Starting phenix.real_space_refine on Wed Aug 5 09:31:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f0x_50117/08_2026/9f0x_50117.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f0x_50117/08_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_50117/08_2026/9f0x_50117.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f0x_50117/08_2026/9f0x_50117.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9f0x_50117/08_2026/9f0x_50117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f0x_50117/08_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-2.2rc3-6140/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: 2.21, per 1000 atoms: 0.23 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: 0.94 Conformation dependent library (CDL) restraints added in 231.4 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: 1.21 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: 1.97 Time building geometry restraints manager: 1.20 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: 12968 1.42 - 2.84: 1100 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: 11.860 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.920 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.200 ------------------------------------------------------------------------------- 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= 0.558 Angle : 0.775 7.111 14146 Z= 0.684 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 0.77513 / 0.68 (14146) hydrogen bonds : bond 0.12746 / 14.96 ( 485) hydrogen bonds : angle 5.85956 / 7.38 ( 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 : 0.287 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: 0.6164 (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: 0.0949 time to fit residues: 28.2272 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 : 0.256 ------------------------------------------------------------------------------- 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: 9.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 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: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 13 GLN E 56 ASN H 803 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.074454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.060633 restraints weight = 48840.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.062150 restraints weight = 26738.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.063131 restraints weight = 18230.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.063758 restraints weight = 14208.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.064150 restraints weight = 12084.614| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9932 Z= 0.188 Angle : 0.742 10.254 14146 Z= 0.426 Chirality : 0.046 0.267 1608 Planarity : 0.005 0.048 1241 Dihedral : 28.795 171.842 2786 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.75 % Allowed : 14.86 % Favored : 82.39 % 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: 1.25 (0.28), residues: 331 sheet: -0.84 (0.38), residues: 169 loop : -1.08 (0.40), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 3 TYR 0.016 0.002 TYR F 62 PHE 0.021 0.002 PHE F 55 TRP 0.008 0.001 TRP H 659 HIS 0.007 0.001 HIS E 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.19 ( 9932) covalent geometry : angle 0.74182 / 0.43 (14146) hydrogen bonds : bond 0.05230 / 5.89 ( 485) hydrogen bonds : angle 4.73848 / 6.32 ( 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 158 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 8 MET cc_start: 0.7501 (mtp) cc_final: 0.7290 (mtp) REVERT: C 28 GLU cc_start: 0.8681 (tp30) cc_final: 0.8035 (tm-30) REVERT: D 1 MET cc_start: 0.7472 (ttp) cc_final: 0.7025 (ptm) REVERT: D 29 MET cc_start: 0.8330 (mtm) cc_final: 0.8029 (mtm) REVERT: E 61 ILE cc_start: 0.8747 (mt) cc_final: 0.8511 (tt) REVERT: F 24 SER cc_start: 0.9304 (t) cc_final: 0.9072 (p) REVERT: F 72 MET cc_start: 0.7017 (ttm) cc_final: 0.6629 (tmm) REVERT: G 39 PHE cc_start: 0.7451 (t80) cc_final: 0.7032 (t80) REVERT: G 71 THR cc_start: 0.8212 (m) cc_final: 0.7970 (p) REVERT: H 654 MET cc_start: 0.6719 (mtt) cc_final: 0.6396 (mtt) outliers start: 17 outliers final: 9 residues processed: 149 average time/residue: 0.0759 time to fit residues: 16.3405 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 : 0.204 ------------------------------------------------------------------------------- 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: 0.5980 chunk 78 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 59 GLN D 54 HIS E 56 ASN H 691 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.072843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.059048 restraints weight = 49359.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.060483 restraints weight = 27775.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.061399 restraints weight = 19241.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.062003 restraints weight = 15203.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.062337 restraints weight = 13020.989| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9932 Z= 0.216 Angle : 0.744 9.048 14146 Z= 0.422 Chirality : 0.045 0.297 1608 Planarity : 0.005 0.031 1241 Dihedral : 28.878 170.285 2785 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.39 % Allowed : 16.32 % Favored : 80.29 % 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: -0.27 (0.31), residues: 773 helix: 1.10 (0.28), residues: 331 sheet: -1.00 (0.39), residues: 164 loop : -1.11 (0.40), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 100 TYR 0.012 0.002 TYR H 669 PHE 0.021 0.002 PHE F 55 TRP 0.010 0.001 TRP H 659 HIS 0.005 0.001 HIS E 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.22 ( 9932) covalent geometry : angle 0.74394 / 0.42 (14146) hydrogen bonds : bond 0.05375 / 6.15 ( 485) hydrogen bonds : angle 4.60024 / 6.29 ( 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 148 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 GLU cc_start: 0.8728 (tp30) cc_final: 0.8044 (tm-30) REVERT: D 1 MET cc_start: 0.7167 (ttp) cc_final: 0.6671 (ttp) REVERT: D 29 MET cc_start: 0.8322 (mtm) cc_final: 0.7031 (mtm) REVERT: D 33 MET cc_start: 0.8653 (mpp) cc_final: 0.7278 (mpp) REVERT: E 61 ILE cc_start: 0.8775 (mt) cc_final: 0.8519 (tt) REVERT: E 95 ASP cc_start: 0.7782 (m-30) cc_final: 0.7541 (m-30) REVERT: F 72 MET cc_start: 0.7191 (ttm) cc_final: 0.6627 (tmm) REVERT: F 74 LEU cc_start: 0.8943 (mt) cc_final: 0.8426 (mt) REVERT: G 39 PHE cc_start: 0.7472 (t80) cc_final: 0.7089 (t80) REVERT: H 654 MET cc_start: 0.6854 (mtt) cc_final: 0.6614 (mtt) outliers start: 21 outliers final: 18 residues processed: 138 average time/residue: 0.0690 time to fit residues: 13.9904 Evaluate side-chains 129 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 SER 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 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 F residue 117 PHE 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 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: 0.9980 chunk 18 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 6 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 32 HIS E 56 ASN ** H 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.073243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.059442 restraints weight = 49453.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.060892 restraints weight = 27804.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.061819 restraints weight = 19189.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.062402 restraints weight = 15115.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.062730 restraints weight = 12998.762| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9932 Z= 0.181 Angle : 0.693 9.863 14146 Z= 0.399 Chirality : 0.042 0.269 1608 Planarity : 0.004 0.034 1241 Dihedral : 28.847 169.241 2785 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 5.01 % Allowed : 16.16 % 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: -0.21 (0.31), residues: 773 helix: 1.31 (0.28), residues: 324 sheet: -1.12 (0.37), residues: 177 loop : -1.11 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 32 TYR 0.007 0.001 TYR H 669 PHE 0.011 0.002 PHE C 49 TRP 0.011 0.001 TRP H 702 HIS 0.005 0.001 HIS H 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.18 ( 9932) covalent geometry : angle 0.69253 / 0.40 (14146) hydrogen bonds : bond 0.04828 / 5.59 ( 485) hydrogen bonds : angle 4.42978 / 6.08 ( 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: 31 poor density : 119 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 GLU cc_start: 0.8716 (tp30) cc_final: 0.7973 (tm-30) REVERT: C 32 GLU cc_start: 0.8492 (tp30) cc_final: 0.8102 (tp30) REVERT: D 29 MET cc_start: 0.8127 (mtm) cc_final: 0.6835 (mtt) REVERT: D 33 MET cc_start: 0.8570 (mpp) cc_final: 0.7121 (mpp) REVERT: E 61 ILE cc_start: 0.8787 (mt) cc_final: 0.8517 (tt) REVERT: E 95 ASP cc_start: 0.7778 (m-30) cc_final: 0.7569 (m-30) REVERT: F 72 MET cc_start: 0.7309 (ttm) cc_final: 0.6694 (tmm) REVERT: F 81 LEU cc_start: 0.8716 (mm) cc_final: 0.7818 (mm) REVERT: F 83 ILE cc_start: 0.6009 (OUTLIER) cc_final: 0.5746 (mm) REVERT: G 39 PHE cc_start: 0.7452 (t80) cc_final: 0.7043 (t80) REVERT: G 99 ASP cc_start: 0.8257 (m-30) cc_final: 0.7893 (p0) REVERT: H 654 MET cc_start: 0.7014 (mtt) cc_final: 0.6784 (mtt) REVERT: H 802 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8200 (mt) outliers start: 31 outliers final: 20 residues processed: 132 average time/residue: 0.0545 time to fit residues: 11.0399 Evaluate side-chains 131 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.157 ------------------------------------------------------------------------------- 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 78 THR Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 83 ILE 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 623 VAL Chi-restraints excluded: chain H residue 655 VAL Chi-restraints excluded: chain H residue 683 LEU Chi-restraints excluded: chain H residue 687 GLN Chi-restraints excluded: chain H residue 692 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: 0.5980 chunk 92 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 50 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3855 r_free = 0.3855 target = 0.073405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.059634 restraints weight = 49704.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.061024 restraints weight = 28740.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.061910 restraints weight = 20186.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.062482 restraints weight = 16109.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.062801 restraints weight = 13955.595| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9932 Z= 0.177 Angle : 0.699 10.268 14146 Z= 0.398 Chirality : 0.042 0.265 1608 Planarity : 0.004 0.049 1241 Dihedral : 28.848 168.233 2785 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.85 % Allowed : 17.29 % Favored : 77.87 % 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: -0.13 (0.31), residues: 773 helix: 1.44 (0.29), residues: 324 sheet: -1.11 (0.37), residues: 183 loop : -1.13 (0.41), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 32 TYR 0.010 0.001 TYR H 669 PHE 0.012 0.001 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 0.00327 / 0.18 ( 9932) covalent geometry : angle 0.69868 / 0.40 (14146) hydrogen bonds : bond 0.04730 / 5.47 ( 485) hydrogen bonds : angle 4.31977 / 5.95 ( 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 148 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 GLU cc_start: 0.8701 (tp30) cc_final: 0.7986 (tm-30) REVERT: C 32 GLU cc_start: 0.8406 (tp30) cc_final: 0.8194 (tp30) REVERT: D 29 MET cc_start: 0.8171 (mtm) cc_final: 0.7091 (mtt) REVERT: D 33 MET cc_start: 0.8576 (mpp) cc_final: 0.7275 (mpp) REVERT: E 61 ILE cc_start: 0.8748 (mt) cc_final: 0.8501 (tt) REVERT: E 95 ASP cc_start: 0.7749 (m-30) cc_final: 0.7492 (m-30) REVERT: F 72 MET cc_start: 0.7265 (ttm) cc_final: 0.6725 (tmm) REVERT: F 81 LEU cc_start: 0.8522 (mm) cc_final: 0.8197 (tp) REVERT: G 39 PHE cc_start: 0.7409 (t80) cc_final: 0.7035 (t80) REVERT: H 654 MET cc_start: 0.7187 (mtt) cc_final: 0.6964 (mtt) outliers start: 30 outliers final: 26 residues processed: 130 average time/residue: 0.0788 time to fit residues: 14.6854 Evaluate side-chains 135 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.191 ------------------------------------------------------------------------------- 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 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 E residue 78 THR 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 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 687 GLN Chi-restraints excluded: chain H residue 692 VAL Chi-restraints excluded: chain H residue 695 ILE Chi-restraints excluded: chain H residue 735 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 52 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 77 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 50 HIS E 56 ASN ** H 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.070874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.057229 restraints weight = 50846.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.058533 restraints weight = 30231.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.059381 restraints weight = 21602.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.059933 restraints weight = 17328.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.060232 restraints weight = 15025.069| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 9932 Z= 0.279 Angle : 0.802 11.128 14146 Z= 0.443 Chirality : 0.046 0.223 1608 Planarity : 0.006 0.038 1241 Dihedral : 29.009 169.377 2785 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 6.62 % Allowed : 16.64 % Favored : 76.74 % 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: -0.79 (0.30), residues: 773 helix: 0.84 (0.28), residues: 327 sheet: -1.30 (0.39), residues: 166 loop : -1.59 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 60 TYR 0.015 0.002 TYR H 669 PHE 0.026 0.003 PHE C 49 TRP 0.016 0.002 TRP H 774 HIS 0.006 0.002 HIS H 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.28 ( 9932) covalent geometry : angle 0.80160 / 0.44 (14146) hydrogen bonds : bond 0.06368 / 7.16 ( 485) hydrogen bonds : angle 4.61587 / 6.42 ( 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 147 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 106 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 28 GLU cc_start: 0.8773 (tp30) cc_final: 0.8071 (tm-30) REVERT: C 32 GLU cc_start: 0.8433 (tp30) cc_final: 0.8226 (tp30) REVERT: D 79 HIS cc_start: 0.8010 (OUTLIER) cc_final: 0.7039 (t70) REVERT: E 1 MET cc_start: 0.6907 (pmm) cc_final: 0.6522 (pmm) REVERT: E 61 ILE cc_start: 0.8764 (mt) cc_final: 0.8508 (tt) REVERT: F 72 MET cc_start: 0.7411 (ttm) cc_final: 0.6975 (tmm) REVERT: G 39 PHE cc_start: 0.7479 (t80) cc_final: 0.7158 (t80) REVERT: G 99 ASP cc_start: 0.8383 (m-30) cc_final: 0.7968 (p0) REVERT: H 647 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7620 (ptt90) REVERT: H 802 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8386 (mm) outliers start: 41 outliers final: 31 residues processed: 130 average time/residue: 0.0815 time to fit residues: 15.4923 Evaluate side-chains 133 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 99 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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 73 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 78 THR Chi-restraints excluded: chain E residue 82 LEU 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 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 45 LEU 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 775 VAL Chi-restraints excluded: chain H residue 798 ASP Chi-restraints excluded: chain H residue 802 LEU Chi-restraints excluded: chain H residue 812 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 23 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 87 optimal weight: 0.9980 chunk 4 optimal weight: 8.9990 chunk 42 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3833 r_free = 0.3833 target = 0.071976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.058230 restraints weight = 50151.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.059606 restraints weight = 28680.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.060498 restraints weight = 20150.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.061089 restraints weight = 16027.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.061443 restraints weight = 13798.760| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9932 Z= 0.188 Angle : 0.712 10.750 14146 Z= 0.401 Chirality : 0.042 0.261 1608 Planarity : 0.004 0.047 1241 Dihedral : 28.991 167.614 2785 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 5.01 % Allowed : 19.71 % 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: -0.50 (0.31), residues: 773 helix: 1.13 (0.28), residues: 326 sheet: -1.14 (0.39), residues: 165 loop : -1.51 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 100 TYR 0.012 0.001 TYR H 669 PHE 0.016 0.002 PHE F 55 TRP 0.010 0.001 TRP H 659 HIS 0.005 0.001 HIS F 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.19 ( 9932) covalent geometry : angle 0.71174 / 0.40 (14146) hydrogen bonds : bond 0.04890 / 5.65 ( 485) hydrogen bonds : angle 4.35905 / 6.05 ( 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 139 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 28 GLU cc_start: 0.8733 (tp30) cc_final: 0.8112 (tm-30) REVERT: C 32 GLU cc_start: 0.8471 (tp30) cc_final: 0.8267 (tp30) REVERT: D 29 MET cc_start: 0.7399 (mtp) cc_final: 0.6701 (mtt) REVERT: D 33 MET cc_start: 0.8738 (mpp) cc_final: 0.7451 (mpp) REVERT: D 79 HIS cc_start: 0.7832 (OUTLIER) cc_final: 0.6896 (t70) REVERT: E 61 ILE cc_start: 0.8759 (mt) cc_final: 0.8486 (tt) REVERT: E 95 ASP cc_start: 0.7894 (m-30) cc_final: 0.7693 (m-30) REVERT: F 72 MET cc_start: 0.7469 (ttm) cc_final: 0.6895 (tmm) REVERT: F 99 ASP cc_start: 0.7596 (t0) cc_final: 0.7364 (m-30) REVERT: G 39 PHE cc_start: 0.7471 (t80) cc_final: 0.7114 (t80) REVERT: G 99 ASP cc_start: 0.8451 (m-30) cc_final: 0.7997 (p0) REVERT: H 802 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8358 (mm) outliers start: 31 outliers final: 28 residues processed: 122 average time/residue: 0.0674 time to fit residues: 12.2262 Evaluate side-chains 137 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 78 THR Chi-restraints excluded: chain E residue 82 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 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 623 VAL Chi-restraints excluded: chain H residue 655 VAL Chi-restraints excluded: chain H residue 683 LEU Chi-restraints excluded: chain H residue 687 GLN 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 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: 0.8980 chunk 76 optimal weight: 0.0970 chunk 12 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 91 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 56 ASN G 31 ASN ** H 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.072236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.058562 restraints weight = 50093.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.059958 restraints weight = 28730.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.060851 restraints weight = 20034.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.061382 restraints weight = 15905.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.061783 restraints weight = 13762.553| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9932 Z= 0.171 Angle : 0.709 10.607 14146 Z= 0.397 Chirality : 0.042 0.259 1608 Planarity : 0.004 0.041 1241 Dihedral : 28.966 166.063 2785 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 5.17 % Allowed : 19.55 % 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: -0.39 (0.31), residues: 773 helix: 1.23 (0.28), residues: 326 sheet: -1.07 (0.40), residues: 165 loop : -1.46 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 32 TYR 0.011 0.001 TYR F 52 PHE 0.027 0.002 PHE G 111 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 0.00318 / 0.17 ( 9932) covalent geometry : angle 0.70882 / 0.40 (14146) hydrogen bonds : bond 0.04736 / 5.47 ( 485) hydrogen bonds : angle 4.26843 / 5.96 ( 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 139 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 107 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 28 GLU cc_start: 0.8719 (tp30) cc_final: 0.8107 (tm-30) REVERT: D 29 MET cc_start: 0.7623 (mtp) cc_final: 0.7153 (mtt) REVERT: D 33 MET cc_start: 0.8739 (mpp) cc_final: 0.7406 (mpp) REVERT: D 79 HIS cc_start: 0.7777 (OUTLIER) cc_final: 0.6895 (t70) REVERT: E 61 ILE cc_start: 0.8724 (mt) cc_final: 0.8445 (tt) REVERT: E 95 ASP cc_start: 0.7897 (m-30) cc_final: 0.7684 (m-30) REVERT: F 72 MET cc_start: 0.7442 (ttm) cc_final: 0.6969 (tmm) REVERT: F 99 ASP cc_start: 0.7605 (t0) cc_final: 0.7355 (m-30) REVERT: F 106 ILE cc_start: 0.7750 (mm) cc_final: 0.7462 (tt) REVERT: G 39 PHE cc_start: 0.7476 (t80) cc_final: 0.7114 (t80) REVERT: G 99 ASP cc_start: 0.8450 (m-30) cc_final: 0.8004 (p0) REVERT: H 802 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8332 (mm) outliers start: 32 outliers final: 29 residues processed: 122 average time/residue: 0.0618 time to fit residues: 11.3615 Evaluate side-chains 138 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 78 THR 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 62 TYR 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 31 ASN 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 683 LEU Chi-restraints excluded: chain H residue 687 GLN 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 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: 2.9990 chunk 77 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 17 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 chunk 15 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 chunk 75 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 31 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 = 0.3839 r_free = 0.3839 target = 0.072105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.058442 restraints weight = 50318.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.059796 restraints weight = 28865.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.060727 restraints weight = 20247.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.061308 restraints weight = 16045.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.061626 restraints weight = 13782.628| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3836 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= 0.181 Angle : 0.716 10.514 14146 Z= 0.400 Chirality : 0.042 0.255 1608 Planarity : 0.004 0.041 1241 Dihedral : 28.966 165.862 2785 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 5.33 % Allowed : 19.71 % Favored : 74.96 % 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: 1.20 (0.28), residues: 326 sheet: -1.10 (0.38), residues: 177 loop : -1.48 (0.39), residues: 270 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 0.013 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 0.00343 / 0.18 ( 9932) covalent geometry : angle 0.71623 / 0.40 (14146) hydrogen bonds : bond 0.04766 / 5.47 ( 485) hydrogen bonds : angle 4.29116 / 5.98 ( 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 139 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 28 GLU cc_start: 0.8710 (tp30) cc_final: 0.8096 (tm-30) REVERT: D 28 GLU cc_start: 0.7735 (tp30) cc_final: 0.7183 (tp30) REVERT: D 29 MET cc_start: 0.7566 (mtp) cc_final: 0.7200 (mtt) REVERT: D 33 MET cc_start: 0.8736 (mpp) cc_final: 0.7421 (mpp) REVERT: D 79 HIS cc_start: 0.7797 (OUTLIER) cc_final: 0.6922 (t70) REVERT: E 61 ILE cc_start: 0.8722 (mt) cc_final: 0.8437 (tt) REVERT: E 95 ASP cc_start: 0.7914 (m-30) cc_final: 0.7699 (m-30) REVERT: F 72 MET cc_start: 0.7462 (ttm) cc_final: 0.6966 (tmm) REVERT: F 99 ASP cc_start: 0.7649 (t0) cc_final: 0.7373 (m-30) REVERT: F 106 ILE cc_start: 0.7773 (mm) cc_final: 0.7489 (tt) REVERT: G 39 PHE cc_start: 0.7491 (t80) cc_final: 0.7125 (t80) REVERT: H 647 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7556 (ptt90) REVERT: H 802 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8376 (mm) outliers start: 33 outliers final: 28 residues processed: 123 average time/residue: 0.0738 time to fit residues: 13.4856 Evaluate side-chains 137 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 106 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 78 THR 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 62 TYR 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 687 GLN 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 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: 9.9990 chunk 32 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 41 optimal weight: 0.1980 chunk 63 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 31 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 = 0.3751 r_free = 0.3751 target = 0.069891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.056245 restraints weight = 49372.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.057650 restraints weight = 27540.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.058581 restraints weight = 18716.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.059166 restraints weight = 14563.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.059570 restraints weight = 12347.736| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9932 Z= 0.203 Angle : 0.740 10.298 14146 Z= 0.411 Chirality : 0.043 0.243 1608 Planarity : 0.004 0.040 1241 Dihedral : 29.020 166.338 2785 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.52 % Allowed : 20.68 % Favored : 74.80 % 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: -0.61 (0.30), residues: 773 helix: 1.03 (0.28), residues: 327 sheet: -1.15 (0.38), residues: 177 loop : -1.58 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 100 TYR 0.011 0.001 TYR F 52 PHE 0.017 0.002 PHE C 49 TRP 0.011 0.002 TRP H 659 HIS 0.005 0.001 HIS E 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.20 ( 9932) covalent geometry : angle 0.73990 / 0.41 (14146) hydrogen bonds : bond 0.05128 / 5.81 ( 485) hydrogen bonds : angle 4.36366 / 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 133 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 28 GLU cc_start: 0.8761 (tp30) cc_final: 0.8112 (tm-30) REVERT: C 32 GLU cc_start: 0.8522 (tp30) cc_final: 0.8301 (tp30) REVERT: D 28 GLU cc_start: 0.7678 (tp30) cc_final: 0.7176 (tp30) REVERT: D 69 LYS cc_start: 0.7818 (tmtt) cc_final: 0.7613 (tptt) REVERT: D 79 HIS cc_start: 0.7793 (OUTLIER) cc_final: 0.6959 (t70) REVERT: E 61 ILE cc_start: 0.8746 (mt) cc_final: 0.8453 (tt) REVERT: E 95 ASP cc_start: 0.7889 (m-30) cc_final: 0.7666 (m-30) REVERT: F 72 MET cc_start: 0.7511 (ttm) cc_final: 0.6907 (tmm) REVERT: F 83 ILE cc_start: 0.6501 (mm) cc_final: 0.6288 (mm) REVERT: F 99 ASP cc_start: 0.7706 (t0) cc_final: 0.7413 (m-30) REVERT: F 106 ILE cc_start: 0.7803 (mm) cc_final: 0.7516 (tt) REVERT: G 39 PHE cc_start: 0.7534 (t80) cc_final: 0.7148 (t80) REVERT: G 99 ASP cc_start: 0.8461 (m-30) cc_final: 0.8002 (p0) REVERT: H 647 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7628 (ptt90) REVERT: H 802 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8060 (mt) outliers start: 28 outliers final: 25 residues processed: 122 average time/residue: 0.0762 time to fit residues: 13.6702 Evaluate side-chains 132 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 647 ARG Chi-restraints excluded: chain H residue 655 VAL Chi-restraints excluded: chain H residue 683 LEU Chi-restraints excluded: chain H residue 687 GLN 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 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: 4.9990 chunk 88 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 736 GLN ** H 830 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 = 0.3720 r_free = 0.3720 target = 0.068629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.055130 restraints weight = 49429.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.056496 restraints weight = 27866.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.057345 restraints weight = 19116.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.057940 restraints weight = 15009.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.058290 restraints weight = 12740.325| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9932 Z= 0.259 Angle : 0.794 8.705 14146 Z= 0.438 Chirality : 0.045 0.230 1608 Planarity : 0.005 0.041 1241 Dihedral : 29.173 167.689 2785 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % 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: -1.05 (0.29), residues: 773 helix: 0.67 (0.27), residues: 328 sheet: -1.45 (0.38), residues: 170 loop : -1.76 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 100 TYR 0.013 0.001 TYR H 669 PHE 0.026 0.003 PHE C 49 TRP 0.014 0.002 TRP H 774 HIS 0.006 0.002 HIS F 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.26 ( 9932) covalent geometry : angle 0.79402 / 0.44 (14146) hydrogen bonds : bond 0.06015 / 6.71 ( 485) hydrogen bonds : angle 4.57536 / 6.39 ( 1230) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1573.44 seconds wall clock time: 27 minutes 51.72 seconds (1671.72 seconds total)