Starting phenix.real_space_refine on Wed Jun 18 15:32:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ruq_19514/06_2025/8ruq_19514.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ruq_19514/06_2025/8ruq_19514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ruq_19514/06_2025/8ruq_19514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ruq_19514/06_2025/8ruq_19514.map" model { file = "/net/cci-nas-00/data/ceres_data/8ruq_19514/06_2025/8ruq_19514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ruq_19514/06_2025/8ruq_19514.cif" } resolution = 2.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.004 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 35 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 293 5.49 5 S 12 5.16 5 C 6715 2.51 5 N 2289 2.21 5 O 2838 1.98 5 H 9671 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21818 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1634 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1303 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1676 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1472 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "E" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1622 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1303 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1691 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1444 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 4679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 4679 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 4632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 4632 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "L" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 362 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 1, 'TRANS': 20} Time building chain proxies: 11.59, per 1000 atoms: 0.53 Number of scatterers: 21818 At special positions: 0 Unit cell: (78.02, 129.48, 123.67, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 12 16.00 P 293 15.00 O 2838 8.00 N 2289 7.00 C 6715 6.00 H 9671 1.00 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: 6.25 Conformation dependent library (CDL) restraints added in 1.2 seconds 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1474 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 10 sheets defined 72.1% alpha, 3.1% beta 147 base pairs and 267 stacking pairs defined. Time for finding SS restraints: 11.90 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.518A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.702A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.537A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.978A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.558A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.623A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.501A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.939A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.679A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.665A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 23 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.009A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.176A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.767A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.913A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.158A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 413 hydrogen bonds defined for protein. 1212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 377 hydrogen bonds 754 hydrogen bond angles 0 basepair planarities 147 basepair parallelities 267 stacking parallelities Total time for adding SS restraints: 9.13 Time building geometry restraints manager: 7.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9669 1.03 - 1.22: 108 1.22 - 1.42: 5673 1.42 - 1.61: 7158 1.61 - 1.80: 23 Bond restraints: 22631 Sorted by residual: bond pdb=" C3' DG I 36 " pdb=" O3' DG I 36 " ideal model delta sigma weight residual 1.422 1.463 -0.041 3.00e-02 1.11e+03 1.88e+00 bond pdb=" C3' DG I 38 " pdb=" C2' DG I 38 " ideal model delta sigma weight residual 1.525 1.506 0.019 2.00e-02 2.50e+03 9.09e-01 bond pdb=" C4' DC I 47 " pdb=" C3' DC I 47 " ideal model delta sigma weight residual 1.523 1.505 0.018 2.00e-02 2.50e+03 7.94e-01 bond pdb=" C4' DC I 48 " pdb=" C3' DC I 48 " ideal model delta sigma weight residual 1.523 1.505 0.018 2.00e-02 2.50e+03 7.84e-01 bond pdb=" C2' DA I 89 " pdb=" C1' DA I 89 " ideal model delta sigma weight residual 1.525 1.507 0.018 2.00e-02 2.50e+03 7.76e-01 ... (remaining 22626 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 37609 1.23 - 2.46: 3242 2.46 - 3.69: 133 3.69 - 4.91: 10 4.91 - 6.14: 2 Bond angle restraints: 40996 Sorted by residual: angle pdb=" C3' DG I 36 " pdb=" O3' DG I 36 " pdb=" P DG I 37 " ideal model delta sigma weight residual 120.20 123.66 -3.46 1.50e+00 4.44e-01 5.33e+00 angle pdb=" C3' DG I 36 " pdb=" C2' DG I 36 " pdb=" C1' DG I 36 " ideal model delta sigma weight residual 101.60 104.96 -3.36 1.50e+00 4.44e-01 5.03e+00 angle pdb=" C3' DC I 122 " pdb=" C2' DC I 122 " pdb=" C1' DC I 122 " ideal model delta sigma weight residual 101.60 104.85 -3.25 1.50e+00 4.44e-01 4.71e+00 angle pdb=" C2' DC I 47 " pdb=" C1' DC I 47 " pdb=" N1 DC I 47 " ideal model delta sigma weight residual 113.50 116.71 -3.21 1.50e+00 4.44e-01 4.58e+00 angle pdb=" CG LYS D 57 " pdb=" CD LYS D 57 " pdb=" CE LYS D 57 " ideal model delta sigma weight residual 111.30 116.16 -4.86 2.30e+00 1.89e-01 4.47e+00 ... (remaining 40991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.88: 7681 33.88 - 67.75: 1712 67.75 - 101.63: 20 101.63 - 135.50: 0 135.50 - 169.38: 1 Dihedral angle restraints: 9414 sinusoidal: 6877 harmonic: 2537 Sorted by residual: dihedral pdb=" C4' DG I 36 " pdb=" C3' DG I 36 " pdb=" O3' DG I 36 " pdb=" P DG I 37 " ideal model delta sinusoidal sigma weight residual 220.00 50.62 169.38 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" CG ARG A 52 " pdb=" CD ARG A 52 " pdb=" NE ARG A 52 " pdb=" CZ ARG A 52 " ideal model delta sinusoidal sigma weight residual 180.00 136.33 43.67 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" CB GLU H 76 " pdb=" CG GLU H 76 " pdb=" CD GLU H 76 " pdb=" OE1 GLU H 76 " ideal model delta sinusoidal sigma weight residual 0.00 85.31 -85.31 1 3.00e+01 1.11e-03 9.79e+00 ... (remaining 9411 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1178 0.025 - 0.050: 539 0.050 - 0.075: 273 0.075 - 0.100: 118 0.100 - 0.125: 44 Chirality restraints: 2152 Sorted by residual: chirality pdb=" CA ILE F 29 " pdb=" N ILE F 29 " pdb=" C ILE F 29 " pdb=" CB ILE F 29 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" C3' DA J 206 " pdb=" C4' DA J 206 " pdb=" O3' DA J 206 " pdb=" C2' DA J 206 " both_signs ideal model delta sigma weight residual False -2.66 -2.54 -0.12 2.00e-01 2.50e+01 3.60e-01 chirality pdb=" CA ILE C 111 " pdb=" N ILE C 111 " pdb=" C ILE C 111 " pdb=" CB ILE C 111 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.58e-01 ... (remaining 2149 not shown) Planarity restraints: 2337 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT I 87 " 0.025 2.00e-02 2.50e+03 1.06e-02 3.38e+00 pdb=" N1 DT I 87 " -0.025 2.00e-02 2.50e+03 pdb=" C2 DT I 87 " -0.004 2.00e-02 2.50e+03 pdb=" O2 DT I 87 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DT I 87 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DT I 87 " 0.001 2.00e-02 2.50e+03 pdb=" O4 DT I 87 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DT I 87 " 0.001 2.00e-02 2.50e+03 pdb=" C7 DT I 87 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DT I 87 " -0.002 2.00e-02 2.50e+03 pdb=" H3 DT I 87 " 0.003 2.00e-02 2.50e+03 pdb=" H6 DT I 87 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 120 " -0.025 2.00e-02 2.50e+03 1.01e-02 3.30e+00 pdb=" N9 DA I 120 " 0.025 2.00e-02 2.50e+03 pdb=" C8 DA I 120 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA I 120 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DA I 120 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DA I 120 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA I 120 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DA I 120 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA I 120 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DA I 120 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DA I 120 " 0.002 2.00e-02 2.50e+03 pdb=" H8 DA I 120 " 0.000 2.00e-02 2.50e+03 pdb=" H2 DA I 120 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 99 " -0.024 2.00e-02 2.50e+03 9.94e-03 3.21e+00 pdb=" N9 DA I 99 " 0.025 2.00e-02 2.50e+03 pdb=" C8 DA I 99 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DA I 99 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 99 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DA I 99 " -0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 99 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DA I 99 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA I 99 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DA I 99 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DA I 99 " 0.002 2.00e-02 2.50e+03 pdb=" H8 DA I 99 " 0.001 2.00e-02 2.50e+03 pdb=" H2 DA I 99 " 0.003 2.00e-02 2.50e+03 ... (remaining 2334 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.05: 195 2.05 - 2.69: 27770 2.69 - 3.33: 56544 3.33 - 3.96: 80966 3.96 - 4.60: 124126 Nonbonded interactions: 289601 Sorted by model distance: nonbonded pdb=" OE1 GLU G 91 " pdb=" H GLU G 91 " model vdw 1.413 2.450 nonbonded pdb=" OE1 GLU A 59 " pdb=" H GLU A 59 " model vdw 1.503 2.450 nonbonded pdb=" OE1 GLU E 59 " pdb=" H GLU E 59 " model vdw 1.665 2.450 nonbonded pdb=" OE1 GLU G 92 " pdb="HH11 ARG L 9 " model vdw 1.666 2.450 nonbonded pdb=" HG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 1.699 2.450 ... (remaining 289596 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 37 and (name N or name CA or name C or name O or name CB \ or name HA )) or resid 38 through 76 or (resid 77 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 78 through 80 or (resid \ 81 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 82 through 134)) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 11 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 42 through 118)) selection = (chain 'G' and (resid 11 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 75 through 90 or (resid \ 91 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 92 through 118)) } ncs_group { reference = (chain 'D' and (resid 31 through 50 or (resid 51 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 52 through 56 or (resid \ 57 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 58 through 70 or (resid 71 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 72 through 125)) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.340 Extract box with map and model: 0.970 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 58.890 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.070 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:13.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 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 : 0.004 0.041 12960 Z= 0.206 Angle : 0.574 6.142 18779 Z= 0.356 Chirality : 0.039 0.125 2152 Planarity : 0.004 0.041 1358 Dihedral : 28.426 169.376 5559 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.64 % Allowed : 16.88 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.96 (0.30), residues: 766 helix: 2.97 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.87 (0.35), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 75 PHE 0.007 0.001 PHE F 61 TYR 0.008 0.001 TYR B 51 ARG 0.003 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.10466 ( 790) hydrogen bonds : angle 3.38092 ( 1966) covalent geometry : bond 0.00447 (12960) covalent geometry : angle 0.57379 (18779) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Evaluate side-chains 80 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 1.383 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 80 average time/residue: 4.0708 time to fit residues: 344.1118 Evaluate side-chains 76 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 49 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.055089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.043277 restraints weight = 77995.348| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 1.29 r_work: 0.2641 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2518 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.0392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12960 Z= 0.183 Angle : 0.574 4.458 18779 Z= 0.358 Chirality : 0.038 0.132 2152 Planarity : 0.004 0.041 1358 Dihedral : 30.662 169.232 4085 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.96 % Allowed : 16.56 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.96 (0.30), residues: 766 helix: 2.92 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.84 (0.35), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 75 PHE 0.006 0.001 PHE F 61 TYR 0.007 0.001 TYR B 51 ARG 0.003 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.05305 ( 790) hydrogen bonds : angle 3.03151 ( 1966) covalent geometry : bond 0.00392 (12960) covalent geometry : angle 0.57444 (18779) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Evaluate side-chains 84 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 1.411 Fit side-chains REVERT: A 133 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8555 (pt0) REVERT: C 95 LYS cc_start: 0.9412 (OUTLIER) cc_final: 0.9123 (ttpt) outliers start: 6 outliers final: 3 residues processed: 82 average time/residue: 4.0442 time to fit residues: 352.0408 Evaluate side-chains 80 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain L residue 8 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 62 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.054685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.042818 restraints weight = 77433.240| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 1.27 r_work: 0.2630 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2508 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.0526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12960 Z= 0.229 Angle : 0.574 4.485 18779 Z= 0.358 Chirality : 0.041 0.126 2152 Planarity : 0.004 0.043 1358 Dihedral : 30.559 168.869 4083 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.64 % Allowed : 16.56 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.04 (0.30), residues: 766 helix: 3.00 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.88 (0.36), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.007 0.001 PHE F 61 TYR 0.008 0.001 TYR B 51 ARG 0.004 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.05320 ( 790) hydrogen bonds : angle 2.88601 ( 1966) covalent geometry : bond 0.00501 (12960) covalent geometry : angle 0.57373 (18779) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Evaluate side-chains 79 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 1.353 Fit side-chains REVERT: C 95 LYS cc_start: 0.9406 (OUTLIER) cc_final: 0.9114 (ttpt) outliers start: 4 outliers final: 2 residues processed: 78 average time/residue: 4.0083 time to fit residues: 330.3895 Evaluate side-chains 75 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 88 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.054797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.042763 restraints weight = 78481.123| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 1.30 r_work: 0.2628 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2505 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.0553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12960 Z= 0.216 Angle : 0.577 8.149 18779 Z= 0.358 Chirality : 0.040 0.126 2152 Planarity : 0.004 0.041 1358 Dihedral : 30.561 168.847 4083 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.80 % Allowed : 16.56 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.04 (0.30), residues: 766 helix: 3.01 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.89 (0.36), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.007 0.001 PHE F 61 TYR 0.008 0.001 TYR B 51 ARG 0.004 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.05211 ( 790) hydrogen bonds : angle 2.88061 ( 1966) covalent geometry : bond 0.00470 (12960) covalent geometry : angle 0.57698 (18779) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Evaluate side-chains 78 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 1.447 Fit side-chains REVERT: C 95 LYS cc_start: 0.9406 (OUTLIER) cc_final: 0.9114 (ttpt) outliers start: 5 outliers final: 4 residues processed: 76 average time/residue: 4.4934 time to fit residues: 364.8356 Evaluate side-chains 77 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain L residue 8 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 17 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.053801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.041806 restraints weight = 78534.104| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 1.30 r_work: 0.2587 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2465 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.0697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 12960 Z= 0.311 Angle : 0.603 4.913 18779 Z= 0.374 Chirality : 0.045 0.141 2152 Planarity : 0.005 0.041 1358 Dihedral : 30.584 170.075 4082 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.11 % Allowed : 15.92 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.30), residues: 766 helix: 2.86 (0.21), residues: 556 sheet: None (None), residues: 0 loop : -1.00 (0.35), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 31 PHE 0.008 0.001 PHE H 65 TYR 0.009 0.001 TYR B 51 ARG 0.003 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.06213 ( 790) hydrogen bonds : angle 2.99826 ( 1966) covalent geometry : bond 0.00687 (12960) covalent geometry : angle 0.60317 (18779) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Evaluate side-chains 80 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 1.371 Fit side-chains REVERT: A 59 GLU cc_start: 0.8674 (pm20) cc_final: 0.8442 (pm20) REVERT: A 131 ARG cc_start: 0.9259 (OUTLIER) cc_final: 0.8523 (mtp85) REVERT: C 95 LYS cc_start: 0.9412 (OUTLIER) cc_final: 0.9144 (ttpp) outliers start: 7 outliers final: 5 residues processed: 78 average time/residue: 3.9937 time to fit residues: 328.7016 Evaluate side-chains 78 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain L residue 8 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 78 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.054329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.042359 restraints weight = 77791.883| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 1.28 r_work: 0.2608 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2486 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.0694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12960 Z= 0.188 Angle : 0.591 8.854 18779 Z= 0.367 Chirality : 0.038 0.125 2152 Planarity : 0.004 0.043 1358 Dihedral : 30.615 169.803 4082 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.96 % Allowed : 16.40 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.79 (0.30), residues: 766 helix: 2.82 (0.21), residues: 556 sheet: None (None), residues: 0 loop : -0.98 (0.35), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.006 0.001 PHE F 61 TYR 0.009 0.001 TYR B 51 ARG 0.005 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.05736 ( 790) hydrogen bonds : angle 2.98130 ( 1966) covalent geometry : bond 0.00400 (12960) covalent geometry : angle 0.59145 (18779) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Evaluate side-chains 82 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 1.261 Fit side-chains REVERT: A 59 GLU cc_start: 0.8666 (pm20) cc_final: 0.8393 (pm20) REVERT: A 131 ARG cc_start: 0.9243 (OUTLIER) cc_final: 0.8462 (mtp85) REVERT: C 95 LYS cc_start: 0.9408 (OUTLIER) cc_final: 0.9136 (ttpp) outliers start: 6 outliers final: 4 residues processed: 80 average time/residue: 3.9987 time to fit residues: 337.1242 Evaluate side-chains 78 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain L residue 8 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 12 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.054298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.042191 restraints weight = 78387.223| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 1.29 r_work: 0.2605 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2483 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.0687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12960 Z= 0.244 Angle : 0.592 8.596 18779 Z= 0.365 Chirality : 0.042 0.129 2152 Planarity : 0.004 0.044 1358 Dihedral : 30.595 169.710 4082 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.96 % Allowed : 15.92 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.30), residues: 766 helix: 2.90 (0.21), residues: 556 sheet: None (None), residues: 0 loop : -0.97 (0.35), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.006 0.001 PHE F 61 TYR 0.009 0.001 TYR B 51 ARG 0.004 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.05566 ( 790) hydrogen bonds : angle 2.95469 ( 1966) covalent geometry : bond 0.00537 (12960) covalent geometry : angle 0.59152 (18779) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Evaluate side-chains 80 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 1.401 Fit side-chains REVERT: A 59 GLU cc_start: 0.8678 (pm20) cc_final: 0.8393 (pm20) REVERT: A 131 ARG cc_start: 0.9253 (OUTLIER) cc_final: 0.8475 (mtp85) REVERT: C 95 LYS cc_start: 0.9414 (OUTLIER) cc_final: 0.9146 (ttpp) outliers start: 6 outliers final: 4 residues processed: 79 average time/residue: 3.9744 time to fit residues: 331.3016 Evaluate side-chains 79 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 67 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.054343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.042268 restraints weight = 78234.020| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 1.28 r_work: 0.2608 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2486 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.0699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12960 Z= 0.243 Angle : 0.592 9.305 18779 Z= 0.366 Chirality : 0.041 0.125 2152 Planarity : 0.004 0.044 1358 Dihedral : 30.590 169.584 4082 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.11 % Allowed : 15.92 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.91 (0.30), residues: 766 helix: 2.92 (0.21), residues: 556 sheet: None (None), residues: 0 loop : -0.97 (0.35), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.007 0.001 PHE F 61 TYR 0.009 0.001 TYR B 51 ARG 0.006 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.05534 ( 790) hydrogen bonds : angle 2.94076 ( 1966) covalent geometry : bond 0.00534 (12960) covalent geometry : angle 0.59214 (18779) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Evaluate side-chains 80 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 1.358 Fit side-chains REVERT: A 131 ARG cc_start: 0.9251 (OUTLIER) cc_final: 0.8476 (mtp85) REVERT: C 95 LYS cc_start: 0.9412 (OUTLIER) cc_final: 0.9144 (ttpp) outliers start: 7 outliers final: 5 residues processed: 78 average time/residue: 4.0778 time to fit residues: 337.5647 Evaluate side-chains 79 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain L residue 8 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 9 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.054404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.042326 restraints weight = 78330.893| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 1.29 r_work: 0.2609 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2489 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.0698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12960 Z= 0.231 Angle : 0.592 9.539 18779 Z= 0.365 Chirality : 0.041 0.124 2152 Planarity : 0.004 0.042 1358 Dihedral : 30.591 169.543 4082 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.11 % Allowed : 15.92 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.30), residues: 766 helix: 2.91 (0.21), residues: 556 sheet: None (None), residues: 0 loop : -0.96 (0.35), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.007 0.001 PHE F 61 TYR 0.009 0.001 TYR B 51 ARG 0.005 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.05486 ( 790) hydrogen bonds : angle 2.93748 ( 1966) covalent geometry : bond 0.00506 (12960) covalent geometry : angle 0.59165 (18779) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Evaluate side-chains 79 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 1.397 Fit side-chains REVERT: A 131 ARG cc_start: 0.9251 (OUTLIER) cc_final: 0.8473 (mtp85) REVERT: C 95 LYS cc_start: 0.9414 (OUTLIER) cc_final: 0.9146 (ttpp) outliers start: 7 outliers final: 5 residues processed: 77 average time/residue: 4.0234 time to fit residues: 327.2838 Evaluate side-chains 79 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain L residue 8 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 56 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.054555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.042530 restraints weight = 77983.635| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 1.27 r_work: 0.2614 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2493 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.0698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12960 Z= 0.191 Angle : 0.589 9.652 18779 Z= 0.363 Chirality : 0.039 0.125 2152 Planarity : 0.004 0.042 1358 Dihedral : 30.597 169.411 4082 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.11 % Allowed : 16.08 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.30), residues: 766 helix: 2.91 (0.21), residues: 556 sheet: None (None), residues: 0 loop : -0.95 (0.35), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.006 0.001 PHE F 61 TYR 0.009 0.001 TYR B 51 ARG 0.007 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.05386 ( 790) hydrogen bonds : angle 2.93652 ( 1966) covalent geometry : bond 0.00414 (12960) covalent geometry : angle 0.58943 (18779) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Evaluate side-chains 79 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 1.292 Fit side-chains REVERT: A 131 ARG cc_start: 0.9246 (OUTLIER) cc_final: 0.8466 (mtp85) REVERT: C 95 LYS cc_start: 0.9414 (OUTLIER) cc_final: 0.9115 (ttpt) outliers start: 7 outliers final: 5 residues processed: 77 average time/residue: 4.7535 time to fit residues: 386.6852 Evaluate side-chains 79 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain L residue 8 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 87 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 19 optimal weight: 0.0970 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.054529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.042602 restraints weight = 78433.211| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 1.27 r_work: 0.2617 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2497 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.0702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12960 Z= 0.211 Angle : 0.588 9.706 18779 Z= 0.363 Chirality : 0.039 0.125 2152 Planarity : 0.004 0.043 1358 Dihedral : 30.595 169.459 4082 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.11 % Allowed : 15.92 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.30), residues: 766 helix: 2.93 (0.21), residues: 556 sheet: None (None), residues: 0 loop : -0.94 (0.35), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.006 0.001 PHE F 61 TYR 0.009 0.001 TYR B 51 ARG 0.007 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.05347 ( 790) hydrogen bonds : angle 2.92799 ( 1966) covalent geometry : bond 0.00459 (12960) covalent geometry : angle 0.58755 (18779) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17641.36 seconds wall clock time: 303 minutes 47.64 seconds (18227.64 seconds total)