Starting phenix.real_space_refine on Fri Jul 3 03:36:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hr1_34956/07_2026/8hr1_34956.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hr1_34956/07_2026/8hr1_34956.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hr1_34956/07_2026/8hr1_34956.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hr1_34956/07_2026/8hr1_34956.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hr1_34956/07_2026/8hr1_34956.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hr1_34956/07_2026/8hr1_34956.map" } resolution = 3.02 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= 0.002 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 294 5.49 5 S 11 5.16 5 C 6695 2.51 5 N 2275 2.21 5 O 2835 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12110 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 668 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 707 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 783 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 815 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 707 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "S" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'CIS': 1, 'TRANS': 12} Chain: "I" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Time building chain proxies: 2.82, per 1000 atoms: 0.23 Number of scatterers: 12110 At special positions: 0 Unit cell: (119.214, 92.364, 117.066, 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 11 16.00 P 294 15.00 O 2835 8.00 N 2275 7.00 C 6695 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: 0.99 Conformation dependent library (CDL) restraints added in 192.6 milliseconds 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1430 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 9 sheets defined 70.2% alpha, 2.6% beta 136 base pairs and 260 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 removed outlier: 4.401A pdb=" N ARG A 72 " --> pdb=" O GLN A 68 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 113 removed outlier: 3.761A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 130 removed outlier: 4.044A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 removed outlier: 3.772A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.793A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.562A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.372A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.819A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.554A pdb=" N GLU D 71 " --> pdb=" O ASN D 67 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS D 82 " --> pdb=" O SER D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.564A pdb=" N ALA D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.606A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.553A pdb=" N GLU E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.940A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.625A pdb=" N ARG E 129 " --> pdb=" O GLN E 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 48 through 51 removed outlier: 3.803A pdb=" N TYR F 51 " --> pdb=" O GLY F 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 48 through 51' Processing helix chain 'F' and resid 54 through 76 removed outlier: 3.631A pdb=" N VAL F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU F 63 " --> pdb=" O LYS F 59 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR F 73 " --> pdb=" O ALA F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.705A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.384A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU G 63 " --> pdb=" O THR G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.562A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.553A pdb=" N GLU H 71 " --> pdb=" O ASN H 67 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA H 81 " --> pdb=" O ALA H 77 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS H 82 " --> pdb=" O SER H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.565A pdb=" N ALA H 97 " --> pdb=" O GLU H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.606A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.904A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.259A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.314A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.057A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.382A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 354 hydrogen bonds defined for protein. 1050 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 326 hydrogen bonds 584 hydrogen bond angles 0 basepair planarities 136 basepair parallelities 260 stacking parallelities Total time for adding SS restraints: 1.81 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2260 1.33 - 1.45: 4320 1.45 - 1.57: 5738 1.57 - 1.69: 586 1.69 - 1.80: 21 Bond restraints: 12925 Sorted by residual: bond pdb=" C3' DG J -7 " pdb=" O3' DG J -7 " ideal model delta sigma weight residual 1.435 1.385 0.050 1.30e-02 5.92e+03 1.46e+01 bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.435 1.483 -0.048 1.30e-02 5.92e+03 1.35e+01 bond pdb=" C3' DT I 14 " pdb=" O3' DT I 14 " ideal model delta sigma weight residual 1.435 1.389 0.046 1.30e-02 5.92e+03 1.28e+01 bond pdb=" C3' DC I 34 " pdb=" O3' DC I 34 " ideal model delta sigma weight residual 1.435 1.390 0.045 1.30e-02 5.92e+03 1.18e+01 bond pdb=" C3' DA J -5 " pdb=" O3' DA J -5 " ideal model delta sigma weight residual 1.435 1.392 0.043 1.30e-02 5.92e+03 1.09e+01 ... (remaining 12920 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 17095 1.63 - 3.26: 1505 3.26 - 4.89: 84 4.89 - 6.51: 22 6.51 - 8.14: 9 Bond angle restraints: 18715 Sorted by residual: angle pdb=" O4' DC J -62 " pdb=" C4' DC J -62 " pdb=" C3' DC J -62 " ideal model delta sigma weight residual 106.00 103.21 2.79 6.00e-01 2.78e+00 2.16e+01 angle pdb=" N3 DT I -67 " pdb=" C4 DT I -67 " pdb=" O4 DT I -67 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT J 68 " pdb=" C4 DT J 68 " pdb=" O4 DT J 68 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" N3 DT I -23 " pdb=" C4 DT I -23 " pdb=" O4 DT I -23 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 angle pdb=" N3 DT I -17 " pdb=" C4 DT I -17 " pdb=" O4 DT I -17 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 ... (remaining 18710 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.36: 5757 35.36 - 70.72: 1232 70.72 - 106.08: 15 106.08 - 141.44: 2 141.44 - 176.80: 1 Dihedral angle restraints: 7007 sinusoidal: 4791 harmonic: 2216 Sorted by residual: dihedral pdb=" CA ALA A 127 " pdb=" C ALA A 127 " pdb=" N ARG A 128 " pdb=" CA ARG A 128 " ideal model delta harmonic sigma weight residual 180.00 155.70 24.30 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA ALA A 114 " pdb=" C ALA A 114 " pdb=" N LYS A 115 " pdb=" CA LYS A 115 " ideal model delta harmonic sigma weight residual 180.00 158.56 21.44 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA ARG S 169 " pdb=" C ARG S 169 " pdb=" N GLU S 170 " pdb=" CA GLU S 170 " ideal model delta harmonic sigma weight residual 180.00 159.89 20.11 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 7004 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1213 0.045 - 0.090: 630 0.090 - 0.136: 233 0.136 - 0.181: 49 0.181 - 0.226: 6 Chirality restraints: 2131 Sorted by residual: chirality pdb=" C3' DG I 20 " pdb=" C4' DG I 20 " pdb=" O3' DG I 20 " pdb=" C2' DG I 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.50 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB ILE H 54 " pdb=" CA ILE H 54 " pdb=" CG1 ILE H 54 " pdb=" CG2 ILE H 54 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.08e-01 chirality pdb=" CB ILE D 54 " pdb=" CA ILE D 54 " pdb=" CG1 ILE D 54 " pdb=" CG2 ILE D 54 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 9.00e-01 ... (remaining 2128 not shown) Planarity restraints: 1346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 65 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.98e+00 pdb=" N PRO A 66 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " -0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO G 80 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE H 69 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.30e+00 pdb=" C ILE H 69 " -0.031 2.00e-02 2.50e+03 pdb=" O ILE H 69 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE H 70 " 0.011 2.00e-02 2.50e+03 ... (remaining 1343 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2666 2.78 - 3.31: 10387 3.31 - 3.84: 24457 3.84 - 4.37: 28931 4.37 - 4.90: 40663 Nonbonded interactions: 107104 Sorted by model distance: nonbonded pdb=" OE1 GLN A 68 " pdb=" NH1 ARG A 72 " model vdw 2.255 3.120 nonbonded pdb=" OH TYR G 57 " pdb=" OE2 GLU G 61 " model vdw 2.305 3.040 nonbonded pdb=" O THR C 16 " pdb=" OG SER C 19 " model vdw 2.310 3.040 nonbonded pdb=" OG SER C 40 " pdb=" O ARG C 42 " model vdw 2.340 3.040 nonbonded pdb=" N4 DC I 40 " pdb=" O6 DG J -40 " model vdw 2.340 3.120 ... (remaining 107099 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' and resid 39 through 133) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 13 through 117 or (resid 118 and (name N or name CA or nam \ e C or name O or name CB )))) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 1.460 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: 0.030 Set scattering table: 0.030 Process input model: 11.710 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 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 : 0.010 0.077 12925 Z= 0.812 Angle : 0.916 8.143 18715 Z= 0.722 Chirality : 0.059 0.226 2131 Planarity : 0.005 0.050 1346 Dihedral : 26.086 176.798 5577 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.16 % Allowed : 3.60 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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: -5.09 (0.20), residues: 747 helix: -3.62 (0.12), residues: 530 sheet: None (None), residues: 0 loop : -2.00 (0.36), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 45 TYR 0.013 0.002 TYR F 88 PHE 0.031 0.004 PHE E 104 TRP 0.030 0.007 TRP S 164 HIS 0.014 0.002 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.01024 / 0.81 (12925) covalent geometry : angle 0.91563 / 0.72 (18715) hydrogen bonds : bond 0.32606 / 21.52 ( 680) hydrogen bonds : angle 9.58888 / 6.76 ( 1634) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 229 time to evaluate : 0.355 Fit side-chains REVERT: A 68 GLN cc_start: 0.8635 (tm130) cc_final: 0.8354 (tm-30) REVERT: A 79 LYS cc_start: 0.7632 (tttp) cc_final: 0.7367 (tttt) REVERT: A 125 GLN cc_start: 0.8576 (mt0) cc_final: 0.8318 (mt0) REVERT: B 59 LYS cc_start: 0.8150 (tptt) cc_final: 0.7779 (tptp) REVERT: B 63 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7864 (mt-10) REVERT: B 74 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8290 (mt-10) REVERT: B 88 TYR cc_start: 0.8163 (m-10) cc_final: 0.7671 (m-80) REVERT: B 91 LYS cc_start: 0.8526 (ttmt) cc_final: 0.7920 (ttpt) REVERT: B 95 ARG cc_start: 0.7903 (mtt90) cc_final: 0.7572 (mtt-85) REVERT: C 36 LYS cc_start: 0.8576 (ptpt) cc_final: 0.8192 (pptt) REVERT: C 41 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8133 (tt0) REVERT: C 56 GLU cc_start: 0.8050 (tt0) cc_final: 0.7738 (tt0) REVERT: C 95 LYS cc_start: 0.8930 (ttmp) cc_final: 0.8670 (tttm) REVERT: C 107 VAL cc_start: 0.8706 (t) cc_final: 0.8098 (m) REVERT: D 36 SER cc_start: 0.8174 (t) cc_final: 0.7921 (t) REVERT: D 46 LYS cc_start: 0.8764 (mmpt) cc_final: 0.8458 (mmmt) REVERT: D 57 LYS cc_start: 0.8282 (mmtp) cc_final: 0.8001 (mmtt) REVERT: D 71 GLU cc_start: 0.8139 (pm20) cc_final: 0.7915 (pm20) REVERT: D 82 HIS cc_start: 0.8301 (m-70) cc_final: 0.7819 (m-70) REVERT: D 105 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7695 (mm-30) REVERT: D 108 LYS cc_start: 0.8481 (mttt) cc_final: 0.7820 (mtpp) REVERT: E 41 TYR cc_start: 0.6964 (m-80) cc_final: 0.6592 (m-10) REVERT: E 64 LYS cc_start: 0.7668 (mtmt) cc_final: 0.7280 (mttp) REVERT: E 79 LYS cc_start: 0.7849 (tttp) cc_final: 0.7279 (ttpt) REVERT: E 129 ARG cc_start: 0.8467 (tmt-80) cc_final: 0.7955 (tpt90) REVERT: F 25 ASN cc_start: 0.8932 (OUTLIER) cc_final: 0.8380 (t0) REVERT: F 27 GLN cc_start: 0.8655 (mm-40) cc_final: 0.8404 (mm-40) REVERT: F 44 LYS cc_start: 0.8357 (ttpt) cc_final: 0.8127 (ttmt) REVERT: F 63 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7927 (mt-10) REVERT: F 74 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8421 (mt-10) REVERT: F 91 LYS cc_start: 0.8512 (ttmt) cc_final: 0.7925 (ttpt) REVERT: G 64 GLU cc_start: 0.8468 (tp30) cc_final: 0.8261 (tp30) REVERT: G 95 LYS cc_start: 0.8722 (mtmt) cc_final: 0.8323 (ttmm) REVERT: G 107 VAL cc_start: 0.8493 (t) cc_final: 0.8151 (m) REVERT: H 40 TYR cc_start: 0.8462 (m-80) cc_final: 0.8159 (m-80) REVERT: H 68 ASP cc_start: 0.8848 (t70) cc_final: 0.8416 (t0) REVERT: H 71 GLU cc_start: 0.7967 (pm20) cc_final: 0.7303 (mp0) REVERT: H 76 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7889 (tp30) REVERT: H 85 LYS cc_start: 0.8493 (mptm) cc_final: 0.8222 (mmtt) REVERT: H 93 GLU cc_start: 0.8368 (mm-30) cc_final: 0.7897 (mm-30) REVERT: H 108 LYS cc_start: 0.8757 (mttt) cc_final: 0.8446 (mmtp) outliers start: 1 outliers final: 0 residues processed: 230 average time/residue: 0.1955 time to fit residues: 55.8365 Evaluate side-chains 151 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 25 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 20.0000 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS A 76 GLN B 25 ASN D 84 ASN E 68 GLN E 125 GLN G 94 ASN H 84 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.089139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.059943 restraints weight = 27118.301| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.65 r_work: 0.2754 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12925 Z= 0.190 Angle : 0.733 11.634 18715 Z= 0.433 Chirality : 0.049 0.334 2131 Planarity : 0.006 0.056 1346 Dihedral : 30.702 178.227 4063 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.35 % Allowed : 7.82 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.31 (0.26), residues: 747 helix: -1.22 (0.19), residues: 542 sheet: None (None), residues: 0 loop : -1.96 (0.38), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 20 TYR 0.015 0.002 TYR D 40 PHE 0.012 0.002 PHE G 25 TRP 0.011 0.006 TRP S 164 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.19 (12925) covalent geometry : angle 0.73309 / 0.43 (18715) hydrogen bonds : bond 0.11975 / 7.65 ( 680) hydrogen bonds : angle 3.99234 / 2.78 ( 1634) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 186 time to evaluate : 0.344 Fit side-chains REVERT: A 79 LYS cc_start: 0.8370 (tttp) cc_final: 0.8152 (tttt) REVERT: A 93 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.8923 (tt0) REVERT: A 94 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8277 (mm-30) REVERT: B 91 LYS cc_start: 0.8887 (ttmt) cc_final: 0.8545 (tttt) REVERT: D 57 LYS cc_start: 0.8529 (mmtp) cc_final: 0.8324 (mmtt) REVERT: D 105 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7867 (mm-30) REVERT: D 108 LYS cc_start: 0.8780 (mttt) cc_final: 0.8475 (mtpp) REVERT: E 41 TYR cc_start: 0.8267 (m-80) cc_final: 0.7879 (m-10) REVERT: E 73 GLU cc_start: 0.8606 (pt0) cc_final: 0.8345 (pt0) REVERT: E 79 LYS cc_start: 0.8275 (tttp) cc_final: 0.7761 (ttpt) REVERT: F 91 LYS cc_start: 0.8976 (ttmt) cc_final: 0.8668 (ttpt) outliers start: 15 outliers final: 5 residues processed: 194 average time/residue: 0.1559 time to fit residues: 39.5115 Evaluate side-chains 148 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 141 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain S residue 168 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 79 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 89 optimal weight: 10.0000 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 76 GLN D 82 HIS E 68 GLN E 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.088996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.059451 restraints weight = 27473.827| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 1.69 r_work: 0.2732 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12925 Z= 0.154 Angle : 0.636 7.398 18715 Z= 0.386 Chirality : 0.045 0.234 2131 Planarity : 0.005 0.082 1346 Dihedral : 30.728 176.726 4063 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.35 % Allowed : 12.36 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.56 (0.29), residues: 747 helix: 0.21 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -1.74 (0.40), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 69 TYR 0.010 0.001 TYR F 88 PHE 0.011 0.002 PHE A 67 TRP 0.014 0.005 TRP S 164 HIS 0.004 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.15 (12925) covalent geometry : angle 0.63649 / 0.39 (18715) hydrogen bonds : bond 0.10569 / 6.65 ( 680) hydrogen bonds : angle 3.33491 / 2.30 ( 1634) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.304 Fit side-chains REVERT: A 79 LYS cc_start: 0.8474 (tttp) cc_final: 0.8237 (tttt) REVERT: B 91 LYS cc_start: 0.9061 (ttmt) cc_final: 0.8693 (tttt) REVERT: D 86 ARG cc_start: 0.8653 (mtp85) cc_final: 0.8240 (mmt90) REVERT: D 105 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7909 (mm-30) REVERT: D 108 LYS cc_start: 0.8767 (mttt) cc_final: 0.8504 (mtpp) REVERT: E 41 TYR cc_start: 0.8320 (m-80) cc_final: 0.8041 (m-10) REVERT: E 64 LYS cc_start: 0.8770 (mttt) cc_final: 0.8420 (mttp) REVERT: E 73 GLU cc_start: 0.8605 (pt0) cc_final: 0.8300 (pt0) REVERT: E 79 LYS cc_start: 0.8163 (tttp) cc_final: 0.7705 (ttpt) REVERT: F 74 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8291 (mt-10) REVERT: F 91 LYS cc_start: 0.9029 (ttmt) cc_final: 0.8725 (ttpt) REVERT: G 13 LYS cc_start: 0.5822 (OUTLIER) cc_final: 0.5508 (pttm) outliers start: 15 outliers final: 10 residues processed: 163 average time/residue: 0.1352 time to fit residues: 29.5027 Evaluate side-chains 154 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain S residue 168 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 83 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN B 25 ASN D 82 HIS E 93 GLN F 25 ASN F 93 GLN G 68 ASN H 49 HIS H 95 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.087979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.057853 restraints weight = 27187.086| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 1.63 r_work: 0.2674 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2534 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12925 Z= 0.188 Angle : 0.659 9.915 18715 Z= 0.387 Chirality : 0.046 0.271 2131 Planarity : 0.005 0.043 1346 Dihedral : 30.893 171.085 4063 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.66 % Allowed : 12.36 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.30 (0.30), residues: 747 helix: 0.88 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -1.58 (0.41), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 116 TYR 0.013 0.002 TYR D 40 PHE 0.022 0.003 PHE G 25 TRP 0.005 0.002 TRP S 164 HIS 0.010 0.002 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.19 (12925) covalent geometry : angle 0.65905 / 0.39 (18715) hydrogen bonds : bond 0.09925 / 6.12 ( 680) hydrogen bonds : angle 3.18691 / 2.21 ( 1634) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.313 Fit side-chains REVERT: A 79 LYS cc_start: 0.8609 (tttp) cc_final: 0.8372 (tttt) REVERT: D 86 ARG cc_start: 0.8754 (mtp85) cc_final: 0.8407 (mmt90) REVERT: D 105 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8288 (mm-30) REVERT: D 108 LYS cc_start: 0.9035 (mttt) cc_final: 0.8762 (mtpp) REVERT: E 41 TYR cc_start: 0.8513 (m-80) cc_final: 0.8150 (m-10) REVERT: E 64 LYS cc_start: 0.9016 (mttt) cc_final: 0.8680 (mttp) REVERT: E 73 GLU cc_start: 0.8901 (pt0) cc_final: 0.8610 (pt0) REVERT: E 93 GLN cc_start: 0.9088 (tp-100) cc_final: 0.8847 (tt0) REVERT: F 59 LYS cc_start: 0.8584 (tptm) cc_final: 0.8298 (tptm) REVERT: F 91 LYS cc_start: 0.9221 (ttmt) cc_final: 0.8925 (ttpt) outliers start: 17 outliers final: 9 residues processed: 161 average time/residue: 0.1260 time to fit residues: 27.2859 Evaluate side-chains 151 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain S residue 168 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 88 optimal weight: 40.0000 chunk 41 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 100 optimal weight: 20.0000 chunk 71 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN D 82 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.088675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.058554 restraints weight = 27261.212| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 1.63 r_work: 0.2691 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2553 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 12925 Z= 0.143 Angle : 0.612 6.907 18715 Z= 0.368 Chirality : 0.044 0.254 2131 Planarity : 0.004 0.042 1346 Dihedral : 30.835 171.152 4061 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.97 % Allowed : 12.68 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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: 0.75 (0.30), residues: 747 helix: 1.23 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -1.50 (0.41), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 55 TYR 0.015 0.001 TYR D 40 PHE 0.011 0.002 PHE G 25 TRP 0.003 0.001 TRP S 164 HIS 0.003 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.14 (12925) covalent geometry : angle 0.61234 / 0.37 (18715) hydrogen bonds : bond 0.09753 / 6.02 ( 680) hydrogen bonds : angle 3.01096 / 2.08 ( 1634) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.320 Fit side-chains REVERT: A 79 LYS cc_start: 0.8619 (tttp) cc_final: 0.8373 (tttt) REVERT: D 86 ARG cc_start: 0.8743 (mtp85) cc_final: 0.8433 (mmt90) REVERT: D 105 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8281 (mm-30) REVERT: D 108 LYS cc_start: 0.9111 (mttt) cc_final: 0.8781 (mtpp) REVERT: E 41 TYR cc_start: 0.8522 (m-80) cc_final: 0.8175 (m-10) REVERT: E 64 LYS cc_start: 0.8983 (mttt) cc_final: 0.8660 (mttp) REVERT: E 73 GLU cc_start: 0.8881 (pt0) cc_final: 0.8611 (pt0) REVERT: F 91 LYS cc_start: 0.9187 (ttmt) cc_final: 0.8878 (ttpt) REVERT: G 13 LYS cc_start: 0.5611 (OUTLIER) cc_final: 0.5227 (pttm) outliers start: 19 outliers final: 13 residues processed: 155 average time/residue: 0.1398 time to fit residues: 29.1093 Evaluate side-chains 159 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain S residue 168 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 20 optimal weight: 0.7980 chunk 88 optimal weight: 40.0000 chunk 89 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 54 optimal weight: 0.3980 chunk 77 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN D 82 HIS F 75 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.087672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.057370 restraints weight = 27083.004| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 1.62 r_work: 0.2650 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2510 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12925 Z= 0.194 Angle : 0.649 10.157 18715 Z= 0.380 Chirality : 0.045 0.270 2131 Planarity : 0.005 0.042 1346 Dihedral : 30.975 167.481 4061 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.66 % Allowed : 13.46 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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: 1.00 (0.30), residues: 747 helix: 1.43 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -1.42 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 171 TYR 0.015 0.002 TYR D 40 PHE 0.021 0.003 PHE G 25 TRP 0.005 0.002 TRP S 164 HIS 0.010 0.002 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.19 (12925) covalent geometry : angle 0.64883 / 0.38 (18715) hydrogen bonds : bond 0.09582 / 5.90 ( 680) hydrogen bonds : angle 3.07421 / 2.12 ( 1634) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.306 Fit side-chains REVERT: A 59 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8004 (pm20) REVERT: A 79 LYS cc_start: 0.8618 (tttp) cc_final: 0.8322 (tttt) REVERT: B 88 TYR cc_start: 0.9187 (m-10) cc_final: 0.8816 (m-80) REVERT: D 86 ARG cc_start: 0.8789 (mtp85) cc_final: 0.8502 (mmt90) REVERT: D 105 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8410 (mm-30) REVERT: D 108 LYS cc_start: 0.9163 (mttt) cc_final: 0.8898 (mtpt) REVERT: E 41 TYR cc_start: 0.8592 (m-80) cc_final: 0.8265 (m-10) REVERT: E 64 LYS cc_start: 0.9064 (mttt) cc_final: 0.8736 (mttp) REVERT: F 91 LYS cc_start: 0.9305 (ttmt) cc_final: 0.8967 (ttpt) REVERT: S 172 LYS cc_start: 0.7908 (mmmt) cc_final: 0.7569 (mmmm) outliers start: 17 outliers final: 14 residues processed: 151 average time/residue: 0.1263 time to fit residues: 25.7996 Evaluate side-chains 152 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 168 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 78 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 75 optimal weight: 10.9990 chunk 77 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN D 82 HIS F 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.088155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.057882 restraints weight = 27075.715| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 1.60 r_work: 0.2666 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2525 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12925 Z= 0.152 Angle : 0.626 8.553 18715 Z= 0.370 Chirality : 0.044 0.262 2131 Planarity : 0.004 0.043 1346 Dihedral : 30.974 167.683 4061 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.82 % Allowed : 13.77 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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: 1.25 (0.30), residues: 747 helix: 1.63 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -1.37 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 55 TYR 0.015 0.001 TYR D 40 PHE 0.013 0.002 PHE G 25 TRP 0.010 0.004 TRP S 164 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.15 (12925) covalent geometry : angle 0.62562 / 0.37 (18715) hydrogen bonds : bond 0.09471 / 5.82 ( 680) hydrogen bonds : angle 2.97954 / 2.05 ( 1634) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.315 Fit side-chains REVERT: A 59 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8034 (pm20) REVERT: A 79 LYS cc_start: 0.8644 (tttp) cc_final: 0.8344 (tttt) REVERT: D 86 ARG cc_start: 0.8775 (mtp85) cc_final: 0.8514 (mmt90) REVERT: D 105 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8413 (mm-30) REVERT: D 108 LYS cc_start: 0.9161 (mttt) cc_final: 0.8916 (mtpt) REVERT: E 41 TYR cc_start: 0.8568 (m-80) cc_final: 0.8244 (m-10) REVERT: E 64 LYS cc_start: 0.9041 (mttt) cc_final: 0.8723 (mttp) REVERT: F 91 LYS cc_start: 0.9270 (ttmt) cc_final: 0.8952 (ttpt) outliers start: 18 outliers final: 15 residues processed: 151 average time/residue: 0.1301 time to fit residues: 26.6266 Evaluate side-chains 157 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain S residue 168 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 44 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 78 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN D 82 HIS F 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.088385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.057994 restraints weight = 27234.873| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 1.62 r_work: 0.2669 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2529 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12925 Z= 0.151 Angle : 0.616 11.287 18715 Z= 0.366 Chirality : 0.044 0.259 2131 Planarity : 0.004 0.042 1346 Dihedral : 30.939 167.487 4061 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.66 % Allowed : 14.08 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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: 1.35 (0.30), residues: 747 helix: 1.71 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -1.35 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 55 TYR 0.018 0.001 TYR D 40 PHE 0.012 0.002 PHE G 25 TRP 0.003 0.001 TRP S 164 HIS 0.004 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.15 (12925) covalent geometry : angle 0.61594 / 0.37 (18715) hydrogen bonds : bond 0.09426 / 5.79 ( 680) hydrogen bonds : angle 2.92417 / 2.01 ( 1634) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.334 Fit side-chains REVERT: A 59 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8033 (pm20) REVERT: A 79 LYS cc_start: 0.8651 (tttp) cc_final: 0.8347 (tttt) REVERT: D 86 ARG cc_start: 0.8766 (mtp85) cc_final: 0.8502 (mmt90) REVERT: D 105 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8396 (mm-30) REVERT: D 108 LYS cc_start: 0.9143 (mttt) cc_final: 0.8904 (mtpt) REVERT: E 41 TYR cc_start: 0.8572 (m-80) cc_final: 0.8254 (m-10) REVERT: E 64 LYS cc_start: 0.9028 (mttt) cc_final: 0.8713 (mttp) REVERT: F 91 LYS cc_start: 0.9267 (ttmt) cc_final: 0.8907 (ttpt) outliers start: 17 outliers final: 14 residues processed: 149 average time/residue: 0.1181 time to fit residues: 23.7336 Evaluate side-chains 154 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 168 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 67 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 6 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN D 82 HIS F 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.088799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.058566 restraints weight = 26995.984| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 1.60 r_work: 0.2685 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2545 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 12925 Z= 0.141 Angle : 0.599 10.696 18715 Z= 0.359 Chirality : 0.043 0.257 2131 Planarity : 0.004 0.043 1346 Dihedral : 30.908 167.170 4061 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.82 % Allowed : 14.24 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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: 1.52 (0.31), residues: 747 helix: 1.85 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -1.34 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 45 TYR 0.016 0.001 TYR D 40 PHE 0.011 0.002 PHE H 65 TRP 0.004 0.002 TRP S 164 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.14 (12925) covalent geometry : angle 0.59934 / 0.36 (18715) hydrogen bonds : bond 0.09380 / 5.76 ( 680) hydrogen bonds : angle 2.85333 / 1.96 ( 1634) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.315 Fit side-chains REVERT: A 59 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8029 (pm20) REVERT: A 79 LYS cc_start: 0.8649 (tttp) cc_final: 0.8340 (tttt) REVERT: B 88 TYR cc_start: 0.9057 (m-10) cc_final: 0.8663 (m-80) REVERT: D 86 ARG cc_start: 0.8755 (mtp85) cc_final: 0.8508 (mmt90) REVERT: D 105 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8374 (mm-30) REVERT: D 108 LYS cc_start: 0.9107 (mttt) cc_final: 0.8885 (mtpt) REVERT: E 41 TYR cc_start: 0.8566 (m-80) cc_final: 0.8256 (m-10) REVERT: E 64 LYS cc_start: 0.9023 (mttt) cc_final: 0.8723 (mttp) REVERT: F 91 LYS cc_start: 0.9275 (ttmt) cc_final: 0.8956 (ttpt) REVERT: G 64 GLU cc_start: 0.9059 (tm-30) cc_final: 0.8448 (tm-30) REVERT: H 93 GLU cc_start: 0.8516 (mp0) cc_final: 0.8255 (mp0) outliers start: 18 outliers final: 15 residues processed: 152 average time/residue: 0.1376 time to fit residues: 28.1698 Evaluate side-chains 155 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 168 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 25 optimal weight: 0.2980 chunk 64 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 94 optimal weight: 10.0000 chunk 59 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 91 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN D 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.089090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.058775 restraints weight = 27251.446| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 1.60 r_work: 0.2694 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2552 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 12925 Z= 0.138 Angle : 0.593 11.140 18715 Z= 0.356 Chirality : 0.042 0.256 2131 Planarity : 0.004 0.037 1346 Dihedral : 30.873 166.677 4061 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.66 % Allowed : 14.55 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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: 1.64 (0.31), residues: 747 helix: 1.94 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -1.32 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 55 TYR 0.017 0.001 TYR D 40 PHE 0.012 0.002 PHE H 65 TRP 0.004 0.001 TRP S 164 HIS 0.004 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.14 (12925) covalent geometry : angle 0.59285 / 0.36 (18715) hydrogen bonds : bond 0.09308 / 5.71 ( 680) hydrogen bonds : angle 2.81019 / 1.94 ( 1634) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.236 Fit side-chains REVERT: A 59 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8041 (pm20) REVERT: A 79 LYS cc_start: 0.8652 (tttp) cc_final: 0.8341 (tttt) REVERT: B 88 TYR cc_start: 0.9055 (m-10) cc_final: 0.8676 (m-80) REVERT: D 86 ARG cc_start: 0.8752 (mtp85) cc_final: 0.8519 (mmt90) REVERT: D 102 LEU cc_start: 0.9391 (mp) cc_final: 0.9175 (mp) REVERT: D 105 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8322 (mm-30) REVERT: D 108 LYS cc_start: 0.9123 (mttt) cc_final: 0.8917 (mtpt) REVERT: E 41 TYR cc_start: 0.8564 (m-80) cc_final: 0.8256 (m-10) REVERT: E 64 LYS cc_start: 0.9014 (mttt) cc_final: 0.8736 (mttt) REVERT: F 91 LYS cc_start: 0.9272 (ttmt) cc_final: 0.8965 (ttpt) REVERT: G 64 GLU cc_start: 0.9024 (tm-30) cc_final: 0.8491 (tm-30) REVERT: S 172 LYS cc_start: 0.7846 (mmmm) cc_final: 0.7408 (mmmm) outliers start: 17 outliers final: 13 residues processed: 153 average time/residue: 0.1215 time to fit residues: 24.7664 Evaluate side-chains 155 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 168 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 78 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 chunk 96 optimal weight: 10.0000 chunk 6 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 chunk 83 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 0.3980 chunk 57 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 4 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN D 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.089622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.059325 restraints weight = 27161.060| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 1.62 r_work: 0.2707 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2567 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 12925 Z= 0.136 Angle : 0.580 10.314 18715 Z= 0.351 Chirality : 0.042 0.253 2131 Planarity : 0.004 0.046 1346 Dihedral : 30.844 166.044 4061 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.19 % Allowed : 15.02 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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 (0.31), residues: 747 helix: 2.07 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -1.26 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 55 TYR 0.017 0.001 TYR D 40 PHE 0.013 0.001 PHE H 65 TRP 0.004 0.002 TRP S 164 HIS 0.019 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.14 (12925) covalent geometry : angle 0.58004 / 0.35 (18715) hydrogen bonds : bond 0.09216 / 5.65 ( 680) hydrogen bonds : angle 2.76293 / 1.90 ( 1634) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3035.47 seconds wall clock time: 52 minutes 24.01 seconds (3144.01 seconds total)