 TYR A 111 PHE 0.009 0.001 PHE B 112 TRP 0.006 0.001 TRP A 91 HIS 0.002 0.001 HIS D 74 Details of bonding type rmsd covalent geometry : bond 0.00189 ( 7932) covalent geometry : angle 0.42673 (10710) hydrogen bonds : bond 0.02562 ( 98) hydrogen bonds : angle 4.30648 ( 240) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.299 Fit side-chains REVERT: A 73 LYS cc_start: 0.7271 (tmtt) cc_final: 0.6988 (tmtt) REVERT: B 55 MET cc_start: 0.8617 (mmm) cc_final: 0.8058 (mmm) REVERT: B 73 LYS cc_start: 0.8099 (tptp) cc_final: 0.7819 (tptp) REVERT: D 73 LYS cc_start: 0.7261 (tmtt) cc_final: 0.6999 (tmtt) REVERT: D 126 GLU cc_start: 0.8133 (pm20) cc_final: 0.7574 (pm20) REVERT: E 55 MET cc_start: 0.8604 (mmm) cc_final: 0.8001 (mmm) outliers start: 8 outliers final: 7 residues processed: 100 average time/residue: 0.0683 time to fit residues: 9.5916 Evaluate side-chains 97 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain F residue 70 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 4 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 66 optimal weight: 0.0570 chunk 48 optimal weight: 7.9990 chunk 59 optimal weight: 0.3980 chunk 42 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.6904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.174049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.152453 restraints weight = 7702.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.152453 restraints weight = 7449.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.152453 restraints weight = 7449.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.152453 restraints weight = 7449.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.152453 restraints weight = 7449.568| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 7932 Z= 0.129 Angle : 0.464 6.067 10710 Z= 0.257 Chirality : 0.043 0.125 1194 Planarity : 0.002 0.023 1392 Dihedral : 4.360 17.323 1044 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.20 % Favored : 93.60 % Rotamer: Outliers : 1.20 % Allowed : 10.91 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.27), residues: 984 helix: 0.05 (0.51), residues: 114 sheet: -0.16 (0.25), residues: 444 loop : -1.73 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D 40 TYR 0.009 0.001 TYR F 111 PHE 0.013 0.001 PHE E 112 TRP 0.007 0.001 TRP C 26 HIS 0.002 0.001 HIS B 34 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 7932) covalent geometry : angle 0.46384 (10710) hydrogen bonds : bond 0.02764 ( 98) hydrogen bonds : angle 4.35361 ( 240) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.214 Fit side-chains REVERT: A 73 LYS cc_start: 0.7159 (tmtt) cc_final: 0.6897 (tmtt) REVERT: D 73 LYS cc_start: 0.7218 (tmtt) cc_final: 0.6969 (tmtt) outliers start: 10 outliers final: 7 residues processed: 98 average time/residue: 0.0784 time to fit residues: 10.6113 Evaluate side-chains 95 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain F residue 70 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 76 optimal weight: 0.8980 chunk 57 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 0.1980 chunk 16 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.151019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.118039 restraints weight = 8167.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.119343 restraints weight = 6959.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.120602 restraints weight = 6243.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.121095 restraints weight = 5795.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.121302 restraints weight = 5532.799| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 7932 Z= 0.123 Angle : 0.459 6.054 10710 Z= 0.254 Chirality : 0.043 0.123 1194 Planarity : 0.002 0.022 1392 Dihedral : 4.316 17.130 1044 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.71 % Favored : 93.09 % Rotamer: Outliers : 1.80 % Allowed : 11.51 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.34 (0.27), residues: 984 helix: 0.07 (0.51), residues: 114 sheet: -0.36 (0.25), residues: 444 loop : -1.69 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D 40 TYR 0.009 0.001 TYR B 111 PHE 0.013 0.001 PHE B 112 TRP 0.006 0.001 TRP F 26 HIS 0.003 0.001 HIS B 74 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 7932) covalent geometry : angle 0.45857 (10710) hydrogen bonds : bond 0.02545 ( 98) hydrogen bonds : angle 4.22031 ( 240) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.312 Fit side-chains REVERT: A 73 LYS cc_start: 0.7221 (tmtt) cc_final: 0.6863 (tmtt) REVERT: C 103 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.8301 (p0) REVERT: D 73 LYS cc_start: 0.7196 (tmtt) cc_final: 0.6953 (tmtt) REVERT: F 103 ASP cc_start: 0.8521 (OUTLIER) cc_final: 0.8303 (p0) outliers start: 15 outliers final: 8 residues processed: 104 average time/residue: 0.0709 time to fit residues: 10.4145 Evaluate side-chains 100 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 103 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 73 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 77 optimal weight: 0.5980 chunk 61 optimal weight: 0.0170 chunk 32 optimal weight: 6.9990 chunk 50 optimal weight: 0.3980 chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 88 optimal weight: 0.0980 chunk 34 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 overall best weight: 0.3618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.157329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.125110 restraints weight = 8088.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.126689 restraints weight = 6790.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.127664 restraints weight = 6020.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.128613 restraints weight = 5540.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.128867 restraints weight = 5221.476| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.017 7932 Z= 0.066 Angle : 0.403 5.993 10710 Z= 0.225 Chirality : 0.042 0.123 1194 Planarity : 0.001 0.015 1392 Dihedral : 3.556 13.226 1044 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.27 % Favored : 95.53 % Rotamer: Outliers : 1.20 % Allowed : 11.75 % Favored : 87.05 % 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: -0.98 (0.27), residues: 984 helix: 0.43 (0.53), residues: 114 sheet: -0.08 (0.25), residues: 438 loop : -1.52 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 40 TYR 0.004 0.001 TYR E 111 PHE 0.007 0.001 PHE C 112 TRP 0.007 0.001 TRP C 91 HIS 0.002 0.001 HIS C 74 Details of bonding type rmsd covalent geometry : bond 0.00138 ( 7932) covalent geometry : angle 0.40306 (10710) hydrogen bonds : bond 0.01776 ( 98) hydrogen bonds : angle 3.78829 ( 240) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.286 Fit side-chains REVERT: A 165 LYS cc_start: 0.4218 (mptt) cc_final: 0.4017 (mmtt) REVERT: B 55 MET cc_start: 0.8623 (mmm) cc_final: 0.7997 (mmm) REVERT: C 103 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.8244 (p0) REVERT: E 55 MET cc_start: 0.8619 (mmm) cc_final: 0.8009 (mmm) REVERT: F 103 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8288 (p0) outliers start: 10 outliers final: 5 residues processed: 100 average time/residue: 0.0623 time to fit residues: 9.0985 Evaluate side-chains 92 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 103 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 51 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.144359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.111230 restraints weight = 8474.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.112655 restraints weight = 7194.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.113620 restraints weight = 6408.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.114369 restraints weight = 5918.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.114877 restraints weight = 5606.456| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 7932 Z= 0.262 Angle : 0.589 6.105 10710 Z= 0.327 Chirality : 0.045 0.131 1194 Planarity : 0.003 0.030 1392 Dihedral : 5.167 21.452 1044 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.42 % Favored : 92.48 % Rotamer: Outliers : 0.72 % Allowed : 12.71 % Favored : 86.57 % 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: -2.03 (0.26), residues: 984 helix: -0.02 (0.50), residues: 114 sheet: -1.10 (0.25), residues: 444 loop : -1.88 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 15 TYR 0.012 0.002 TYR F 111 PHE 0.017 0.002 PHE E 112 TRP 0.013 0.002 TRP E 26 HIS 0.004 0.002 HIS B 74 Details of bonding type rmsd covalent geometry : bond 0.00639 ( 7932) covalent geometry : angle 0.58917 (10710) hydrogen bonds : bond 0.04194 ( 98) hydrogen bonds : angle 4.75127 ( 240) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.293 Fit side-chains REVERT: A 73 LYS cc_start: 0.7610 (tmtt) cc_final: 0.7281 (tmtt) REVERT: B 55 MET cc_start: 0.8531 (mmm) cc_final: 0.7970 (mmm) REVERT: C 103 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.8382 (p0) REVERT: D 73 LYS cc_start: 0.7590 (tmtt) cc_final: 0.7278 (tmtt) REVERT: D 126 GLU cc_start: 0.8728 (pm20) cc_final: 0.7713 (pm20) REVERT: E 55 MET cc_start: 0.8517 (mmm) cc_final: 0.7961 (mmm) REVERT: F 103 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.8342 (p0) outliers start: 6 outliers final: 4 residues processed: 100 average time/residue: 0.0772 time to fit residues: 10.6379 Evaluate side-chains 97 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 28 MET Chi-restraints excluded: chain F residue 103 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 73 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 68 optimal weight: 20.0000 chunk 67 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.142612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.110923 restraints weight = 8397.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.112652 restraints weight = 6585.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.114132 restraints weight = 5599.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.115065 restraints weight = 5008.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.115559 restraints weight = 4629.023| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 7932 Z= 0.109 Angle : 0.460 6.070 10710 Z= 0.254 Chirality : 0.043 0.128 1194 Planarity : 0.002 0.022 1392 Dihedral : 4.446 19.129 1044 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.39 % Favored : 94.51 % Rotamer: Outliers : 1.08 % Allowed : 12.71 % Favored : 86.21 % 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: -1.81 (0.27), residues: 984 helix: 0.28 (0.51), residues: 114 sheet: -1.00 (0.25), residues: 444 loop : -1.73 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 40 TYR 0.009 0.001 TYR B 111 PHE 0.011 0.001 PHE B 112 TRP 0.006 0.001 TRP B 26 HIS 0.002 0.001 HIS C 74 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 7932) covalent geometry : angle 0.45977 (10710) hydrogen bonds : bond 0.02538 ( 98) hydrogen bonds : angle 4.17220 ( 240) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.325 Fit side-chains REVERT: A 73 LYS cc_start: 0.7218 (tmtt) cc_final: 0.6826 (tmtt) REVERT: C 103 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.8202 (p0) REVERT: D 73 LYS cc_start: 0.7213 (tmtt) cc_final: 0.6835 (tmtt) REVERT: F 103 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.8214 (p0) outliers start: 9 outliers final: 4 residues processed: 94 average time/residue: 0.0734 time to fit residues: 9.6786 Evaluate side-chains 91 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 164 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 32 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 77 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.143443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.111898 restraints weight = 8395.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.113802 restraints weight = 6548.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.115228 restraints weight = 5510.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.116118 restraints weight = 4917.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.116118 restraints weight = 4545.092| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 7932 Z= 0.096 Angle : 0.434 6.029 10710 Z= 0.241 Chirality : 0.042 0.124 1194 Planarity : 0.002 0.020 1392 Dihedral : 4.069 16.503 1044 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.22 % Favored : 92.68 % Rotamer: Outliers : 0.72 % Allowed : 12.95 % Favored : 86.33 % 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: -1.67 (0.27), residues: 984 helix: 0.49 (0.52), residues: 114 sheet: -0.90 (0.25), residues: 444 loop : -1.69 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 40 TYR 0.008 0.001 TYR B 111 PHE 0.010 0.001 PHE B 112 TRP 0.006 0.001 TRP E 26 HIS 0.002 0.001 HIS B 34 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 7932) covalent geometry : angle 0.43425 (10710) hydrogen bonds : bond 0.02578 ( 98) hydrogen bonds : angle 3.93898 ( 240) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.225 Fit side-chains REVERT: A 73 LYS cc_start: 0.7097 (tmtt) cc_final: 0.6739 (tmtt) REVERT: C 103 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.8179 (p0) REVERT: D 73 LYS cc_start: 0.7121 (tmtt) cc_final: 0.6774 (tmtt) REVERT: F 103 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.8179 (p0) outliers start: 6 outliers final: 4 residues processed: 88 average time/residue: 0.0766 time to fit residues: 9.5312 Evaluate side-chains 89 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 164 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 88 optimal weight: 0.0020 chunk 65 optimal weight: 2.9990 chunk 33 optimal weight: 0.0980 chunk 18 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.146110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.114618 restraints weight = 8394.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.116570 restraints weight = 6555.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.118019 restraints weight = 5506.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.118789 restraints weight = 4881.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.119672 restraints weight = 4527.180| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7932 Z= 0.075 Angle : 0.416 5.487 10710 Z= 0.231 Chirality : 0.042 0.142 1194 Planarity : 0.002 0.017 1392 Dihedral : 3.834 19.927 1044 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.96 % Allowed : 12.95 % Favored : 86.09 % 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: -1.44 (0.27), residues: 984 helix: 0.66 (0.53), residues: 114 sheet: -0.74 (0.26), residues: 444 loop : -1.55 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 40 TYR 0.009 0.001 TYR B 115 PHE 0.008 0.001 PHE D 112 TRP 0.005 0.001 TRP F 91 HIS 0.001 0.000 HIS B 34 Details of bonding type rmsd covalent geometry : bond 0.00167 ( 7932) covalent geometry : angle 0.41647 (10710) hydrogen bonds : bond 0.02274 ( 98) hydrogen bonds : angle 3.78229 ( 240) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.325 Fit side-chains REVERT: A 165 LYS cc_start: 0.4000 (mptt) cc_final: 0.3639 (mmtt) REVERT: B 18 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8114 (pttm) REVERT: C 103 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.8256 (p0) REVERT: F 103 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.8257 (p0) outliers start: 8 outliers final: 5 residues processed: 90 average time/residue: 0.0756 time to fit residues: 9.6851 Evaluate side-chains 89 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 LYS Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 164 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 3 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.140304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.107576 restraints weight = 8578.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.110083 restraints weight = 6183.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.111825 restraints weight = 4954.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.113208 restraints weight = 4274.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.114176 restraints weight = 3841.830| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7932 Z= 0.133 Angle : 0.467 4.854 10710 Z= 0.257 Chirality : 0.043 0.127 1194 Planarity : 0.002 0.021 1392 Dihedral : 4.307 17.788 1044 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 0.96 % Allowed : 12.71 % Favored : 86.33 % 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: -1.62 (0.27), residues: 984 helix: 0.54 (0.52), residues: 114 sheet: -0.90 (0.26), residues: 444 loop : -1.61 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D 40 TYR 0.011 0.001 TYR C 111 PHE 0.014 0.001 PHE E 112 TRP 0.009 0.001 TRP E 26 HIS 0.002 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 7932) covalent geometry : angle 0.46726 (10710) hydrogen bonds : bond 0.02974 ( 98) hydrogen bonds : angle 4.08897 ( 240) =============================================================================== Job complete usr+sys time: 1117.59 seconds wall clock time: 19 minutes 55.03 seconds (1195.03 seconds total)