Starting phenix.real_space_refine on Thu Jul 2 16:25:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f0x_50117/07_2026/9f0x_50117.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f0x_50117/07_2026/9f0x_50117.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9f0x_50117/07_2026/9f0x_50117.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f0x_50117/07_2026/9f0x_50117.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9f0x_50117/07_2026/9f0x_50117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f0x_50117/07_2026/9f0x_50117.map" } resolution = 3.78 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= 0.001 sd= 0.031 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 166 5.49 5 S 22 5.16 5 C 5408 2.51 5 N 1700 2.21 5 O 2127 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s 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: 9423 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1705 Classifications: {'DNA': 83} Link IDs: {'rna3p': 82} Chain: "B" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1698 Classifications: {'DNA': 83} Link IDs: {'rna3p': 82} Chain: "C" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 759 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 90} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 726 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 88} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 900 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 109} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 924 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "G" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 764 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain breaks: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "H" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 1947 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 14, 'TRANS': 251} Chain breaks: 2 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 5, 'GLN:plan1': 1, 'GLU:plan': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 74 Time building chain proxies: 1.86, per 1000 atoms: 0.20 Number of scatterers: 9423 At special positions: 0 Unit cell: (94.05, 94.05, 183.15, 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 22 16.00 P 166 15.00 O 2127 8.00 N 1700 7.00 C 5408 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: 0.91 Conformation dependent library (CDL) restraints added in 245.1 milliseconds 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1490 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 11 sheets defined 45.1% alpha, 16.6% beta 77 base pairs and 142 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'C' and resid 4 through 17 Processing helix chain 'C' and resid 19 through 40 removed outlier: 3.676A pdb=" N PHE C 31 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE C 34 " --> pdb=" O PHE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 90 Processing helix chain 'D' and resid 2 through 14 removed outlier: 3.723A pdb=" N GLU D 8 " --> pdb=" O SER D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 39 Processing helix chain 'D' and resid 83 through 91 Processing helix chain 'E' and resid 19 through 33 removed outlier: 4.556A pdb=" N LEU E 25 " --> pdb=" O ASP E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 52 removed outlier: 3.622A pdb=" N ARG E 44 " --> pdb=" O GLU E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 90 removed outlier: 4.247A pdb=" N LEU E 81 " --> pdb=" O GLU E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 108 Processing helix chain 'F' and resid 22 through 34 removed outlier: 3.656A pdb=" N LEU F 26 " --> pdb=" O VAL F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 52 Processing helix chain 'F' and resid 75 through 90 Processing helix chain 'F' and resid 92 through 108 Processing helix chain 'G' and resid 19 through 34 removed outlier: 4.807A pdb=" N LEU G 25 " --> pdb=" O ASP G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 52 removed outlier: 4.184A pdb=" N LEU G 49 " --> pdb=" O LEU G 45 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N HIS G 50 " --> pdb=" O LYS G 46 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG G 51 " --> pdb=" O ASP G 47 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N TYR G 52 " --> pdb=" O HIS G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 65 Processing helix chain 'G' and resid 75 through 90 removed outlier: 3.794A pdb=" N ARG G 88 " --> pdb=" O ALA G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 108 removed outlier: 3.771A pdb=" N LYS G 107 " --> pdb=" O ASP G 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 577 through 594 removed outlier: 3.627A pdb=" N ALA H 581 " --> pdb=" O ASN H 577 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG H 582 " --> pdb=" O VAL H 578 " (cutoff:3.500A) Processing helix chain 'H' and resid 604 through 622 Processing helix chain 'H' and resid 646 through 650 Processing helix chain 'H' and resid 696 through 698 No H-bonds generated for 'chain 'H' and resid 696 through 698' Processing helix chain 'H' and resid 763 through 767 Processing helix chain 'H' and resid 793 through 797 removed outlier: 3.576A pdb=" N MET H 797 " --> pdb=" O GLN H 794 " (cutoff:3.500A) Processing helix chain 'H' and resid 798 through 808 Processing helix chain 'H' and resid 821 through 825 removed outlier: 3.524A pdb=" N GLU H 825 " --> pdb=" O ARG H 822 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 44 through 46 removed outlier: 4.064A pdb=" N VAL C 44 " --> pdb=" O PHE C 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 54 through 57 Processing sheet with id=AA3, first strand: chain 'C' and resid 60 through 61 removed outlier: 3.713A pdb=" N ARG C 60 " --> pdb=" O ILE C 73 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 43 through 45 Processing sheet with id=AA5, first strand: chain 'D' and resid 60 through 62 Processing sheet with id=AA6, first strand: chain 'E' and resid 13 through 18 Processing sheet with id=AA7, first strand: chain 'F' and resid 13 through 19 Processing sheet with id=AA8, first strand: chain 'G' and resid 13 through 18 Processing sheet with id=AA9, first strand: chain 'H' and resid 568 through 572 removed outlier: 3.540A pdb=" N ALA H 790 " --> pdb=" O ARG H 813 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL H 598 " --> pdb=" O PHE H 789 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N SER H 791 " --> pdb=" O VAL H 598 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLN H 600 " --> pdb=" O SER H 791 " (cutoff:3.500A) removed outlier: 9.209A pdb=" N GLU H 776 " --> pdb=" O SER H 597 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ALA H 599 " --> pdb=" O GLU H 776 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 632 through 637 removed outlier: 4.572A pdb=" N LEU H 704 " --> pdb=" O VAL H 637 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N THR H 682 " --> pdb=" O ASP H 672 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N VAL H 674 " --> pdb=" O SER H 680 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N SER H 680 " --> pdb=" O VAL H 674 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 756 through 759 removed outlier: 3.864A pdb=" N SER H 739 " --> pdb=" O THR H 746 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL H 748 " --> pdb=" O VAL H 737 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N VAL H 737 " --> pdb=" O VAL H 748 " (cutoff:3.500A) 314 hydrogen bonds defined for protein. 888 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 171 hydrogen bonds 342 hydrogen bond angles 0 basepair planarities 77 basepair parallelities 142 stacking parallelities Total time for adding SS restraints: 1.50 Time building geometry restraints manager: 1.19 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: 1735 1.33 - 1.45: 3012 1.45 - 1.57: 4814 1.57 - 1.68: 330 1.68 - 1.80: 41 Bond restraints: 9932 Sorted by residual: bond pdb=" C3' DC B 75 " pdb=" C2' DC B 75 " ideal model delta sigma weight residual 1.516 1.551 -0.035 8.00e-03 1.56e+04 1.88e+01 bond pdb=" C3' DT A 30 " pdb=" O3' DT A 30 " ideal model delta sigma weight residual 1.435 1.385 0.050 1.30e-02 5.92e+03 1.47e+01 bond pdb=" C3' DT B 73 " pdb=" O3' DT B 73 " ideal model delta sigma weight residual 1.435 1.388 0.047 1.30e-02 5.92e+03 1.31e+01 bond pdb=" C3' DA B 74 " pdb=" O3' DA B 74 " ideal model delta sigma weight residual 1.435 1.390 0.045 1.30e-02 5.92e+03 1.21e+01 bond pdb=" C1' DT B 34 " pdb=" N1 DT B 34 " ideal model delta sigma weight residual 1.468 1.516 -0.048 1.40e-02 5.10e+03 1.18e+01 ... (remaining 9927 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 12984 1.42 - 2.84: 1084 2.84 - 4.27: 69 4.27 - 5.69: 7 5.69 - 7.11: 2 Bond angle restraints: 14146 Sorted by residual: angle pdb=" O4' DG B 26 " pdb=" C4' DG B 26 " pdb=" C3' DG B 26 " ideal model delta sigma weight residual 106.00 102.78 3.22 6.00e-01 2.78e+00 2.88e+01 angle pdb=" O4' DA A 41 " pdb=" C4' DA A 41 " pdb=" C3' DA A 41 " ideal model delta sigma weight residual 106.00 103.00 3.00 6.00e-01 2.78e+00 2.50e+01 angle pdb=" N3 DT B 35 " pdb=" C4 DT B 35 " pdb=" O4 DT B 35 " ideal model delta sigma weight residual 119.90 122.62 -2.72 6.00e-01 2.78e+00 2.05e+01 angle pdb=" N3 DT B 34 " pdb=" C4 DT B 34 " pdb=" O4 DT B 34 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 angle pdb=" O4' DT B 35 " pdb=" C4' DT B 35 " pdb=" C3' DT B 35 " ideal model delta sigma weight residual 106.00 103.33 2.67 6.00e-01 2.78e+00 1.98e+01 ... (remaining 14141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.29: 4901 35.29 - 70.58: 759 70.58 - 105.87: 12 105.87 - 141.15: 1 141.15 - 176.44: 1 Dihedral angle restraints: 5674 sinusoidal: 3384 harmonic: 2290 Sorted by residual: dihedral pdb=" C4' DG B 47 " pdb=" C3' DG B 47 " pdb=" O3' DG B 47 " pdb=" P DA B 48 " ideal model delta sinusoidal sigma weight residual -140.00 36.44 -176.44 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA LYS G 68 " pdb=" C LYS G 68 " pdb=" N TYR G 69 " pdb=" CA TYR G 69 " ideal model delta harmonic sigma weight residual -180.00 -160.52 -19.48 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA SER H 665 " pdb=" C SER H 665 " pdb=" N HIS H 666 " pdb=" CA HIS H 666 " ideal model delta harmonic sigma weight residual -180.00 -162.01 -17.99 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 5671 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1025 0.036 - 0.071: 386 0.071 - 0.107: 150 0.107 - 0.143: 42 0.143 - 0.179: 5 Chirality restraints: 1608 Sorted by residual: chirality pdb=" C3' DG B 47 " pdb=" C4' DG B 47 " pdb=" O3' DG B 47 " pdb=" C2' DG B 47 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.97e-01 chirality pdb=" C3' DA B 74 " pdb=" C4' DA B 74 " pdb=" O3' DA B 74 " pdb=" C2' DA B 74 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.19e-01 chirality pdb=" C3' DA A 70 " pdb=" C4' DA A 70 " pdb=" O3' DA A 70 " pdb=" C2' DA A 70 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.83e-01 ... (remaining 1605 not shown) Planarity restraints: 1241 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA A 63 " -0.027 2.00e-02 2.50e+03 1.18e-02 3.80e+00 pdb=" N9 DA A 63 " 0.024 2.00e-02 2.50e+03 pdb=" C8 DA A 63 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA A 63 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DA A 63 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA A 63 " -0.004 2.00e-02 2.50e+03 pdb=" N6 DA A 63 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DA A 63 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA A 63 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DA A 63 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DA A 63 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT A 93 " 0.006 2.00e-02 2.50e+03 1.10e-02 3.01e+00 pdb=" N1 DT A 93 " -0.018 2.00e-02 2.50e+03 pdb=" C2 DT A 93 " 0.021 2.00e-02 2.50e+03 pdb=" O2 DT A 93 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DT A 93 " -0.016 2.00e-02 2.50e+03 pdb=" C4 DT A 93 " 0.010 2.00e-02 2.50e+03 pdb=" O4 DT A 93 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DT A 93 " 0.001 2.00e-02 2.50e+03 pdb=" C7 DT A 93 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DT A 93 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA B 61 " 0.023 2.00e-02 2.50e+03 1.02e-02 2.83e+00 pdb=" N9 DA B 61 " -0.022 2.00e-02 2.50e+03 pdb=" C8 DA B 61 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DA B 61 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DA B 61 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DA B 61 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA B 61 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DA B 61 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DA B 61 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DA B 61 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA B 61 " -0.003 2.00e-02 2.50e+03 ... (remaining 1238 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 127 2.64 - 3.20: 8406 3.20 - 3.77: 16879 3.77 - 4.33: 21350 4.33 - 4.90: 31138 Nonbonded interactions: 77900 Sorted by model distance: nonbonded pdb=" OP1 DT A 61 " pdb=" OG1 THR E 6 " model vdw 2.069 3.040 nonbonded pdb=" OP1 DG A 71 " pdb=" OG1 THR F 6 " model vdw 2.158 3.040 nonbonded pdb=" OG SER H 761 " pdb=" OG1 THR H 766 " model vdw 2.181 3.040 nonbonded pdb=" NE2 HIS F 48 " pdb=" OD2 ASP F 103 " model vdw 2.195 3.120 nonbonded pdb=" OD1 ASP H 699 " pdb=" OG SER H 701 " model vdw 2.201 3.040 ... (remaining 77895 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 'E' and (resid 12 through 16 or (resid 17 and (name N or name CA or name \ C or name O or name CB )) or resid 18 through 22 or (resid 23 and (name N or nam \ e CA or name C or name O or name CB )) or resid 24 through 45 or (resid 46 and ( \ name N or name CA or name C or name O or name CB )) or resid 47 or (resid 48 and \ (name N or name CA or name C or name O or name CB )) or resid 49 or (resid 50 t \ hrough 51 and (name N or name CA or name C or name O or name CB )) or resid 52 t \ hrough 53 or (resid 54 and (name N or name CA or name C or name O or name CB )) \ or resid 55 or (resid 61 through 62 and (name N or name CA or name C or name O o \ r name CB )) or resid 63 or (resid 64 and (name N or name CA or name C or name O \ or name CB )) or resid 65 or (resid 66 and (name N or name CA or name C or name \ O or name CB )) or resid 67 through 73 or (resid 74 through 75 and (name N or n \ ame CA or name C or name O or name CB )) or resid 76 or (resid 77 and (name N or \ name CA or name C or name O or name CB )) or resid 78 or (resid 79 through 80 a \ nd (name N or name CA or name C or name O or name CB )) or resid 81 through 85 o \ r (resid 86 and (name N or name CA or name C or name O or name CB )) or resid 87 \ through 92 or (resid 93 and (name N or name CA or name C or name O or name CB ) \ ) or resid 94 or (resid 95 and (name N or name CA or name C or name O or name CB \ )) or resid 96 through 101 or (resid 102 and (name N or name CA or name C or na \ me O or name CB )) or resid 103 through 107 or (resid 108 and (name N or name CA \ or name C or name O or name CB )) or resid 109 through 111 or (resid 112 and (n \ ame N or name CA or name C or name O or name CB )) or resid 113)) selection = (chain 'F' and (resid 12 through 25 or (resid 26 and (name N or name CA or name \ C or name O or name CB )) or resid 27 or (resid 28 through 29 and (name N or nam \ e CA or name C or name O or name CB )) or resid 30 through 47 or (resid 48 and ( \ name N or name CA or name C or name O or name CB )) or resid 49 through 55 or (r \ esid 61 through 62 and (name N or name CA or name C or name O or name CB )) or r \ esid 63 through 65 or (resid 66 and (name N or name CA or name C or name O or na \ me CB )) or resid 67 or (resid 68 and (name N or name CA or name C or name O or \ name CB )) or resid 69 through 73 or (resid 74 through 75 and (name N or name CA \ or name C or name O or name CB )) or resid 76 or (resid 77 and (name N or name \ CA or name C or name O or name CB )) or resid 78 or (resid 79 through 80 and (na \ me N or name CA or name C or name O or name CB )) or resid 81 through 85 or (res \ id 86 and (name N or name CA or name C or name O or name CB )) or resid 87 throu \ gh 92 or (resid 93 and (name N or name CA or name C or name O or name CB )) or r \ esid 94 or (resid 95 and (name N or name CA or name C or name O or name CB )) or \ resid 96 through 101 or (resid 102 and (name N or name CA or name C or name O o \ r name CB )) or resid 103 through 107 or (resid 108 and (name N or name CA or na \ me C or name O or name CB )) or resid 109 through 113)) selection = (chain 'G' and (resid 12 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 25 or (resid 26 and (name N or nam \ e CA or name C or name O or name CB )) or resid 27 or (resid 28 through 29 and ( \ name N or name CA or name C or name O or name CB )) or resid 30 through 45 or (r \ esid 46 and (name N or name CA or name C or name O or name CB )) or resid 47 thr \ ough 49 or (resid 50 through 51 and (name N or name CA or name C or name O or na \ me CB )) or resid 52 through 67 or (resid 68 and (name N or name CA or name C or \ name O or name CB )) or resid 69 through 79 or (resid 80 and (name N or name CA \ or name C or name O or name CB )) or resid 81 through 111 or (resid 112 and (na \ me N or name CA or name C or name O or name CB )) or resid 113)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 17.560 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: 0.020 Set scattering table: 0.020 Process input model: 9.530 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 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 : 0.006 0.050 9932 Z= 0.557 Angle : 0.771 7.111 14146 Z= 0.681 Chirality : 0.045 0.179 1608 Planarity : 0.004 0.038 1241 Dihedral : 24.698 176.442 4184 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.81 % Allowed : 2.91 % Favored : 96.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.31), residues: 773 helix: 1.10 (0.28), residues: 321 sheet: -0.67 (0.41), residues: 155 loop : -0.92 (0.39), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 90 TYR 0.019 0.001 TYR H 669 PHE 0.021 0.002 PHE C 49 TRP 0.011 0.002 TRP H 774 HIS 0.002 0.001 HIS D 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00637 / 0.56 ( 9932) covalent geometry : angle 0.77112 / 0.68 (14146) hydrogen bonds : bond 0.12746 / 14.87 ( 485) hydrogen bonds : angle 5.85956 / 7.39 ( 1230) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 212 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.7020 (ttp) cc_final: 0.6163 (ptm) REVERT: E 61 ILE cc_start: 0.8880 (mt) cc_final: 0.8678 (mm) REVERT: E 95 ASP cc_start: 0.7720 (m-30) cc_final: 0.7416 (m-30) REVERT: F 22 VAL cc_start: 0.8605 (m) cc_final: 0.8362 (p) REVERT: G 39 PHE cc_start: 0.6983 (t80) cc_final: 0.6710 (t80) REVERT: H 719 ARG cc_start: 0.8114 (ptp90) cc_final: 0.7732 (mtm-85) outliers start: 5 outliers final: 3 residues processed: 216 average time/residue: 0.0913 time to fit residues: 27.1036 Evaluate side-chains 137 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 134 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 655 VAL Chi-restraints excluded: chain H residue 692 VAL Chi-restraints excluded: chain H residue 729 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 13 GLN D 54 HIS E 56 ASN H 803 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.073822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.059978 restraints weight = 49064.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.061495 restraints weight = 26917.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.062455 restraints weight = 18327.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.063062 restraints weight = 14355.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.063455 restraints weight = 12252.649| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9932 Z= 0.220 Angle : 0.756 10.564 14146 Z= 0.434 Chirality : 0.046 0.244 1608 Planarity : 0.005 0.048 1241 Dihedral : 28.823 171.640 2786 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.58 % Allowed : 16.64 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.30), residues: 773 helix: 1.19 (0.28), residues: 331 sheet: -0.84 (0.38), residues: 169 loop : -1.16 (0.39), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 3 TYR 0.016 0.002 TYR F 62 PHE 0.023 0.002 PHE F 117 TRP 0.008 0.001 TRP H 659 HIS 0.009 0.001 HIS E 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.22 ( 9932) covalent geometry : angle 0.75597 / 0.43 (14146) hydrogen bonds : bond 0.05541 / 6.19 ( 485) hydrogen bonds : angle 4.88406 / 6.48 ( 1230) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 21 ARG cc_start: 0.8154 (ttt90) cc_final: 0.7691 (ttt90) REVERT: C 28 GLU cc_start: 0.8720 (tp30) cc_final: 0.8092 (tm-30) REVERT: D 1 MET cc_start: 0.7554 (ttp) cc_final: 0.6839 (ptm) REVERT: D 29 MET cc_start: 0.8410 (mtm) cc_final: 0.7968 (mtm) REVERT: E 61 ILE cc_start: 0.8749 (mt) cc_final: 0.8511 (tt) REVERT: F 24 SER cc_start: 0.9298 (t) cc_final: 0.8997 (p) REVERT: F 69 TYR cc_start: 0.7693 (m-80) cc_final: 0.7237 (m-80) REVERT: F 72 MET cc_start: 0.7052 (ttm) cc_final: 0.6544 (tmm) REVERT: G 39 PHE cc_start: 0.7466 (t80) cc_final: 0.7005 (t80) REVERT: G 71 THR cc_start: 0.8212 (m) cc_final: 0.7937 (p) REVERT: H 673 ARG cc_start: 0.8861 (ttm-80) cc_final: 0.8218 (ttm110) outliers start: 16 outliers final: 9 residues processed: 146 average time/residue: 0.0839 time to fit residues: 17.2428 Evaluate side-chains 127 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain H residue 655 VAL Chi-restraints excluded: chain H residue 692 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 88 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 59 GLN D 32 HIS E 56 ASN E 80 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.071600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.058026 restraints weight = 49711.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.059371 restraints weight = 28773.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.060250 restraints weight = 20293.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.060814 restraints weight = 16125.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.061133 restraints weight = 13903.912| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9932 Z= 0.268 Angle : 0.775 8.764 14146 Z= 0.440 Chirality : 0.046 0.300 1608 Planarity : 0.005 0.038 1241 Dihedral : 28.976 171.237 2785 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.88 % Allowed : 17.29 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.30), residues: 773 helix: 0.93 (0.28), residues: 331 sheet: -0.89 (0.40), residues: 155 loop : -1.39 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 100 TYR 0.014 0.002 TYR H 669 PHE 0.024 0.003 PHE C 49 TRP 0.011 0.002 TRP H 659 HIS 0.007 0.002 HIS E 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.27 ( 9932) covalent geometry : angle 0.77495 / 0.44 (14146) hydrogen bonds : bond 0.05883 / 6.62 ( 485) hydrogen bonds : angle 4.77843 / 6.47 ( 1230) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 GLU cc_start: 0.8746 (tp30) cc_final: 0.8084 (tm-30) REVERT: C 93 ASN cc_start: 0.7789 (p0) cc_final: 0.7565 (p0) REVERT: D 1 MET cc_start: 0.7799 (ttp) cc_final: 0.7347 (ttp) REVERT: E 61 ILE cc_start: 0.8764 (mt) cc_final: 0.8518 (tt) REVERT: E 95 ASP cc_start: 0.7843 (m-30) cc_final: 0.7611 (m-30) REVERT: F 69 TYR cc_start: 0.7725 (m-80) cc_final: 0.7347 (m-80) REVERT: F 72 MET cc_start: 0.7264 (ttm) cc_final: 0.6799 (tmm) REVERT: F 74 LEU cc_start: 0.8960 (mt) cc_final: 0.8483 (mt) REVERT: G 39 PHE cc_start: 0.7496 (t80) cc_final: 0.7137 (t80) REVERT: H 736 GLN cc_start: 0.7855 (tp40) cc_final: 0.7410 (tm-30) outliers start: 24 outliers final: 19 residues processed: 138 average time/residue: 0.0903 time to fit residues: 17.6966 Evaluate side-chains 131 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 113 ASN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain H residue 646 LEU Chi-restraints excluded: chain H residue 655 VAL Chi-restraints excluded: chain H residue 683 LEU Chi-restraints excluded: chain H residue 692 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 29 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 84 optimal weight: 0.4980 chunk 6 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 56 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.073090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.059496 restraints weight = 49906.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.060829 restraints weight = 28923.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.061732 restraints weight = 20546.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.062306 restraints weight = 16341.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.062608 restraints weight = 14095.593| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9932 Z= 0.166 Angle : 0.683 10.154 14146 Z= 0.395 Chirality : 0.042 0.262 1608 Planarity : 0.005 0.055 1241 Dihedral : 28.913 169.948 2785 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.36 % Allowed : 16.80 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.31), residues: 773 helix: 1.39 (0.29), residues: 325 sheet: -0.95 (0.38), residues: 171 loop : -1.11 (0.40), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 32 TYR 0.010 0.001 TYR H 669 PHE 0.014 0.001 PHE F 55 TRP 0.011 0.001 TRP H 702 HIS 0.004 0.001 HIS E 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.17 ( 9932) covalent geometry : angle 0.68272 / 0.39 (14146) hydrogen bonds : bond 0.04720 / 5.49 ( 485) hydrogen bonds : angle 4.49562 / 6.18 ( 1230) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 GLU cc_start: 0.8673 (tp30) cc_final: 0.7988 (tm-30) REVERT: C 32 GLU cc_start: 0.8424 (tp30) cc_final: 0.8118 (tp30) REVERT: D 29 MET cc_start: 0.7894 (mtm) cc_final: 0.6685 (mtt) REVERT: D 33 MET cc_start: 0.8575 (mpp) cc_final: 0.7413 (mpp) REVERT: E 61 ILE cc_start: 0.8729 (mt) cc_final: 0.8492 (tt) REVERT: E 95 ASP cc_start: 0.7788 (m-30) cc_final: 0.7517 (m-30) REVERT: F 69 TYR cc_start: 0.7646 (m-80) cc_final: 0.7251 (m-80) REVERT: F 72 MET cc_start: 0.7249 (ttm) cc_final: 0.6793 (tmm) REVERT: F 81 LEU cc_start: 0.8641 (mm) cc_final: 0.7713 (mm) REVERT: F 99 ASP cc_start: 0.7657 (t0) cc_final: 0.7280 (m-30) REVERT: G 39 PHE cc_start: 0.7367 (t80) cc_final: 0.6988 (t80) REVERT: H 802 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8205 (mt) outliers start: 27 outliers final: 21 residues processed: 136 average time/residue: 0.0735 time to fit residues: 15.1551 Evaluate side-chains 132 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 57 ARG Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain H residue 623 VAL Chi-restraints excluded: chain H residue 655 VAL Chi-restraints excluded: chain H residue 683 LEU Chi-restraints excluded: chain H residue 692 VAL Chi-restraints excluded: chain H residue 740 VAL Chi-restraints excluded: chain H residue 802 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 73 optimal weight: 0.1980 chunk 92 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 50 optimal weight: 0.0870 chunk 71 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 overall best weight: 1.2362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 56 ASN ** H 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.071984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.058421 restraints weight = 49742.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.059793 restraints weight = 28433.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.060680 restraints weight = 19860.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.061187 restraints weight = 15773.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.061566 restraints weight = 13738.943| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9932 Z= 0.199 Angle : 0.707 10.045 14146 Z= 0.401 Chirality : 0.043 0.236 1608 Planarity : 0.004 0.036 1241 Dihedral : 28.933 170.389 2785 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 5.01 % Allowed : 17.77 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.31), residues: 773 helix: 1.43 (0.29), residues: 325 sheet: -1.18 (0.39), residues: 168 loop : -1.24 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 32 TYR 0.011 0.001 TYR H 669 PHE 0.016 0.002 PHE C 49 TRP 0.009 0.001 TRP H 659 HIS 0.004 0.001 HIS E 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.20 ( 9932) covalent geometry : angle 0.70673 / 0.40 (14146) hydrogen bonds : bond 0.05040 / 5.78 ( 485) hydrogen bonds : angle 4.46143 / 6.19 ( 1230) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 GLU cc_start: 0.8745 (tp30) cc_final: 0.8022 (tm-30) REVERT: C 32 GLU cc_start: 0.8506 (tp30) cc_final: 0.8246 (tp30) REVERT: D 29 MET cc_start: 0.8067 (mtm) cc_final: 0.6738 (mtp) REVERT: D 33 MET cc_start: 0.8700 (mpp) cc_final: 0.7370 (mpp) REVERT: D 79 HIS cc_start: 0.7821 (OUTLIER) cc_final: 0.6859 (t70) REVERT: E 1 MET cc_start: 0.6812 (pmm) cc_final: 0.6387 (pmm) REVERT: E 61 ILE cc_start: 0.8764 (mt) cc_final: 0.8508 (tt) REVERT: F 69 TYR cc_start: 0.7724 (m-80) cc_final: 0.7296 (m-80) REVERT: F 72 MET cc_start: 0.7333 (ttm) cc_final: 0.6721 (tmm) REVERT: F 81 LEU cc_start: 0.8571 (mm) cc_final: 0.8169 (mm) REVERT: G 39 PHE cc_start: 0.7471 (t80) cc_final: 0.7129 (t80) REVERT: G 72 MET cc_start: 0.6507 (tpt) cc_final: 0.6113 (tpt) REVERT: H 802 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8416 (mm) outliers start: 31 outliers final: 26 residues processed: 128 average time/residue: 0.0821 time to fit residues: 15.6675 Evaluate side-chains 137 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 57 ARG Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 113 ASN Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain H residue 623 VAL Chi-restraints excluded: chain H residue 655 VAL Chi-restraints excluded: chain H residue 683 LEU Chi-restraints excluded: chain H residue 692 VAL Chi-restraints excluded: chain H residue 695 ILE Chi-restraints excluded: chain H residue 735 LEU Chi-restraints excluded: chain H residue 740 VAL Chi-restraints excluded: chain H residue 775 VAL Chi-restraints excluded: chain H residue 802 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 52 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 56 ASN ** F 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 691 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.071011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.057342 restraints weight = 50533.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.058661 restraints weight = 29472.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.059540 restraints weight = 20903.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.060098 restraints weight = 16704.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.060454 restraints weight = 14436.150| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9932 Z= 0.241 Angle : 0.746 9.752 14146 Z= 0.420 Chirality : 0.044 0.238 1608 Planarity : 0.005 0.040 1241 Dihedral : 29.032 171.170 2785 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 6.62 % Allowed : 17.12 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.30), residues: 773 helix: 1.08 (0.28), residues: 328 sheet: -1.23 (0.38), residues: 166 loop : -1.56 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 100 TYR 0.021 0.002 TYR H 815 PHE 0.022 0.002 PHE C 49 TRP 0.012 0.002 TRP H 659 HIS 0.005 0.002 HIS E 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.24 ( 9932) covalent geometry : angle 0.74563 / 0.42 (14146) hydrogen bonds : bond 0.05697 / 6.47 ( 485) hydrogen bonds : angle 4.59833 / 6.38 ( 1230) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 109 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 GLU cc_start: 0.8806 (tp30) cc_final: 0.8083 (tm-30) REVERT: D 1 MET cc_start: 0.7956 (ttm) cc_final: 0.7421 (ttp) REVERT: D 29 MET cc_start: 0.8123 (mtm) cc_final: 0.6906 (mtp) REVERT: D 33 MET cc_start: 0.8781 (mpp) cc_final: 0.7440 (mpp) REVERT: D 79 HIS cc_start: 0.7879 (OUTLIER) cc_final: 0.6928 (t70) REVERT: E 61 ILE cc_start: 0.8775 (mt) cc_final: 0.8500 (tt) REVERT: E 95 ASP cc_start: 0.7930 (m-30) cc_final: 0.7696 (m-30) REVERT: F 69 TYR cc_start: 0.7883 (m-80) cc_final: 0.7552 (m-80) REVERT: F 72 MET cc_start: 0.7445 (ttm) cc_final: 0.6935 (tmm) REVERT: G 39 PHE cc_start: 0.7556 (t80) cc_final: 0.7222 (t80) REVERT: G 72 MET cc_start: 0.6529 (tpt) cc_final: 0.6198 (tpp) REVERT: G 99 ASP cc_start: 0.8456 (m-30) cc_final: 0.8005 (p0) REVERT: H 647 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7629 (ptt90) REVERT: H 802 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8426 (mm) outliers start: 41 outliers final: 27 residues processed: 130 average time/residue: 0.0856 time to fit residues: 16.2785 Evaluate side-chains 133 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 103 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 57 ARG Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 113 ASN Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain H residue 647 ARG Chi-restraints excluded: chain H residue 655 VAL Chi-restraints excluded: chain H residue 683 LEU Chi-restraints excluded: chain H residue 692 VAL Chi-restraints excluded: chain H residue 695 ILE Chi-restraints excluded: chain H residue 735 LEU Chi-restraints excluded: chain H residue 740 VAL Chi-restraints excluded: chain H residue 775 VAL Chi-restraints excluded: chain H residue 802 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 23 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 56 ASN ** H 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.070841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.057087 restraints weight = 50426.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.058462 restraints weight = 29063.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.059338 restraints weight = 20304.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.059853 restraints weight = 16178.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.060246 restraints weight = 14048.984| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9932 Z= 0.236 Angle : 0.745 10.124 14146 Z= 0.419 Chirality : 0.043 0.220 1608 Planarity : 0.005 0.043 1241 Dihedral : 29.089 170.399 2785 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 5.98 % Allowed : 18.74 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.30), residues: 773 helix: 0.97 (0.28), residues: 328 sheet: -1.32 (0.38), residues: 161 loop : -1.65 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 32 TYR 0.013 0.002 TYR H 669 PHE 0.020 0.002 PHE C 49 TRP 0.012 0.002 TRP H 659 HIS 0.005 0.001 HIS F 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.24 ( 9932) covalent geometry : angle 0.74534 / 0.42 (14146) hydrogen bonds : bond 0.05474 / 6.24 ( 485) hydrogen bonds : angle 4.56318 / 6.32 ( 1230) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 108 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 GLU cc_start: 0.8826 (tp30) cc_final: 0.8146 (tm-30) REVERT: D 29 MET cc_start: 0.8182 (mtm) cc_final: 0.6904 (mtt) REVERT: D 33 MET cc_start: 0.8778 (mpp) cc_final: 0.7437 (mpp) REVERT: D 79 HIS cc_start: 0.7896 (OUTLIER) cc_final: 0.7007 (t70) REVERT: E 61 ILE cc_start: 0.8754 (mt) cc_final: 0.8475 (tt) REVERT: F 69 TYR cc_start: 0.7872 (m-80) cc_final: 0.7541 (m-80) REVERT: F 72 MET cc_start: 0.7534 (ttm) cc_final: 0.6983 (tmm) REVERT: F 81 LEU cc_start: 0.8550 (mm) cc_final: 0.8230 (mm) REVERT: G 39 PHE cc_start: 0.7578 (t80) cc_final: 0.7249 (t80) REVERT: G 72 MET cc_start: 0.6541 (tpt) cc_final: 0.6328 (tpp) REVERT: H 647 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7645 (ptt90) REVERT: H 802 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8411 (mm) outliers start: 37 outliers final: 31 residues processed: 130 average time/residue: 0.0907 time to fit residues: 17.1161 Evaluate side-chains 139 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 57 ARG Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 113 ASN Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain H residue 647 ARG Chi-restraints excluded: chain H residue 655 VAL Chi-restraints excluded: chain H residue 656 MET Chi-restraints excluded: chain H residue 683 LEU Chi-restraints excluded: chain H residue 692 VAL Chi-restraints excluded: chain H residue 695 ILE Chi-restraints excluded: chain H residue 735 LEU Chi-restraints excluded: chain H residue 740 VAL Chi-restraints excluded: chain H residue 775 VAL Chi-restraints excluded: chain H residue 802 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 19 optimal weight: 1.9990 chunk 76 optimal weight: 0.0570 chunk 12 optimal weight: 8.9990 chunk 78 optimal weight: 0.2980 chunk 87 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 overall best weight: 0.8502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 31 ASN H 666 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.071866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.058104 restraints weight = 49619.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.059562 restraints weight = 27491.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.060515 restraints weight = 18801.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.061073 restraints weight = 14736.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.061481 restraints weight = 12640.444| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9932 Z= 0.168 Angle : 0.688 10.691 14146 Z= 0.392 Chirality : 0.041 0.243 1608 Planarity : 0.004 0.050 1241 Dihedral : 29.057 168.783 2785 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 5.33 % Allowed : 20.52 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.43 (0.31), residues: 773 helix: 1.25 (0.29), residues: 328 sheet: -1.17 (0.39), residues: 165 loop : -1.53 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 100 TYR 0.011 0.001 TYR H 815 PHE 0.026 0.002 PHE G 111 TRP 0.008 0.001 TRP H 659 HIS 0.005 0.001 HIS F 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.17 ( 9932) covalent geometry : angle 0.68811 / 0.39 (14146) hydrogen bonds : bond 0.04667 / 5.41 ( 485) hydrogen bonds : angle 4.38999 / 6.12 ( 1230) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 GLU cc_start: 0.8813 (tp30) cc_final: 0.8121 (tm-30) REVERT: D 29 MET cc_start: 0.7955 (mtm) cc_final: 0.7106 (mtt) REVERT: D 33 MET cc_start: 0.8766 (mpp) cc_final: 0.7527 (mpp) REVERT: D 79 HIS cc_start: 0.7742 (OUTLIER) cc_final: 0.6838 (t70) REVERT: E 61 ILE cc_start: 0.8709 (mt) cc_final: 0.8415 (tt) REVERT: F 69 TYR cc_start: 0.7876 (m-80) cc_final: 0.7476 (m-80) REVERT: F 72 MET cc_start: 0.7478 (ttm) cc_final: 0.6963 (tmm) REVERT: F 81 LEU cc_start: 0.8597 (mm) cc_final: 0.8283 (mm) REVERT: F 99 ASP cc_start: 0.7691 (t0) cc_final: 0.7372 (m-30) REVERT: G 39 PHE cc_start: 0.7551 (t80) cc_final: 0.7207 (t80) REVERT: G 99 ASP cc_start: 0.8417 (m-30) cc_final: 0.7957 (p0) REVERT: H 647 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7352 (ptt90) REVERT: H 802 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8342 (mm) outliers start: 33 outliers final: 28 residues processed: 127 average time/residue: 0.0873 time to fit residues: 16.2653 Evaluate side-chains 134 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 57 ARG Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 31 ASN Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain H residue 647 ARG Chi-restraints excluded: chain H residue 655 VAL Chi-restraints excluded: chain H residue 656 MET Chi-restraints excluded: chain H residue 683 LEU Chi-restraints excluded: chain H residue 692 VAL Chi-restraints excluded: chain H residue 695 ILE Chi-restraints excluded: chain H residue 735 LEU Chi-restraints excluded: chain H residue 740 VAL Chi-restraints excluded: chain H residue 775 VAL Chi-restraints excluded: chain H residue 802 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 40 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 76 optimal weight: 0.6980 chunk 15 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.070640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.056915 restraints weight = 48898.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.058339 restraints weight = 27054.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.059288 restraints weight = 18414.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.059845 restraints weight = 14261.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.060279 restraints weight = 12142.800| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9932 Z= 0.168 Angle : 0.702 10.529 14146 Z= 0.397 Chirality : 0.041 0.238 1608 Planarity : 0.004 0.045 1241 Dihedral : 29.043 168.331 2785 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 5.33 % Allowed : 20.84 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.30), residues: 773 helix: 1.16 (0.28), residues: 328 sheet: -1.16 (0.39), residues: 165 loop : -1.53 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 100 TYR 0.011 0.001 TYR H 815 PHE 0.012 0.002 PHE F 55 TRP 0.008 0.001 TRP H 659 HIS 0.004 0.001 HIS F 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.17 ( 9932) covalent geometry : angle 0.70165 / 0.40 (14146) hydrogen bonds : bond 0.04706 / 5.42 ( 485) hydrogen bonds : angle 4.38773 / 6.07 ( 1230) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 105 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 GLU cc_start: 0.8829 (tp30) cc_final: 0.8118 (tm-30) REVERT: D 29 MET cc_start: 0.7886 (mtm) cc_final: 0.7048 (mtt) REVERT: D 33 MET cc_start: 0.8811 (mpp) cc_final: 0.7332 (mpp) REVERT: D 79 HIS cc_start: 0.7668 (OUTLIER) cc_final: 0.6857 (t70) REVERT: E 61 ILE cc_start: 0.8749 (mt) cc_final: 0.8438 (tt) REVERT: F 69 TYR cc_start: 0.7873 (m-80) cc_final: 0.7443 (m-80) REVERT: F 72 MET cc_start: 0.7515 (ttm) cc_final: 0.6910 (tmm) REVERT: F 81 LEU cc_start: 0.8547 (mm) cc_final: 0.8327 (mm) REVERT: F 99 ASP cc_start: 0.7709 (t0) cc_final: 0.7419 (m-30) REVERT: G 39 PHE cc_start: 0.7618 (t80) cc_final: 0.7251 (t80) REVERT: G 99 ASP cc_start: 0.8498 (m-30) cc_final: 0.8017 (p0) REVERT: H 647 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7566 (ptt90) REVERT: H 802 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8340 (mm) outliers start: 33 outliers final: 27 residues processed: 124 average time/residue: 0.0896 time to fit residues: 16.2753 Evaluate side-chains 134 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 57 ARG Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 62 TYR Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 31 ASN Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain H residue 647 ARG Chi-restraints excluded: chain H residue 655 VAL Chi-restraints excluded: chain H residue 683 LEU Chi-restraints excluded: chain H residue 692 VAL Chi-restraints excluded: chain H residue 695 ILE Chi-restraints excluded: chain H residue 735 LEU Chi-restraints excluded: chain H residue 740 VAL Chi-restraints excluded: chain H residue 775 VAL Chi-restraints excluded: chain H residue 802 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 5 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 73 optimal weight: 0.3980 chunk 50 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.070242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.056574 restraints weight = 48859.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.057968 restraints weight = 27208.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.058902 restraints weight = 18626.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.059519 restraints weight = 14455.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.059877 restraints weight = 12197.329| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9932 Z= 0.195 Angle : 0.724 10.114 14146 Z= 0.407 Chirality : 0.042 0.227 1608 Planarity : 0.004 0.043 1241 Dihedral : 29.060 168.583 2785 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 5.33 % Allowed : 20.36 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.30), residues: 773 helix: 1.07 (0.28), residues: 328 sheet: -1.19 (0.39), residues: 165 loop : -1.60 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 100 TYR 0.011 0.001 TYR F 52 PHE 0.015 0.002 PHE C 49 TRP 0.009 0.001 TRP H 659 HIS 0.004 0.001 HIS F 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.20 ( 9932) covalent geometry : angle 0.72401 / 0.41 (14146) hydrogen bonds : bond 0.04883 / 5.58 ( 485) hydrogen bonds : angle 4.40175 / 6.10 ( 1230) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 GLU cc_start: 0.8843 (tp30) cc_final: 0.8107 (tm-30) REVERT: D 28 GLU cc_start: 0.7881 (tp30) cc_final: 0.7426 (tp30) REVERT: D 29 MET cc_start: 0.7995 (mtm) cc_final: 0.7080 (ttm) REVERT: D 33 MET cc_start: 0.8914 (mpp) cc_final: 0.7708 (mpp) REVERT: D 79 HIS cc_start: 0.7695 (OUTLIER) cc_final: 0.6841 (t70) REVERT: E 61 ILE cc_start: 0.8757 (mt) cc_final: 0.8448 (tt) REVERT: F 69 TYR cc_start: 0.7829 (m-80) cc_final: 0.7412 (m-80) REVERT: F 72 MET cc_start: 0.7507 (ttm) cc_final: 0.6887 (tmm) REVERT: G 39 PHE cc_start: 0.7651 (t80) cc_final: 0.7286 (t80) REVERT: G 72 MET cc_start: 0.6358 (tpt) cc_final: 0.5989 (tpt) REVERT: G 99 ASP cc_start: 0.8528 (m-30) cc_final: 0.8053 (p0) REVERT: H 647 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7599 (ptt90) REVERT: H 802 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8374 (mm) outliers start: 33 outliers final: 29 residues processed: 125 average time/residue: 0.0884 time to fit residues: 16.2303 Evaluate side-chains 137 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 57 ARG Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 62 TYR Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 31 ASN Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain H residue 647 ARG Chi-restraints excluded: chain H residue 655 VAL Chi-restraints excluded: chain H residue 683 LEU Chi-restraints excluded: chain H residue 692 VAL Chi-restraints excluded: chain H residue 695 ILE Chi-restraints excluded: chain H residue 735 LEU Chi-restraints excluded: chain H residue 740 VAL Chi-restraints excluded: chain H residue 775 VAL Chi-restraints excluded: chain H residue 802 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 91 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 736 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.069478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.055818 restraints weight = 48820.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.057193 restraints weight = 27507.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.058092 restraints weight = 18851.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.058681 restraints weight = 14741.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.059045 restraints weight = 12519.989| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 9932 Z= 0.240 Angle : 0.755 9.363 14146 Z= 0.423 Chirality : 0.043 0.210 1608 Planarity : 0.005 0.049 1241 Dihedral : 29.121 169.304 2785 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 5.49 % Allowed : 20.36 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.85 (0.30), residues: 773 helix: 0.86 (0.28), residues: 328 sheet: -1.31 (0.39), residues: 165 loop : -1.73 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 32 TYR 0.012 0.001 TYR H 669 PHE 0.022 0.002 PHE C 49 TRP 0.011 0.002 TRP H 659 HIS 0.005 0.001 HIS F 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.24 ( 9932) covalent geometry : angle 0.75544 / 0.42 (14146) hydrogen bonds : bond 0.05407 / 6.10 ( 485) hydrogen bonds : angle 4.49534 / 6.23 ( 1230) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1909.92 seconds wall clock time: 33 minutes 45.50 seconds (2025.50 seconds total)