Starting phenix.real_space_refine on Wed Aug 5 20:41:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lrv_63344/08_2026/9lrv_63344.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lrv_63344/08_2026/9lrv_63344.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lrv_63344/08_2026/9lrv_63344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lrv_63344/08_2026/9lrv_63344.map" model { file = "/net/cci-nas-00/data/ceres_data/9lrv_63344/08_2026/9lrv_63344.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lrv_63344/08_2026/9lrv_63344.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.023 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 287 5.49 5 S 10 5.16 5 C 6416 2.51 5 N 2179 2.21 5 O 2753 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 11645 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 737 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 1, 'TRANS': 94} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 623 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 796 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 723 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 785 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 97} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "F" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 631 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 721 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 92} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 728 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 91} 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: "I" Number of atoms: 2928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2928 Classifications: {'DNA': 144} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 143} Chain: "J" Number of atoms: 2973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2973 Classifications: {'DNA': 144} Link IDs: {'rna3p': 143} Time building chain proxies: 2.17, per 1000 atoms: 0.19 Number of scatterers: 11645 At special positions: 0 Unit cell: (78.11, 117.7, 116.63, 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 10 16.00 P 287 15.00 O 2753 8.00 N 2179 7.00 C 6416 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: 0.84 Conformation dependent library (CDL) restraints added in 231.1 milliseconds 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1398 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 8 sheets defined 74.5% alpha, 2.4% beta 94 base pairs and 245 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 25 through 38 Processing helix chain 'A' and resid 44 through 61 Processing helix chain 'A' and resid 72 through 101 Processing helix chain 'A' and resid 107 through 119 removed outlier: 3.683A pdb=" N MET A 111 " --> pdb=" O MET A 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 30 Processing helix chain 'B' and resid 31 through 43 Processing helix chain 'B' and resid 49 through 77 removed outlier: 4.413A pdb=" N GLU B 53 " --> pdb=" O ALA B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 94 removed outlier: 3.625A pdb=" N VAL B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 23 Processing helix chain 'C' and resid 28 through 38 Processing helix chain 'C' and resid 47 through 75 removed outlier: 4.358A pdb=" N VAL C 51 " --> pdb=" O ALA C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 91 Processing helix chain 'C' and resid 92 through 99 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 122 removed outlier: 3.542A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 38 Processing helix chain 'E' and resid 44 through 62 removed outlier: 3.528A pdb=" N PHE E 48 " --> pdb=" O GLN E 44 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASN E 62 " --> pdb=" O GLU E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 101 removed outlier: 3.678A pdb=" N CYS E 97 " --> pdb=" O ASP E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 119 Processing helix chain 'F' and resid 25 through 30 Processing helix chain 'F' and resid 31 through 42 Processing helix chain 'F' and resid 49 through 77 removed outlier: 4.454A pdb=" N GLU F 53 " --> pdb=" O ALA F 49 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP F 69 " --> pdb=" O ASN F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 removed outlier: 3.658A pdb=" N VAL F 87 " --> pdb=" O THR F 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 24 Processing helix chain 'G' and resid 28 through 38 Processing helix chain 'G' and resid 47 through 75 removed outlier: 4.323A pdb=" N VAL G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 92 Processing helix chain 'G' and resid 92 through 99 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.593A pdb=" N MET H 59 " --> pdb=" O SER H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 removed outlier: 3.523A pdb=" N ALA H 107 " --> pdb=" O PRO H 103 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER H 124 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 71 removed outlier: 7.423A pdb=" N ARG A 70 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 105 through 106 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AA4, first strand: chain 'C' and resid 79 through 80 Processing sheet with id=AA5, first strand: chain 'C' and resid 103 through 104 removed outlier: 6.804A pdb=" N THR C 103 " --> pdb=" O TYR F 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 70 through 71 removed outlier: 6.937A pdb=" N ARG E 70 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 105 through 106 Processing sheet with id=AA8, first strand: chain 'G' and resid 44 through 45 removed outlier: 7.254A pdb=" N ARG G 44 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 408 hydrogen bonds defined for protein. 1209 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 235 hydrogen bonds 470 hydrogen bond angles 0 basepair planarities 94 basepair parallelities 245 stacking parallelities Total time for adding SS restraints: 2.12 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2100 1.33 - 1.45: 4125 1.45 - 1.57: 5624 1.57 - 1.69: 573 1.69 - 1.80: 16 Bond restraints: 12438 Sorted by residual: bond pdb=" C3' DC I 4 " pdb=" C2' DC I 4 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DT J -17 " pdb=" C2' DT J -17 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DA I 65 " pdb=" C2' DA I 65 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DC I 19 " pdb=" C2' DC I 19 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.43e+00 bond pdb=" C3' DC J 19 " pdb=" C2' DC J 19 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.43e+00 ... (remaining 12433 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 16020 1.08 - 2.15: 1582 2.15 - 3.23: 438 3.23 - 4.30: 15 4.30 - 5.38: 6 Bond angle restraints: 18061 Sorted by residual: angle pdb=" N3 DT J -23 " pdb=" C4 DT J -23 " pdb=" O4 DT J -23 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" N3 DT I -42 " pdb=" C4 DT I -42 " pdb=" O4 DT I -42 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT I -16 " pdb=" C4 DT I -16 " pdb=" O4 DT I -16 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+01 angle pdb=" N3 DT I -17 " pdb=" C4 DT I -17 " pdb=" O4 DT I -17 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 angle pdb=" N3 DT J -61 " pdb=" C4 DT J -61 " pdb=" O4 DT J -61 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 ... (remaining 18056 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.68: 5332 34.68 - 69.35: 1337 69.35 - 104.03: 26 104.03 - 138.71: 1 138.71 - 173.39: 1 Dihedral angle restraints: 6697 sinusoidal: 4538 harmonic: 2159 Sorted by residual: dihedral pdb=" CA LYS B 80 " pdb=" C LYS B 80 " pdb=" N THR B 81 " pdb=" CA THR B 81 " ideal model delta harmonic sigma weight residual 180.00 160.22 19.78 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual -140.00 33.39 -173.39 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DC J 34 " pdb=" C3' DC J 34 " pdb=" O3' DC J 34 " pdb=" P DT J 35 " ideal model delta sinusoidal sigma weight residual 220.00 86.28 133.72 1 3.50e+01 8.16e-04 1.33e+01 ... (remaining 6694 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1494 0.044 - 0.088: 485 0.088 - 0.133: 94 0.133 - 0.177: 2 0.177 - 0.221: 1 Chirality restraints: 2076 Sorted by residual: chirality pdb=" CB ILE A 106 " pdb=" CA ILE A 106 " pdb=" CG1 ILE A 106 " pdb=" CG2 ILE A 106 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA LEU D 80 " pdb=" N LEU D 80 " pdb=" C LEU D 80 " pdb=" CB LEU D 80 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 5.15e-01 chirality pdb=" C3' DT J -17 " pdb=" C4' DT J -17 " pdb=" O3' DT J -17 " pdb=" C2' DT J -17 " both_signs ideal model delta sigma weight residual False -2.73 -2.60 -0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 2073 not shown) Planarity restraints: 1287 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG E 23 " -0.023 5.00e-02 4.00e+02 3.60e-02 2.07e+00 pdb=" N PRO E 24 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO E 24 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 24 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 32 " 0.022 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO F 33 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO F 33 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO F 33 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 32 " -0.017 2.00e-02 2.50e+03 8.06e-03 1.79e+00 pdb=" N9 DA I 32 " 0.019 2.00e-02 2.50e+03 pdb=" C8 DA I 32 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA I 32 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DA I 32 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DA I 32 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA I 32 " -0.003 2.00e-02 2.50e+03 pdb=" N1 DA I 32 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 32 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DA I 32 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DA I 32 " 0.001 2.00e-02 2.50e+03 ... (remaining 1284 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1579 2.76 - 3.29: 10269 3.29 - 3.83: 22475 3.83 - 4.36: 27786 4.36 - 4.90: 39567 Nonbonded interactions: 101676 Sorted by model distance: nonbonded pdb=" O2 DC I -64 " pdb=" N2 DG J 64 " model vdw 2.223 3.120 nonbonded pdb=" OG1 THR B 74 " pdb=" OD2 ASP B 86 " model vdw 2.265 3.040 nonbonded pdb=" OG1 THR F 74 " pdb=" OD2 ASP F 86 " model vdw 2.296 3.040 nonbonded pdb=" O HIS B 76 " pdb=" NH2 ARG D 92 " model vdw 2.302 3.120 nonbonded pdb=" OD2 ASP F 69 " pdb=" NE2 GLN F 94 " model vdw 2.305 3.120 ... (remaining 101671 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' selection = (chain 'E' and ((resid 24 and (name N or name CA or name C or name O or name CB \ )) or resid 25 through 36 or (resid 37 and (name N or name CA or name C or name \ O or name CB )) or resid 38 through 39 or (resid 40 and (name N or name CA or na \ me C or name O or name CB )) or resid 41 through 57 or (resid 58 and (name N or \ name CA or name C or name O or name CB )) or resid 59 or (resid 60 through 67 an \ d (name N or name CA or name C or name O or name CB )) or resid 68 through 80 or \ (resid 81 through 83 and (name N or name CA or name C or name O or name CB )) o \ r resid 84 through 119)) } ncs_group { reference = chain 'B' selection = (chain 'F' and ((resid 25 and (name N or name CA or name C or name O or name CB \ )) or resid 26 through 102)) } ncs_group { reference = (chain 'C' and (resid 15 through 16 or (resid 17 and (name N or name CA or name \ C or name O or name CB )) or resid 18 through 92 or (resid 93 and (name N or nam \ e CA or name C or name O or name CB )) or resid 94 through 100 or (resid 101 and \ (name N or name CA or name C or name O or name CB )) or resid 102 through 111)) \ selection = chain 'G' } ncs_group { reference = (chain 'D' and (resid 31 through 70 or (resid 71 and (name N or name CA or name \ C or name O or name CB )) or resid 72 through 123)) selection = (chain 'H' and ((resid 31 through 32 and (name N or name CA or name C or name O \ or name CB )) or resid 33 through 123)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.590 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 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 0.054 12438 Z= 0.512 Angle : 0.701 5.375 18061 Z= 0.628 Chirality : 0.043 0.221 2076 Planarity : 0.004 0.039 1287 Dihedral : 28.128 173.387 5299 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.55 (0.30), residues: 726 helix: 1.74 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -1.12 (0.39), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 37 TYR 0.021 0.002 TYR B 89 PHE 0.008 0.001 PHE B 62 TRP 0.003 0.001 TRP A 71 HIS 0.004 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.51 (12438) covalent geometry : angle 0.70130 / 0.63 (18061) hydrogen bonds : bond 0.21453 / 15.08 ( 643) hydrogen bonds : angle 7.08508 / 5.16 ( 1679) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.221 Fit side-chains REVERT: D 76 GLU cc_start: 0.6780 (tp30) cc_final: 0.6577 (tp30) REVERT: G 91 ASN cc_start: 0.7772 (m-40) cc_final: 0.7540 (m110) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.8040 time to fit residues: 169.0133 Evaluate side-chains 143 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 75 ASN D 63 ASN F 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.086154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.054188 restraints weight = 28900.933| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 2.03 r_work: 0.2585 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12438 Z= 0.163 Angle : 0.631 6.658 18061 Z= 0.369 Chirality : 0.043 0.223 2076 Planarity : 0.005 0.038 1287 Dihedral : 30.953 170.723 3954 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.90 % Allowed : 16.18 % Favored : 80.92 % 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: 2.13 (0.30), residues: 726 helix: 2.14 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.95 (0.40), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 37 TYR 0.010 0.001 TYR C 59 PHE 0.008 0.001 PHE B 62 TRP 0.003 0.001 TRP A 71 HIS 0.006 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.16 (12438) covalent geometry : angle 0.63056 / 0.37 (18061) hydrogen bonds : bond 0.06125 / 4.26 ( 643) hydrogen bonds : angle 3.18729 / 2.29 ( 1679) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 0.219 Fit side-chains REVERT: B 36 ARG cc_start: 0.8511 (mtp85) cc_final: 0.8079 (mtp85) REVERT: B 45 LYS cc_start: 0.8965 (mtpp) cc_final: 0.8493 (mttt) REVERT: B 96 ARG cc_start: 0.8275 (mmt90) cc_final: 0.7915 (tpp-160) REVERT: C 66 GLU cc_start: 0.8990 (tt0) cc_final: 0.8477 (tm-30) REVERT: C 106 GLN cc_start: 0.9263 (mm-40) cc_final: 0.8895 (mm110) REVERT: D 68 ASP cc_start: 0.9134 (t0) cc_final: 0.8848 (t0) REVERT: E 40 ASP cc_start: 0.8898 (p0) cc_final: 0.8666 (p0) REVERT: E 81 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8641 (mm-30) REVERT: G 73 ARG cc_start: 0.8688 (mtm110) cc_final: 0.8483 (ttp80) REVERT: G 97 LYS cc_start: 0.9362 (tppp) cc_final: 0.9159 (ttmp) REVERT: H 60 ARG cc_start: 0.8531 (mmm-85) cc_final: 0.8291 (mmm-85) REVERT: H 68 ASP cc_start: 0.8966 (t0) cc_final: 0.8651 (t0) outliers start: 17 outliers final: 5 residues processed: 165 average time/residue: 0.7348 time to fit residues: 128.3386 Evaluate side-chains 153 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 148 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain F residue 50 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 0 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 chunk 87 optimal weight: 11.9990 chunk 81 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 17 GLN G 43 GLN H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.084580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.052593 restraints weight = 29516.238| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 2.06 r_work: 0.2546 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12438 Z= 0.206 Angle : 0.609 6.022 18061 Z= 0.354 Chirality : 0.042 0.244 2076 Planarity : 0.004 0.038 1287 Dihedral : 31.197 172.339 3954 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.90 % Allowed : 19.25 % Favored : 77.85 % 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: 2.38 (0.30), residues: 726 helix: 2.35 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.96 (0.40), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 96 TYR 0.014 0.002 TYR E 35 PHE 0.015 0.002 PHE E 59 TRP 0.003 0.001 TRP A 71 HIS 0.004 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.21 (12438) covalent geometry : angle 0.60908 / 0.35 (18061) hydrogen bonds : bond 0.05797 / 4.05 ( 643) hydrogen bonds : angle 3.03813 / 2.20 ( 1679) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.196 Fit side-chains REVERT: B 36 ARG cc_start: 0.8544 (mtp85) cc_final: 0.8221 (mtp85) REVERT: B 53 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8614 (mp0) REVERT: C 66 GLU cc_start: 0.9009 (tt0) cc_final: 0.8446 (tm-30) REVERT: C 106 GLN cc_start: 0.9393 (mm-40) cc_final: 0.9093 (mm110) REVERT: D 68 ASP cc_start: 0.9223 (t0) cc_final: 0.8883 (t0) REVERT: E 58 GLU cc_start: 0.8788 (tt0) cc_final: 0.8583 (tm-30) REVERT: F 80 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8564 (mtmt) REVERT: G 73 ARG cc_start: 0.8704 (mtm110) cc_final: 0.8489 (ttp80) REVERT: G 97 LYS cc_start: 0.9392 (tppp) cc_final: 0.9162 (ttmp) REVERT: H 60 ARG cc_start: 0.8528 (mmm-85) cc_final: 0.8279 (mmm-85) REVERT: H 68 ASP cc_start: 0.9058 (t0) cc_final: 0.8643 (t0) outliers start: 17 outliers final: 5 residues processed: 160 average time/residue: 0.7808 time to fit residues: 132.0062 Evaluate side-chains 146 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 140 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 80 LYS Chi-restraints excluded: chain G residue 20 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 81 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 92 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 77 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 43 GLN H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.085538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.053658 restraints weight = 29227.895| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 2.04 r_work: 0.2579 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12438 Z= 0.145 Angle : 0.565 6.139 18061 Z= 0.335 Chirality : 0.041 0.230 2076 Planarity : 0.004 0.039 1287 Dihedral : 31.137 171.841 3954 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 3.07 % Allowed : 20.61 % Favored : 76.32 % 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: 2.67 (0.30), residues: 726 helix: 2.54 (0.21), residues: 548 sheet: None (None), residues: 0 loop : -0.82 (0.41), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 96 TYR 0.020 0.001 TYR D 40 PHE 0.009 0.001 PHE B 62 TRP 0.002 0.001 TRP A 71 HIS 0.004 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.14 (12438) covalent geometry : angle 0.56480 / 0.34 (18061) hydrogen bonds : bond 0.04716 / 3.26 ( 643) hydrogen bonds : angle 2.86004 / 2.07 ( 1679) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: B 45 LYS cc_start: 0.8960 (mtpp) cc_final: 0.8469 (mttt) REVERT: B 92 LYS cc_start: 0.9499 (ttmm) cc_final: 0.9172 (ttpt) REVERT: C 66 GLU cc_start: 0.8992 (tt0) cc_final: 0.8447 (tm-30) REVERT: C 106 GLN cc_start: 0.9373 (mm-40) cc_final: 0.9096 (mm110) REVERT: D 68 ASP cc_start: 0.9229 (t0) cc_final: 0.8842 (t0) REVERT: D 85 LYS cc_start: 0.9383 (OUTLIER) cc_final: 0.8969 (mtmm) REVERT: E 44 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8279 (mm-40) REVERT: F 80 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8574 (mtmt) REVERT: G 73 ARG cc_start: 0.8723 (mtm110) cc_final: 0.8499 (ttp80) REVERT: G 91 ASN cc_start: 0.9159 (m-40) cc_final: 0.8912 (m110) REVERT: G 97 LYS cc_start: 0.9393 (tppp) cc_final: 0.9175 (ttmp) REVERT: H 60 ARG cc_start: 0.8561 (mmm-85) cc_final: 0.8343 (mmm-85) REVERT: H 68 ASP cc_start: 0.9104 (t0) cc_final: 0.8724 (t0) outliers start: 18 outliers final: 3 residues processed: 164 average time/residue: 0.7953 time to fit residues: 138.2203 Evaluate side-chains 155 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 149 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 80 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 97 optimal weight: 30.0000 chunk 58 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 23 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 17 GLN G 43 GLN H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.085247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.053178 restraints weight = 29691.684| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 1.96 r_work: 0.2561 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12438 Z= 0.153 Angle : 0.564 5.981 18061 Z= 0.332 Chirality : 0.040 0.232 2076 Planarity : 0.004 0.040 1287 Dihedral : 31.192 170.541 3954 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.41 % Allowed : 20.27 % Favored : 76.32 % 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: 2.86 (0.30), residues: 726 helix: 2.70 (0.21), residues: 548 sheet: None (None), residues: 0 loop : -0.80 (0.41), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 96 TYR 0.021 0.001 TYR D 40 PHE 0.012 0.002 PHE E 59 TRP 0.002 0.001 TRP A 71 HIS 0.004 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.15 (12438) covalent geometry : angle 0.56365 / 0.33 (18061) hydrogen bonds : bond 0.04673 / 3.26 ( 643) hydrogen bonds : angle 2.81454 / 2.05 ( 1679) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: B 45 LYS cc_start: 0.8960 (mtpp) cc_final: 0.8554 (mttp) REVERT: B 92 LYS cc_start: 0.9480 (OUTLIER) cc_final: 0.9149 (ttpt) REVERT: B 94 GLN cc_start: 0.8876 (mm-40) cc_final: 0.8422 (mp10) REVERT: C 66 GLU cc_start: 0.8963 (tt0) cc_final: 0.8424 (tm-30) REVERT: C 73 ARG cc_start: 0.8845 (ttp80) cc_final: 0.8612 (ttp80) REVERT: C 106 GLN cc_start: 0.9388 (mm-40) cc_final: 0.9093 (mm110) REVERT: D 59 MET cc_start: 0.9280 (tpt) cc_final: 0.9048 (mmm) REVERT: D 68 ASP cc_start: 0.9253 (t0) cc_final: 0.8848 (t0) REVERT: D 85 LYS cc_start: 0.9350 (OUTLIER) cc_final: 0.8927 (mtmm) REVERT: E 44 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8287 (mm-40) REVERT: F 80 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8634 (mtmt) REVERT: G 73 ARG cc_start: 0.8764 (mtm110) cc_final: 0.8558 (ttp80) REVERT: G 97 LYS cc_start: 0.9365 (tppp) cc_final: 0.9121 (ttmt) REVERT: H 35 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8053 (mm-30) REVERT: H 68 ASP cc_start: 0.9124 (t0) cc_final: 0.8753 (t0) outliers start: 20 outliers final: 6 residues processed: 162 average time/residue: 0.8300 time to fit residues: 142.2614 Evaluate side-chains 159 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 149 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 80 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 5 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 chunk 43 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 44 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.085379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.053184 restraints weight = 29611.433| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 2.02 r_work: 0.2565 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12438 Z= 0.148 Angle : 0.557 5.868 18061 Z= 0.328 Chirality : 0.040 0.224 2076 Planarity : 0.004 0.040 1287 Dihedral : 31.201 169.814 3954 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 3.24 % Allowed : 22.66 % Favored : 74.11 % 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: 2.91 (0.30), residues: 726 helix: 2.72 (0.21), residues: 548 sheet: None (None), residues: 0 loop : -0.75 (0.41), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 96 TYR 0.023 0.001 TYR D 40 PHE 0.008 0.001 PHE B 62 TRP 0.002 0.001 TRP A 71 HIS 0.005 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.15 (12438) covalent geometry : angle 0.55705 / 0.33 (18061) hydrogen bonds : bond 0.04374 / 3.04 ( 643) hydrogen bonds : angle 2.74721 / 2.00 ( 1679) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: B 92 LYS cc_start: 0.9472 (ttmm) cc_final: 0.9139 (ttpt) REVERT: C 66 GLU cc_start: 0.8945 (tt0) cc_final: 0.8470 (tm-30) REVERT: C 106 GLN cc_start: 0.9404 (mm-40) cc_final: 0.9110 (mm110) REVERT: D 59 MET cc_start: 0.9276 (tpt) cc_final: 0.9054 (mmm) REVERT: D 68 ASP cc_start: 0.9240 (t0) cc_final: 0.8850 (t0) REVERT: D 85 LYS cc_start: 0.9342 (OUTLIER) cc_final: 0.8939 (mtmm) REVERT: E 44 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8327 (mm-40) REVERT: F 80 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8625 (mtmt) REVERT: G 73 ARG cc_start: 0.8776 (mtm110) cc_final: 0.8559 (ttp80) REVERT: G 91 ASN cc_start: 0.9206 (m-40) cc_final: 0.8993 (m110) REVERT: G 94 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8649 (mm-30) REVERT: G 97 LYS cc_start: 0.9360 (tppp) cc_final: 0.9094 (ttmp) REVERT: H 35 GLU cc_start: 0.8532 (mm-30) cc_final: 0.7932 (mm-30) REVERT: H 68 ASP cc_start: 0.9138 (t0) cc_final: 0.8774 (t0) REVERT: H 119 THR cc_start: 0.9391 (m) cc_final: 0.9113 (p) outliers start: 19 outliers final: 7 residues processed: 166 average time/residue: 0.8246 time to fit residues: 144.9225 Evaluate side-chains 160 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 150 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 80 LYS Chi-restraints excluded: chain G residue 58 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 12 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 52 optimal weight: 0.0470 chunk 61 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 72 optimal weight: 20.0000 chunk 55 optimal weight: 0.9980 chunk 96 optimal weight: 20.0000 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 17 GLN G 43 GLN H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.085599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.053244 restraints weight = 29853.121| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 2.07 r_work: 0.2577 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12438 Z= 0.133 Angle : 0.545 6.158 18061 Z= 0.323 Chirality : 0.039 0.222 2076 Planarity : 0.004 0.047 1287 Dihedral : 31.149 169.558 3954 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.73 % Allowed : 23.51 % Favored : 73.76 % 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: 3.00 (0.30), residues: 726 helix: 2.81 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -0.76 (0.41), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 73 TYR 0.025 0.001 TYR D 40 PHE 0.010 0.001 PHE E 59 TRP 0.002 0.001 TRP A 71 HIS 0.005 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.13 (12438) covalent geometry : angle 0.54473 / 0.32 (18061) hydrogen bonds : bond 0.04183 / 2.90 ( 643) hydrogen bonds : angle 2.69660 / 1.96 ( 1679) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: B 45 LYS cc_start: 0.8912 (mtpp) cc_final: 0.8441 (mttt) REVERT: B 92 LYS cc_start: 0.9471 (ttmm) cc_final: 0.9092 (ttpt) REVERT: B 94 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.7956 (mp10) REVERT: C 66 GLU cc_start: 0.8932 (tt0) cc_final: 0.8544 (tm-30) REVERT: C 106 GLN cc_start: 0.9371 (mm-40) cc_final: 0.9073 (mm110) REVERT: D 68 ASP cc_start: 0.9245 (t0) cc_final: 0.8838 (t0) REVERT: D 85 LYS cc_start: 0.9355 (OUTLIER) cc_final: 0.8968 (mtmm) REVERT: E 44 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8344 (mm-40) REVERT: G 73 ARG cc_start: 0.8777 (mtm110) cc_final: 0.8558 (ttp80) REVERT: G 97 LYS cc_start: 0.9359 (tppp) cc_final: 0.9094 (ttmp) REVERT: H 35 GLU cc_start: 0.8533 (mm-30) cc_final: 0.7933 (mm-30) REVERT: H 68 ASP cc_start: 0.9126 (t0) cc_final: 0.8766 (t0) REVERT: H 116 LYS cc_start: 0.9207 (ttpp) cc_final: 0.8919 (ptmm) REVERT: H 119 THR cc_start: 0.9375 (m) cc_final: 0.9102 (p) outliers start: 16 outliers final: 6 residues processed: 166 average time/residue: 0.7887 time to fit residues: 138.6799 Evaluate side-chains 162 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 153 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain G residue 20 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 78 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 39 optimal weight: 0.4980 chunk 32 optimal weight: 0.7980 chunk 96 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 61 optimal weight: 9.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 17 GLN H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.085050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.052718 restraints weight = 29749.061| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 2.00 r_work: 0.2557 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12438 Z= 0.173 Angle : 0.577 11.026 18061 Z= 0.333 Chirality : 0.040 0.223 2076 Planarity : 0.004 0.042 1287 Dihedral : 31.251 168.437 3954 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.56 % Allowed : 23.51 % Favored : 73.94 % 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: 2.91 (0.30), residues: 726 helix: 2.74 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -0.80 (0.41), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 96 TYR 0.027 0.001 TYR D 40 PHE 0.007 0.001 PHE B 62 TRP 0.003 0.001 TRP A 71 HIS 0.006 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.17 (12438) covalent geometry : angle 0.57748 / 0.33 (18061) hydrogen bonds : bond 0.04448 / 3.12 ( 643) hydrogen bonds : angle 2.77391 / 2.02 ( 1679) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: B 45 LYS cc_start: 0.9027 (mtpp) cc_final: 0.8521 (mttt) REVERT: B 92 LYS cc_start: 0.9474 (ttmm) cc_final: 0.9108 (ttpt) REVERT: B 94 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.7949 (mp10) REVERT: C 66 GLU cc_start: 0.9002 (tt0) cc_final: 0.8487 (tm-30) REVERT: C 106 GLN cc_start: 0.9396 (mm-40) cc_final: 0.9064 (mm110) REVERT: D 68 ASP cc_start: 0.9288 (t0) cc_final: 0.8882 (t0) REVERT: D 85 LYS cc_start: 0.9355 (OUTLIER) cc_final: 0.8958 (mtmm) REVERT: E 44 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8377 (mm-40) REVERT: F 80 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8686 (mtmt) REVERT: G 73 ARG cc_start: 0.8780 (mtm110) cc_final: 0.8562 (ttp80) REVERT: G 97 LYS cc_start: 0.9350 (tppp) cc_final: 0.9046 (ttmp) REVERT: H 68 ASP cc_start: 0.9157 (t0) cc_final: 0.8770 (t0) REVERT: H 116 LYS cc_start: 0.9221 (ttpp) cc_final: 0.8951 (ptmm) REVERT: H 119 THR cc_start: 0.9384 (m) cc_final: 0.9113 (p) outliers start: 15 outliers final: 7 residues processed: 162 average time/residue: 0.8168 time to fit residues: 140.0508 Evaluate side-chains 161 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 80 LYS Chi-restraints excluded: chain G residue 20 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 97 optimal weight: 30.0000 chunk 62 optimal weight: 2.9990 chunk 70 optimal weight: 50.0000 chunk 89 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 17 GLN G 43 GLN H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.084097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.051968 restraints weight = 29154.108| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 2.05 r_work: 0.2561 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12438 Z= 0.188 Angle : 0.585 6.127 18061 Z= 0.337 Chirality : 0.040 0.219 2076 Planarity : 0.004 0.038 1287 Dihedral : 31.325 167.932 3954 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.04 % Allowed : 24.70 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.82 (0.30), residues: 726 helix: 2.69 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -0.86 (0.41), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 96 TYR 0.024 0.001 TYR D 40 PHE 0.008 0.001 PHE F 62 TRP 0.005 0.001 TRP A 71 HIS 0.005 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.19 (12438) covalent geometry : angle 0.58480 / 0.34 (18061) hydrogen bonds : bond 0.04474 / 3.13 ( 643) hydrogen bonds : angle 2.84100 / 2.07 ( 1679) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: B 45 LYS cc_start: 0.8980 (mtpp) cc_final: 0.8506 (mttt) REVERT: B 92 LYS cc_start: 0.9500 (ttmm) cc_final: 0.9141 (ttpt) REVERT: B 94 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8023 (mp10) REVERT: C 66 GLU cc_start: 0.9025 (tt0) cc_final: 0.8544 (tm-30) REVERT: C 92 ASP cc_start: 0.8543 (t70) cc_final: 0.8154 (t70) REVERT: C 106 GLN cc_start: 0.9435 (mm-40) cc_final: 0.9154 (mm-40) REVERT: D 68 ASP cc_start: 0.9311 (t0) cc_final: 0.8938 (t0) REVERT: D 85 LYS cc_start: 0.9368 (OUTLIER) cc_final: 0.8973 (mtmm) REVERT: E 44 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8439 (mm-40) REVERT: G 73 ARG cc_start: 0.8793 (mtm110) cc_final: 0.8581 (ttp80) REVERT: G 97 LYS cc_start: 0.9365 (tppp) cc_final: 0.9059 (ttmt) REVERT: H 35 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8109 (mm-30) REVERT: H 68 ASP cc_start: 0.9190 (t0) cc_final: 0.8803 (t0) REVERT: H 116 LYS cc_start: 0.9245 (ttpp) cc_final: 0.8934 (ptmm) REVERT: H 119 THR cc_start: 0.9418 (m) cc_final: 0.9153 (p) outliers start: 12 outliers final: 7 residues processed: 160 average time/residue: 0.8232 time to fit residues: 139.4138 Evaluate side-chains 160 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 150 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain G residue 20 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 63 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 41 optimal weight: 0.6980 chunk 74 optimal weight: 10.0000 chunk 49 optimal weight: 0.6980 chunk 71 optimal weight: 20.0000 chunk 75 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 97 optimal weight: 30.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 17 GLN H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.084859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.052543 restraints weight = 29916.288| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 2.02 r_work: 0.2554 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12438 Z= 0.162 Angle : 0.572 9.477 18061 Z= 0.332 Chirality : 0.039 0.216 2076 Planarity : 0.004 0.044 1287 Dihedral : 31.289 168.094 3954 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.04 % Allowed : 25.04 % Favored : 72.91 % 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: 2.84 (0.30), residues: 726 helix: 2.69 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -0.81 (0.41), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 73 TYR 0.026 0.001 TYR D 40 PHE 0.008 0.001 PHE F 62 TRP 0.002 0.001 TRP A 71 HIS 0.006 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 (12438) covalent geometry : angle 0.57206 / 0.33 (18061) hydrogen bonds : bond 0.04236 / 2.96 ( 643) hydrogen bonds : angle 2.79691 / 2.04 ( 1679) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 154 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: B 45 LYS cc_start: 0.8994 (mtpp) cc_final: 0.8522 (mttt) REVERT: B 92 LYS cc_start: 0.9475 (ttmm) cc_final: 0.9112 (ttpt) REVERT: B 94 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.7913 (mp10) REVERT: C 66 GLU cc_start: 0.9004 (tt0) cc_final: 0.8520 (tm-30) REVERT: C 78 THR cc_start: 0.9252 (p) cc_final: 0.8956 (t) REVERT: C 92 ASP cc_start: 0.8485 (t70) cc_final: 0.8088 (t70) REVERT: C 106 GLN cc_start: 0.9430 (mm-40) cc_final: 0.9136 (mm-40) REVERT: D 68 ASP cc_start: 0.9253 (t0) cc_final: 0.8881 (t0) REVERT: D 85 LYS cc_start: 0.9358 (OUTLIER) cc_final: 0.9004 (mtmm) REVERT: E 44 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8384 (mm-40) REVERT: F 80 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8695 (mtmt) REVERT: G 73 ARG cc_start: 0.8788 (mtm110) cc_final: 0.8587 (ttp80) REVERT: G 97 LYS cc_start: 0.9339 (tppp) cc_final: 0.9024 (ttmt) REVERT: H 35 GLU cc_start: 0.8587 (mm-30) cc_final: 0.7947 (mm-30) REVERT: H 68 ASP cc_start: 0.9162 (t0) cc_final: 0.8780 (t0) REVERT: H 105 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8563 (mm-30) REVERT: H 108 LYS cc_start: 0.8839 (ttmm) cc_final: 0.8444 (mtmp) REVERT: H 116 LYS cc_start: 0.9232 (ttpp) cc_final: 0.8917 (ptmm) REVERT: H 119 THR cc_start: 0.9394 (m) cc_final: 0.9125 (p) outliers start: 12 outliers final: 7 residues processed: 160 average time/residue: 0.8257 time to fit residues: 139.8356 Evaluate side-chains 161 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 80 LYS Chi-restraints excluded: chain G residue 20 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 54 optimal weight: 0.0020 chunk 11 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 7 optimal weight: 0.3980 chunk 60 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 17 GLN G 43 GLN H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.085387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.053323 restraints weight = 29935.047| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 2.01 r_work: 0.2580 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 12438 Z= 0.129 Angle : 0.556 7.161 18061 Z= 0.327 Chirality : 0.038 0.211 2076 Planarity : 0.004 0.049 1287 Dihedral : 31.209 168.462 3954 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.04 % Allowed : 25.21 % Favored : 72.74 % 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: 2.93 (0.30), residues: 726 helix: 2.75 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -0.75 (0.41), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 73 TYR 0.024 0.001 TYR D 40 PHE 0.013 0.001 PHE E 59 TRP 0.002 0.001 TRP A 71 HIS 0.006 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.13 (12438) covalent geometry : angle 0.55571 / 0.33 (18061) hydrogen bonds : bond 0.03962 / 2.75 ( 643) hydrogen bonds : angle 2.73348 / 1.99 ( 1679) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3715.23 seconds wall clock time: 64 minutes 0.38 seconds (3840.38 seconds total)