Starting phenix.real_space_refine on Wed Feb 4 16:37:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hr1_34956/02_2026/8hr1_34956.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hr1_34956/02_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_34956/02_2026/8hr1_34956.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hr1_34956/02_2026/8hr1_34956.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hr1_34956/02_2026/8hr1_34956.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hr1_34956/02_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-2.0-5952/lib/python3.9/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: 2.81, 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 315.1 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: 2.38 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: 1.83 Time building geometry restraints manager: 1.32 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=" C LEU H 101 " pdb=" N LEU H 102 " ideal model delta sigma weight residual 1.331 1.294 0.037 1.63e-02 3.76e+03 5.28e+00 bond pdb=" CB ARG B 92 " pdb=" CG ARG B 92 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.90e+00 bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.483 -0.061 3.00e-02 1.11e+03 4.10e+00 bond pdb=" CG1 ILE F 50 " pdb=" CD1 ILE F 50 " ideal model delta sigma weight residual 1.513 1.436 0.077 3.90e-02 6.57e+02 3.91e+00 bond pdb=" C ILE A 119 " pdb=" N MET A 120 " ideal model delta sigma weight residual 1.329 1.273 0.055 3.03e-02 1.09e+03 3.33e+00 ... (remaining 12920 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 17648 1.63 - 3.26: 961 3.26 - 4.89: 76 4.89 - 6.51: 21 6.51 - 8.14: 9 Bond angle restraints: 18715 Sorted by residual: angle pdb=" C LEU H 101 " pdb=" N LEU H 102 " pdb=" CA LEU H 102 " ideal model delta sigma weight residual 121.61 116.53 5.08 1.39e+00 5.18e-01 1.33e+01 angle pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sigma weight residual 120.20 125.21 -5.01 1.50e+00 4.44e-01 1.12e+01 angle pdb=" C PHE E 104 " pdb=" N GLU E 105 " pdb=" CA GLU E 105 " ideal model delta sigma weight residual 121.14 115.49 5.65 1.75e+00 3.27e-01 1.04e+01 angle pdb=" C PHE H 70 " pdb=" N GLU H 71 " pdb=" CA GLU H 71 " ideal model delta sigma weight residual 121.94 115.91 6.03 2.00e+00 2.50e-01 9.09e+00 angle pdb=" C PHE D 70 " pdb=" N GLU D 71 " pdb=" CA GLU D 71 " ideal model delta sigma weight residual 121.94 115.96 5.98 2.00e+00 2.50e-01 8.94e+00 ... (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 - 0.038: 1199 0.038 - 0.076: 761 0.076 - 0.114: 120 0.114 - 0.152: 37 0.152 - 0.191: 14 Chirality restraints: 2131 Sorted by residual: 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 chirality pdb=" CA ILE G 79 " pdb=" N ILE G 79 " pdb=" C ILE G 79 " pdb=" CB ILE G 79 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.30e-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: 1.210 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: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.550 Find NCS groups from input model: 0.120 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 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= 0.433 Angle : 0.803 8.143 18715 Z= 0.470 Chirality : 0.047 0.191 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 covalent geometry : bond 0.00972 (12925) covalent geometry : angle 0.80288 (18715) hydrogen bonds : bond 0.32606 ( 680) hydrogen bonds : angle 9.58888 ( 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 : 0.397 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: 0.2127 time to fit residues: 60.2013 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 : 0.333 ------------------------------------------------------------------------------- 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: 2.9990 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: 0.9980 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS B 25 ASN D 84 ASN E 68 GLN E 125 GLN G 94 ASN H 84 ASN H 95 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.090045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.061065 restraints weight = 27380.138| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.65 r_work: 0.2768 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12925 Z= 0.176 Angle : 0.625 9.628 18715 Z= 0.376 Chirality : 0.037 0.156 2131 Planarity : 0.005 0.038 1346 Dihedral : 30.365 169.954 4063 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.35 % Allowed : 7.67 % Favored : 89.98 % 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: -1.69 (0.27), residues: 747 helix: -0.75 (0.20), residues: 545 sheet: None (None), residues: 0 loop : -1.78 (0.40), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 49 TYR 0.012 0.001 TYR D 40 PHE 0.013 0.002 PHE G 25 TRP 0.017 0.004 TRP S 164 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00384 (12925) covalent geometry : angle 0.62514 (18715) hydrogen bonds : bond 0.09704 ( 680) hydrogen bonds : angle 3.48371 ( 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 209 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 194 time to evaluate : 0.397 Fit side-chains REVERT: A 73 GLU cc_start: 0.8882 (tt0) cc_final: 0.8679 (tt0) REVERT: A 79 LYS cc_start: 0.8582 (tttp) cc_final: 0.8341 (tttt) REVERT: A 93 GLN cc_start: 0.9235 (OUTLIER) cc_final: 0.8931 (tt0) REVERT: C 95 LYS cc_start: 0.9139 (ttmp) cc_final: 0.8938 (tttp) REVERT: D 46 LYS cc_start: 0.8883 (mmpt) cc_final: 0.8677 (mmmt) REVERT: D 105 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8171 (mm-30) REVERT: D 108 LYS cc_start: 0.8945 (mttt) cc_final: 0.8674 (mtpp) REVERT: E 41 TYR cc_start: 0.8424 (m-80) cc_final: 0.8160 (m-10) REVERT: E 73 GLU cc_start: 0.8799 (pt0) cc_final: 0.8490 (pt0) REVERT: E 76 GLN cc_start: 0.8726 (tt0) cc_final: 0.8504 (tt0) REVERT: E 79 LYS cc_start: 0.8161 (tttp) cc_final: 0.7619 (ttpt) REVERT: F 35 ARG cc_start: 0.8945 (mtp85) cc_final: 0.8664 (mtp85) REVERT: F 91 LYS cc_start: 0.9140 (ttmt) cc_final: 0.8816 (ttpt) REVERT: G 13 LYS cc_start: 0.5783 (OUTLIER) cc_final: 0.5552 (pttm) REVERT: G 64 GLU cc_start: 0.8804 (tp30) cc_final: 0.8596 (tp30) REVERT: H 85 LYS cc_start: 0.8892 (mptm) cc_final: 0.8687 (mmtt) REVERT: S 172 LYS cc_start: 0.7859 (mmmt) cc_final: 0.7527 (mmmm) outliers start: 15 outliers final: 6 residues processed: 202 average time/residue: 0.1599 time to fit residues: 41.9444 Evaluate side-chains 150 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 142 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 60 VAL 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: 0.8980 chunk 79 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN D 82 HIS E 68 GLN E 93 GLN F 93 GLN G 68 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.090001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.060164 restraints weight = 27353.931| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.64 r_work: 0.2732 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12925 Z= 0.167 Angle : 0.562 5.412 18715 Z= 0.342 Chirality : 0.034 0.126 2131 Planarity : 0.004 0.036 1346 Dihedral : 30.156 165.440 4061 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.35 % Allowed : 13.62 % Favored : 84.04 % 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: 0.11 (0.30), residues: 747 helix: 0.71 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -1.54 (0.41), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 35 TYR 0.010 0.001 TYR G 50 PHE 0.013 0.002 PHE G 25 TRP 0.025 0.006 TRP S 164 HIS 0.009 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00365 (12925) covalent geometry : angle 0.56174 (18715) hydrogen bonds : bond 0.08952 ( 680) hydrogen bonds : angle 2.98593 ( 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 172 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 0.265 Fit side-chains REVERT: A 79 LYS cc_start: 0.8566 (tttp) cc_final: 0.8309 (tttt) REVERT: A 93 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8836 (tt0) REVERT: D 46 LYS cc_start: 0.8856 (mmpt) cc_final: 0.8570 (mmmt) REVERT: D 86 ARG cc_start: 0.8717 (mtp85) cc_final: 0.8478 (mmt90) REVERT: D 105 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8266 (mm-30) REVERT: D 108 LYS cc_start: 0.9082 (mttt) cc_final: 0.8755 (mtpp) REVERT: E 41 TYR cc_start: 0.8530 (m-80) cc_final: 0.8185 (m-10) REVERT: F 35 ARG cc_start: 0.8981 (mtp85) cc_final: 0.8692 (mtp85) REVERT: F 59 LYS cc_start: 0.8625 (tptm) cc_final: 0.8314 (tptm) REVERT: F 91 LYS cc_start: 0.9253 (ttmt) cc_final: 0.8920 (ttpt) REVERT: G 13 LYS cc_start: 0.6161 (OUTLIER) cc_final: 0.5850 (pttm) REVERT: G 64 GLU cc_start: 0.8862 (tp30) cc_final: 0.8653 (tm-30) REVERT: H 85 LYS cc_start: 0.8908 (mptm) cc_final: 0.8468 (mmtp) outliers start: 15 outliers final: 7 residues processed: 165 average time/residue: 0.1499 time to fit residues: 32.8448 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 : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain D residue 113 GLU 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 H residue 88 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 83 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 55 optimal weight: 0.1980 chunk 67 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 125 GLN B 25 ASN C 38 ASN D 82 HIS F 93 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.090663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.060679 restraints weight = 27308.799| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 1.62 r_work: 0.2747 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.3995 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= 0.155 Angle : 0.546 6.118 18715 Z= 0.333 Chirality : 0.034 0.125 2131 Planarity : 0.004 0.036 1346 Dihedral : 30.155 161.622 4061 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.82 % Allowed : 14.08 % Favored : 83.10 % 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: 0.98 (0.31), residues: 747 helix: 1.40 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -1.36 (0.42), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 35 TYR 0.011 0.001 TYR G 50 PHE 0.012 0.002 PHE E 67 TRP 0.006 0.002 TRP S 164 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00340 (12925) covalent geometry : angle 0.54575 (18715) hydrogen bonds : bond 0.08681 ( 680) hydrogen bonds : angle 2.73480 ( 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 165 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.336 Fit side-chains REVERT: A 73 GLU cc_start: 0.9052 (tt0) cc_final: 0.8551 (tt0) REVERT: A 79 LYS cc_start: 0.8597 (tttp) cc_final: 0.8285 (tttt) REVERT: A 93 GLN cc_start: 0.9156 (OUTLIER) cc_final: 0.8808 (tt0) REVERT: B 25 ASN cc_start: 0.8494 (m110) cc_final: 0.8208 (m110) REVERT: D 46 LYS cc_start: 0.8895 (mmpt) cc_final: 0.8606 (mmmt) REVERT: D 105 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8377 (mm-30) REVERT: D 108 LYS cc_start: 0.9075 (mttt) cc_final: 0.8815 (mtpp) REVERT: E 41 TYR cc_start: 0.8529 (m-80) cc_final: 0.8251 (m-10) REVERT: F 91 LYS cc_start: 0.9235 (ttmt) cc_final: 0.8926 (ttpt) REVERT: G 13 LYS cc_start: 0.6041 (OUTLIER) cc_final: 0.5642 (pttm) REVERT: S 172 LYS cc_start: 0.7749 (mmmt) cc_final: 0.7369 (mmmm) outliers start: 18 outliers final: 7 residues processed: 154 average time/residue: 0.1588 time to fit residues: 31.9111 Evaluate side-chains 148 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 139 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 61 GLU 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 101 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 88 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 7 optimal weight: 0.3980 chunk 25 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN C 38 ASN D 82 HIS F 75 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.090623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.060315 restraints weight = 27428.431| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 1.62 r_work: 0.2733 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12925 Z= 0.160 Angle : 0.547 6.295 18715 Z= 0.333 Chirality : 0.034 0.127 2131 Planarity : 0.004 0.035 1346 Dihedral : 30.185 159.625 4061 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.97 % Allowed : 14.08 % 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: 1.40 (0.31), residues: 747 helix: 1.70 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -1.25 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 35 TYR 0.008 0.001 TYR G 50 PHE 0.010 0.002 PHE G 25 TRP 0.003 0.001 TRP S 164 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00353 (12925) covalent geometry : angle 0.54686 (18715) hydrogen bonds : bond 0.08503 ( 680) hydrogen bonds : angle 2.70300 ( 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 165 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 0.358 Fit side-chains REVERT: A 59 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7833 (pm20) REVERT: A 79 LYS cc_start: 0.8557 (tttp) cc_final: 0.8267 (tttt) REVERT: A 93 GLN cc_start: 0.9124 (OUTLIER) cc_final: 0.8722 (tt0) REVERT: B 88 TYR cc_start: 0.8898 (m-10) cc_final: 0.8522 (m-80) REVERT: D 46 LYS cc_start: 0.8917 (mmpt) cc_final: 0.8612 (mmmt) REVERT: D 105 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7931 (mm-30) REVERT: D 108 LYS cc_start: 0.8943 (mttt) cc_final: 0.8685 (mtpt) REVERT: E 41 TYR cc_start: 0.8453 (m-80) cc_final: 0.8235 (m-10) REVERT: F 91 LYS cc_start: 0.9163 (ttmt) cc_final: 0.8868 (ttpt) REVERT: G 13 LYS cc_start: 0.6157 (OUTLIER) cc_final: 0.5721 (pttm) REVERT: H 93 GLU cc_start: 0.8229 (mp0) cc_final: 0.7913 (mp0) outliers start: 19 outliers final: 9 residues processed: 155 average time/residue: 0.1499 time to fit residues: 30.6129 Evaluate side-chains 154 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 61 GLU 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 62 ILE Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 20 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 125 GLN B 25 ASN C 38 ASN D 82 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.090698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.060291 restraints weight = 27246.229| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 1.62 r_work: 0.2729 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12925 Z= 0.163 Angle : 0.550 7.329 18715 Z= 0.333 Chirality : 0.034 0.132 2131 Planarity : 0.004 0.036 1346 Dihedral : 30.235 158.102 4061 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.50 % Allowed : 15.65 % Favored : 81.85 % 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: 1.65 (0.31), residues: 747 helix: 1.90 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -1.19 (0.44), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 35 TYR 0.013 0.001 TYR C 39 PHE 0.011 0.002 PHE G 25 TRP 0.003 0.001 TRP S 164 HIS 0.005 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00364 (12925) covalent geometry : angle 0.55040 (18715) hydrogen bonds : bond 0.08458 ( 680) hydrogen bonds : angle 2.67367 ( 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: 16 poor density : 144 time to evaluate : 0.323 Fit side-chains REVERT: A 59 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7798 (pm20) REVERT: A 79 LYS cc_start: 0.8568 (tttp) cc_final: 0.8336 (tttt) REVERT: A 93 GLN cc_start: 0.9191 (OUTLIER) cc_final: 0.8885 (tt0) REVERT: B 88 TYR cc_start: 0.8889 (m-10) cc_final: 0.8502 (m-80) REVERT: D 46 LYS cc_start: 0.8927 (mmpt) cc_final: 0.8620 (mmmt) REVERT: D 105 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7957 (mm-30) REVERT: D 108 LYS cc_start: 0.8962 (mttt) cc_final: 0.8712 (mtpt) REVERT: F 91 LYS cc_start: 0.9190 (ttmt) cc_final: 0.8895 (ttpt) REVERT: G 64 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8221 (tm-30) REVERT: H 93 GLU cc_start: 0.8269 (mp0) cc_final: 0.8059 (mp0) REVERT: S 172 LYS cc_start: 0.7884 (mmmt) cc_final: 0.7447 (mmmm) outliers start: 16 outliers final: 10 residues processed: 152 average time/residue: 0.1471 time to fit residues: 29.6221 Evaluate side-chains 151 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain D residue 101 LEU 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 168 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 78 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 68 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 125 GLN B 25 ASN C 38 ASN D 82 HIS D 95 GLN F 93 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.089566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.058840 restraints weight = 27164.143| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 1.61 r_work: 0.2690 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2549 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 12925 Z= 0.197 Angle : 0.573 7.487 18715 Z= 0.343 Chirality : 0.035 0.135 2131 Planarity : 0.004 0.036 1346 Dihedral : 30.423 156.467 4061 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.66 % Allowed : 15.02 % Favored : 82.32 % 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: 1.66 (0.31), residues: 747 helix: 1.91 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -1.19 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 99 TYR 0.009 0.001 TYR H 37 PHE 0.017 0.002 PHE G 25 TRP 0.003 0.001 TRP S 164 HIS 0.005 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00448 (12925) covalent geometry : angle 0.57276 (18715) hydrogen bonds : bond 0.08479 ( 680) hydrogen bonds : angle 2.79445 ( 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 158 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.317 Fit side-chains REVERT: A 59 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8049 (pm20) REVERT: A 79 LYS cc_start: 0.8626 (tttp) cc_final: 0.8396 (tttt) REVERT: B 88 TYR cc_start: 0.9064 (m-10) cc_final: 0.8674 (m-80) REVERT: C 64 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8353 (tm-30) REVERT: D 46 LYS cc_start: 0.8997 (mmpt) cc_final: 0.8668 (mmmt) REVERT: D 71 GLU cc_start: 0.8888 (tp30) cc_final: 0.8628 (mm-30) REVERT: D 105 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8291 (mm-30) REVERT: D 108 LYS cc_start: 0.9096 (mttt) cc_final: 0.8826 (mtpt) REVERT: F 91 LYS cc_start: 0.9294 (ttmt) cc_final: 0.8994 (ttpt) REVERT: H 93 GLU cc_start: 0.8633 (mp0) cc_final: 0.8372 (mp0) REVERT: S 172 LYS cc_start: 0.8020 (mmmt) cc_final: 0.7682 (mmmm) outliers start: 17 outliers final: 11 residues processed: 150 average time/residue: 0.1436 time to fit residues: 28.6104 Evaluate side-chains 149 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain D residue 101 LEU 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 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: 5.9990 chunk 1 optimal weight: 0.3980 chunk 59 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 125 GLN D 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.090403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.059838 restraints weight = 27242.673| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.61 r_work: 0.2715 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12925 Z= 0.153 Angle : 0.551 7.779 18715 Z= 0.333 Chirality : 0.034 0.211 2131 Planarity : 0.004 0.038 1346 Dihedral : 30.385 156.593 4061 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.50 % Allowed : 15.65 % Favored : 81.85 % 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: 1.91 (0.31), residues: 747 helix: 2.11 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -1.11 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 69 TYR 0.009 0.001 TYR B 51 PHE 0.012 0.001 PHE H 65 TRP 0.002 0.001 TRP S 164 HIS 0.003 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00337 (12925) covalent geometry : angle 0.55090 (18715) hydrogen bonds : bond 0.08431 ( 680) hydrogen bonds : angle 2.68893 ( 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: 16 poor density : 142 time to evaluate : 0.219 Fit side-chains REVERT: A 59 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8031 (pm20) REVERT: A 73 GLU cc_start: 0.9018 (tt0) cc_final: 0.8724 (tt0) REVERT: A 79 LYS cc_start: 0.8627 (tttp) cc_final: 0.8422 (tttt) REVERT: C 64 GLU cc_start: 0.8883 (tm-30) cc_final: 0.8322 (tm-30) REVERT: D 46 LYS cc_start: 0.8979 (mmpt) cc_final: 0.8648 (mmmt) REVERT: D 71 GLU cc_start: 0.8874 (tp30) cc_final: 0.8606 (mm-30) REVERT: D 105 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8277 (mm-30) REVERT: D 108 LYS cc_start: 0.9083 (mttt) cc_final: 0.8816 (mtpt) REVERT: F 91 LYS cc_start: 0.9269 (ttmt) cc_final: 0.8955 (ttpt) REVERT: G 64 GLU cc_start: 0.8826 (tm-30) cc_final: 0.8453 (tm-30) REVERT: H 93 GLU cc_start: 0.8624 (mp0) cc_final: 0.8347 (mp0) outliers start: 16 outliers final: 11 residues processed: 149 average time/residue: 0.1237 time to fit residues: 24.5964 Evaluate side-chains 150 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.209 ------------------------------------------------------------------------------- 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 17 ARG Chi-restraints excluded: chain C residue 61 GLU 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 118 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 101 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: 5.9990 chunk 95 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN B 25 ASN D 82 HIS H 95 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.090588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.060049 restraints weight = 27066.758| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 1.61 r_work: 0.2721 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12925 Z= 0.163 Angle : 0.553 8.428 18715 Z= 0.333 Chirality : 0.034 0.164 2131 Planarity : 0.004 0.036 1346 Dihedral : 30.332 156.202 4061 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.50 % Allowed : 15.81 % Favored : 81.69 % 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: 2.00 (0.31), residues: 747 helix: 2.18 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -1.08 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 99 TYR 0.007 0.001 TYR B 51 PHE 0.012 0.002 PHE H 65 TRP 0.003 0.001 TRP S 164 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00363 (12925) covalent geometry : angle 0.55273 (18715) hydrogen bonds : bond 0.08393 ( 680) hydrogen bonds : angle 2.66875 ( 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 156 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.305 Fit side-chains REVERT: A 59 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8114 (pm20) REVERT: A 79 LYS cc_start: 0.8627 (tttp) cc_final: 0.8426 (tttt) REVERT: C 64 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8343 (tm-30) REVERT: D 46 LYS cc_start: 0.8990 (mmpt) cc_final: 0.8667 (mmmt) REVERT: D 71 GLU cc_start: 0.8869 (tp30) cc_final: 0.8611 (mm-30) REVERT: D 105 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8270 (mm-30) REVERT: D 108 LYS cc_start: 0.9061 (mttt) cc_final: 0.8808 (mtpt) REVERT: F 91 LYS cc_start: 0.9281 (ttmt) cc_final: 0.8980 (ttpt) REVERT: H 93 GLU cc_start: 0.8610 (mp0) cc_final: 0.8330 (mp0) REVERT: S 172 LYS cc_start: 0.7853 (mmmt) cc_final: 0.7643 (mmmm) outliers start: 16 outliers final: 14 residues processed: 147 average time/residue: 0.1376 time to fit residues: 26.9384 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 : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 76 GLN 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 H residue 47 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 25 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 94 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN B 25 ASN D 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.090373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.059874 restraints weight = 27276.508| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 1.61 r_work: 0.2720 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 12925 Z= 0.169 Angle : 0.551 8.539 18715 Z= 0.332 Chirality : 0.034 0.176 2131 Planarity : 0.004 0.037 1346 Dihedral : 30.351 155.902 4061 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.35 % Allowed : 15.81 % Favored : 81.85 % 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: 2.06 (0.31), residues: 747 helix: 2.24 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -1.12 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 99 TYR 0.008 0.001 TYR B 51 PHE 0.012 0.002 PHE H 65 TRP 0.003 0.001 TRP S 164 HIS 0.004 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00380 (12925) covalent geometry : angle 0.55073 (18715) hydrogen bonds : bond 0.08351 ( 680) hydrogen bonds : angle 2.66852 ( 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 155 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.264 Fit side-chains REVERT: A 59 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8154 (pm20) REVERT: B 88 TYR cc_start: 0.9050 (m-10) cc_final: 0.8657 (m-80) REVERT: C 64 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8338 (tm-30) REVERT: D 46 LYS cc_start: 0.8993 (mmpt) cc_final: 0.8668 (mmmt) REVERT: D 71 GLU cc_start: 0.8878 (tp30) cc_final: 0.8623 (mm-30) REVERT: D 105 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8248 (mm-30) REVERT: D 108 LYS cc_start: 0.9070 (mttt) cc_final: 0.8801 (mtpt) REVERT: F 91 LYS cc_start: 0.9288 (ttmt) cc_final: 0.8981 (ttpt) REVERT: H 93 GLU cc_start: 0.8625 (mp0) cc_final: 0.8323 (mp0) REVERT: S 172 LYS cc_start: 0.7993 (mmmt) cc_final: 0.7700 (mmmm) outliers start: 15 outliers final: 14 residues processed: 146 average time/residue: 0.1446 time to fit residues: 28.1039 Evaluate side-chains 153 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 76 GLN 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 H residue 47 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 78 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN B 25 ASN D 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.090544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.060192 restraints weight = 27195.284| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 1.60 r_work: 0.2724 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12925 Z= 0.164 Angle : 0.549 8.309 18715 Z= 0.331 Chirality : 0.034 0.175 2131 Planarity : 0.004 0.036 1346 Dihedral : 30.344 155.800 4061 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.35 % Allowed : 15.65 % Favored : 82.00 % 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: 2.12 (0.31), residues: 747 helix: 2.28 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -1.09 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 99 TYR 0.008 0.001 TYR B 51 PHE 0.012 0.002 PHE H 65 TRP 0.003 0.001 TRP S 164 HIS 0.004 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00369 (12925) covalent geometry : angle 0.54910 (18715) hydrogen bonds : bond 0.08341 ( 680) hydrogen bonds : angle 2.65338 ( 1634) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3379.00 seconds wall clock time: 58 minutes 20.62 seconds (3500.62 seconds total)