Starting phenix.real_space_refine on Wed Mar 4 06:58:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lrv_63344/03_2026/9lrv_63344.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lrv_63344/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/9lrv_63344/03_2026/9lrv_63344.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lrv_63344/03_2026/9lrv_63344.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lrv_63344/03_2026/9lrv_63344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lrv_63344/03_2026/9lrv_63344.map" } 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-dev-5986/lib/python3.9/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: 2.25, 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: 0.92 Conformation dependent library (CDL) restraints added in 342.2 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: 1.74 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: 2.02 Time building geometry restraints manager: 1.27 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=" CA SER D 78 " pdb=" CB SER D 78 " ideal model delta sigma weight residual 1.529 1.489 0.040 1.55e-02 4.16e+03 6.60e+00 bond pdb=" N LYS D 79 " pdb=" CA LYS D 79 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.19e-02 7.06e+03 3.92e+00 bond pdb=" N LEU D 80 " pdb=" CA LEU D 80 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.21e-02 6.83e+03 3.81e+00 bond pdb=" CA ALA D 82 " pdb=" CB ALA D 82 " ideal model delta sigma weight residual 1.529 1.499 0.030 1.55e-02 4.16e+03 3.74e+00 bond pdb=" N SER D 78 " pdb=" CA SER D 78 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.19e-02 7.06e+03 3.40e+00 ... (remaining 12433 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 17126 1.08 - 2.15: 757 2.15 - 3.23: 159 3.23 - 4.30: 13 4.30 - 5.38: 6 Bond angle restraints: 18061 Sorted by residual: angle pdb=" N LEU D 80 " pdb=" CA LEU D 80 " pdb=" C LEU D 80 " ideal model delta sigma weight residual 111.28 108.14 3.14 1.09e+00 8.42e-01 8.30e+00 angle pdb=" CA LYS D 79 " pdb=" C LYS D 79 " pdb=" O LYS D 79 " ideal model delta sigma weight residual 120.82 117.92 2.90 1.05e+00 9.07e-01 7.63e+00 angle pdb=" O SER D 78 " pdb=" C SER D 78 " pdb=" N LYS D 79 " ideal model delta sigma weight residual 122.07 124.59 -2.52 1.03e+00 9.43e-01 5.96e+00 angle pdb=" C ALA D 82 " pdb=" N TYR D 83 " pdb=" CA TYR D 83 " ideal model delta sigma weight residual 120.38 116.88 3.50 1.46e+00 4.69e-01 5.75e+00 angle pdb=" O ALA D 81 " pdb=" C ALA D 81 " pdb=" N ALA D 82 " ideal model delta sigma weight residual 122.07 124.54 -2.47 1.03e+00 9.43e-01 5.75e+00 ... (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: 1779 0.044 - 0.088: 256 0.088 - 0.133: 39 0.133 - 0.177: 1 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=" CA ILE F 30 " pdb=" N ILE F 30 " pdb=" C ILE F 30 " pdb=" CB ILE F 30 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-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: 1.140 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: 0.040 Set scattering table: 0.030 Process input model: 12.150 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 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 0.054 12438 Z= 0.178 Angle : 0.515 5.375 18061 Z= 0.314 Chirality : 0.032 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 covalent geometry : bond 0.00390 (12438) covalent geometry : angle 0.51479 (18061) hydrogen bonds : bond 0.21453 ( 643) hydrogen bonds : angle 7.08508 ( 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 : 0.327 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: 0.7539 (m110) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 1.0020 time to fit residues: 209.7446 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 : 0.306 ------------------------------------------------------------------------------- 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: 7.9990 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3557 r_free = 0.3557 target = 0.086362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.055091 restraints weight = 29323.791| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 2.05 r_work: 0.2606 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12438 Z= 0.162 Angle : 0.521 5.500 18061 Z= 0.318 Chirality : 0.032 0.123 2076 Planarity : 0.004 0.032 1287 Dihedral : 30.634 176.093 3954 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.73 % Allowed : 15.67 % Favored : 81.60 % 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: 2.49 (0.31), residues: 726 helix: 2.42 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.90 (0.41), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 96 TYR 0.010 0.001 TYR D 40 PHE 0.008 0.001 PHE B 62 TRP 0.004 0.001 TRP A 71 HIS 0.004 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00358 (12438) covalent geometry : angle 0.52127 (18061) hydrogen bonds : bond 0.04161 ( 643) hydrogen bonds : angle 2.79114 ( 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 186 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 0.292 Fit side-chains REVERT: B 45 LYS cc_start: 0.8989 (mtpp) cc_final: 0.8498 (mttt) REVERT: B 92 LYS cc_start: 0.9518 (OUTLIER) cc_final: 0.9218 (ttpt) REVERT: B 96 ARG cc_start: 0.8501 (mmt90) cc_final: 0.8254 (tpp-160) REVERT: C 66 GLU cc_start: 0.8974 (tt0) cc_final: 0.8433 (tm-30) REVERT: C 106 GLN cc_start: 0.9303 (mm-40) cc_final: 0.8954 (mm110) REVERT: D 68 ASP cc_start: 0.9180 (t0) cc_final: 0.8872 (t0) REVERT: E 44 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8221 (mm-40) REVERT: G 73 ARG cc_start: 0.8722 (mtm110) cc_final: 0.8504 (ttp80) REVERT: G 97 LYS cc_start: 0.9353 (tppp) cc_final: 0.9139 (ttmp) REVERT: H 51 ASP cc_start: 0.8480 (p0) cc_final: 0.8267 (p0) REVERT: H 68 ASP cc_start: 0.9016 (t0) cc_final: 0.8783 (t0) outliers start: 16 outliers final: 2 residues processed: 173 average time/residue: 0.8468 time to fit residues: 154.5447 Evaluate side-chains 161 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 157 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain F residue 25 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 39 optimal weight: 0.4980 chunk 0 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.083990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.052307 restraints weight = 29790.598| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 2.10 r_work: 0.2553 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12438 Z= 0.221 Angle : 0.526 5.419 18061 Z= 0.318 Chirality : 0.033 0.122 2076 Planarity : 0.004 0.037 1287 Dihedral : 30.935 172.423 3954 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.58 % Allowed : 19.76 % Favored : 76.66 % 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: 2.68 (0.31), residues: 726 helix: 2.56 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.86 (0.41), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 96 TYR 0.010 0.001 TYR D 40 PHE 0.008 0.001 PHE G 27 TRP 0.003 0.001 TRP A 71 HIS 0.007 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00503 (12438) covalent geometry : angle 0.52614 (18061) hydrogen bonds : bond 0.04352 ( 643) hydrogen bonds : angle 2.84585 ( 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 179 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 0.288 Fit side-chains REVERT: B 36 ARG cc_start: 0.8498 (mtp85) cc_final: 0.8108 (mtp85) REVERT: B 92 LYS cc_start: 0.9511 (ttmm) cc_final: 0.9216 (ttpt) REVERT: B 94 GLN cc_start: 0.8882 (mm-40) cc_final: 0.8483 (mp10) REVERT: C 66 GLU cc_start: 0.8983 (tt0) cc_final: 0.8456 (tm-30) REVERT: C 106 GLN cc_start: 0.9350 (mm-40) cc_final: 0.9132 (mm110) REVERT: D 68 ASP cc_start: 0.9212 (t0) cc_final: 0.8875 (t0) REVERT: E 44 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8457 (mm-40) REVERT: G 97 LYS cc_start: 0.9376 (tppp) cc_final: 0.9087 (ttmt) REVERT: H 35 GLU cc_start: 0.8674 (mm-30) cc_final: 0.7956 (mm-30) REVERT: H 68 ASP cc_start: 0.9094 (t0) cc_final: 0.8787 (t0) REVERT: H 116 LYS cc_start: 0.9266 (ttpp) cc_final: 0.8987 (ttpp) REVERT: H 119 THR cc_start: 0.9422 (m) cc_final: 0.9144 (p) outliers start: 21 outliers final: 7 residues processed: 165 average time/residue: 0.8287 time to fit residues: 144.1191 Evaluate side-chains 161 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 153 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 E residue 38 SER Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain F residue 31 THR 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: 4.9990 chunk 13 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 28 optimal weight: 0.0970 chunk 56 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3539 r_free = 0.3539 target = 0.085021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.053037 restraints weight = 29563.860| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 2.08 r_work: 0.2584 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12438 Z= 0.159 Angle : 0.500 5.266 18061 Z= 0.305 Chirality : 0.031 0.132 2076 Planarity : 0.003 0.035 1287 Dihedral : 30.744 172.669 3954 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.92 % Allowed : 21.29 % Favored : 74.79 % 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 : -0.81 (0.41), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 96 TYR 0.016 0.001 TYR D 40 PHE 0.011 0.001 PHE E 59 TRP 0.002 0.001 TRP A 71 HIS 0.004 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00352 (12438) covalent geometry : angle 0.50000 (18061) hydrogen bonds : bond 0.03744 ( 643) hydrogen bonds : angle 2.69174 ( 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 188 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 0.255 Fit side-chains REVERT: B 36 ARG cc_start: 0.8498 (mtp85) cc_final: 0.8104 (mtp85) REVERT: B 45 LYS cc_start: 0.8964 (mtpp) cc_final: 0.8434 (mttt) REVERT: B 92 LYS cc_start: 0.9500 (ttmm) cc_final: 0.9182 (ttpt) REVERT: C 66 GLU cc_start: 0.8976 (tt0) cc_final: 0.8459 (tm-30) REVERT: C 78 THR cc_start: 0.9253 (p) cc_final: 0.8989 (t) REVERT: C 106 GLN cc_start: 0.9329 (mm-40) cc_final: 0.8795 (mm110) REVERT: D 68 ASP cc_start: 0.9228 (t0) cc_final: 0.8861 (t0) REVERT: D 85 LYS cc_start: 0.9373 (OUTLIER) cc_final: 0.8983 (mtmm) REVERT: E 44 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8452 (mm-40) REVERT: E 60 VAL cc_start: 0.8568 (p) cc_final: 0.8364 (p) REVERT: G 97 LYS cc_start: 0.9357 (tppp) cc_final: 0.9049 (ttmp) REVERT: H 60 ARG cc_start: 0.8517 (mmm-85) cc_final: 0.8195 (mmm-85) REVERT: H 68 ASP cc_start: 0.9115 (t0) cc_final: 0.8823 (t0) REVERT: H 116 LYS cc_start: 0.9302 (ttpp) cc_final: 0.9016 (ttpp) REVERT: H 119 THR cc_start: 0.9407 (m) cc_final: 0.9136 (p) outliers start: 23 outliers final: 5 residues processed: 174 average time/residue: 0.8307 time to fit residues: 152.3214 Evaluate side-chains 167 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 160 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 78 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 G residue 20 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 97 optimal weight: 8.9990 chunk 58 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 GLN F 76 HIS H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.084354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.052671 restraints weight = 29615.424| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 2.08 r_work: 0.2570 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12438 Z= 0.200 Angle : 0.518 7.715 18061 Z= 0.312 Chirality : 0.032 0.126 2076 Planarity : 0.003 0.035 1287 Dihedral : 30.857 171.278 3954 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 4.09 % Allowed : 21.81 % 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: 2.96 (0.31), residues: 726 helix: 2.79 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -0.83 (0.41), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 96 TYR 0.022 0.001 TYR D 40 PHE 0.008 0.001 PHE B 62 TRP 0.003 0.001 TRP A 71 HIS 0.005 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00455 (12438) covalent geometry : angle 0.51785 (18061) hydrogen bonds : bond 0.03869 ( 643) hydrogen bonds : angle 2.69906 ( 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 187 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.299 Fit side-chains REVERT: B 36 ARG cc_start: 0.8522 (mtp85) cc_final: 0.8318 (mtp85) REVERT: B 92 LYS cc_start: 0.9523 (ttmm) cc_final: 0.9163 (ttpt) REVERT: B 94 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.7898 (mp10) REVERT: C 58 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8418 (tt0) REVERT: C 66 GLU cc_start: 0.9027 (tt0) cc_final: 0.8533 (tm-30) REVERT: C 78 THR cc_start: 0.9295 (p) cc_final: 0.9034 (t) REVERT: C 106 GLN cc_start: 0.9384 (mm-40) cc_final: 0.9053 (mm110) REVERT: D 68 ASP cc_start: 0.9247 (t0) cc_final: 0.8892 (t0) REVERT: D 85 LYS cc_start: 0.9374 (OUTLIER) cc_final: 0.9034 (mtmm) REVERT: E 44 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8485 (mm-40) REVERT: G 74 ASP cc_start: 0.8643 (m-30) cc_final: 0.8418 (m-30) REVERT: G 91 ASN cc_start: 0.9196 (m-40) cc_final: 0.8930 (m110) REVERT: H 35 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8029 (mm-30) REVERT: H 36 THR cc_start: 0.9061 (OUTLIER) cc_final: 0.8735 (t) REVERT: H 60 ARG cc_start: 0.8589 (mmm-85) cc_final: 0.8275 (mmm-85) REVERT: H 68 ASP cc_start: 0.9172 (t0) cc_final: 0.8838 (t0) REVERT: H 116 LYS cc_start: 0.9332 (OUTLIER) cc_final: 0.9035 (ttpp) REVERT: H 119 THR cc_start: 0.9418 (m) cc_final: 0.9150 (p) outliers start: 24 outliers final: 6 residues processed: 173 average time/residue: 0.8194 time to fit residues: 149.8921 Evaluate side-chains 164 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 94 GLN Chi-restraints excluded: chain C residue 58 GLU 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 Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 116 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 5 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 97 optimal weight: 8.9990 chunk 43 optimal weight: 0.3980 chunk 66 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 35 optimal weight: 20.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.084973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.052972 restraints weight = 29330.065| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 2.10 r_work: 0.2589 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12438 Z= 0.151 Angle : 0.508 5.463 18061 Z= 0.307 Chirality : 0.032 0.207 2076 Planarity : 0.004 0.040 1287 Dihedral : 30.807 171.863 3954 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.58 % Allowed : 22.66 % 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: 3.01 (0.30), residues: 726 helix: 2.82 (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 0.005 0.000 ARG C 73 TYR 0.023 0.001 TYR D 40 PHE 0.013 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 covalent geometry : bond 0.00333 (12438) covalent geometry : angle 0.50800 (18061) hydrogen bonds : bond 0.03595 ( 643) hydrogen bonds : angle 2.68621 ( 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 182 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 0.283 Fit side-chains REVERT: B 36 ARG cc_start: 0.8498 (mtp85) cc_final: 0.8122 (mtp85) REVERT: B 45 LYS cc_start: 0.8917 (mtpp) cc_final: 0.8361 (mttt) REVERT: B 92 LYS cc_start: 0.9509 (ttmm) cc_final: 0.9152 (ttpt) REVERT: B 94 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.7812 (mp10) REVERT: C 58 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8453 (tt0) REVERT: C 66 GLU cc_start: 0.8988 (tt0) cc_final: 0.8613 (tm-30) REVERT: C 70 ASN cc_start: 0.9148 (m-40) cc_final: 0.8922 (m-40) REVERT: C 78 THR cc_start: 0.9283 (p) cc_final: 0.9027 (t) REVERT: C 106 GLN cc_start: 0.9344 (mm-40) cc_final: 0.9065 (mm110) REVERT: D 68 ASP cc_start: 0.9247 (t0) cc_final: 0.8884 (t0) REVERT: D 85 LYS cc_start: 0.9375 (OUTLIER) cc_final: 0.9018 (mtmm) REVERT: E 44 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8461 (mm-40) REVERT: G 74 ASP cc_start: 0.8618 (m-30) cc_final: 0.8407 (m-30) REVERT: G 91 ASN cc_start: 0.9185 (m-40) cc_final: 0.8917 (m110) REVERT: G 97 LYS cc_start: 0.9319 (tppp) cc_final: 0.9118 (ttmp) REVERT: H 35 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8171 (mm-30) REVERT: H 60 ARG cc_start: 0.8555 (mmm-85) cc_final: 0.8246 (mmm-85) REVERT: H 68 ASP cc_start: 0.9157 (t0) cc_final: 0.8842 (t0) REVERT: H 116 LYS cc_start: 0.9337 (ttpp) cc_final: 0.9042 (ttpp) REVERT: H 119 THR cc_start: 0.9403 (m) cc_final: 0.9133 (p) outliers start: 21 outliers final: 5 residues processed: 169 average time/residue: 0.8103 time to fit residues: 144.6782 Evaluate side-chains 166 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 157 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 C residue 58 GLU 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 12 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 52 optimal weight: 0.0060 chunk 61 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.084348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.052439 restraints weight = 29843.441| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 2.08 r_work: 0.2571 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12438 Z= 0.195 Angle : 0.523 10.099 18061 Z= 0.313 Chirality : 0.032 0.160 2076 Planarity : 0.004 0.038 1287 Dihedral : 30.862 171.140 3954 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.90 % Allowed : 24.36 % 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: 3.04 (0.31), residues: 726 helix: 2.84 (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 0.008 0.000 ARG G 73 TYR 0.024 0.001 TYR D 40 PHE 0.007 0.001 PHE F 62 TRP 0.003 0.001 TRP A 71 HIS 0.006 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00444 (12438) covalent geometry : angle 0.52292 (18061) hydrogen bonds : bond 0.03833 ( 643) hydrogen bonds : angle 2.71196 ( 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 177 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: B 45 LYS cc_start: 0.8974 (mtpp) cc_final: 0.8493 (mttt) REVERT: B 92 LYS cc_start: 0.9506 (ttmm) cc_final: 0.9151 (ttpt) REVERT: B 94 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.7871 (mp10) REVERT: C 58 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8415 (tt0) REVERT: C 66 GLU cc_start: 0.9015 (tt0) cc_final: 0.8521 (tm-30) REVERT: C 78 THR cc_start: 0.9283 (p) cc_final: 0.9020 (t) REVERT: C 106 GLN cc_start: 0.9358 (mm-40) cc_final: 0.9040 (mm110) REVERT: D 68 ASP cc_start: 0.9266 (t0) cc_final: 0.8892 (t0) REVERT: D 85 LYS cc_start: 0.9366 (OUTLIER) cc_final: 0.9016 (mtmm) REVERT: E 44 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8463 (mm-40) REVERT: G 74 ASP cc_start: 0.8661 (m-30) cc_final: 0.8419 (m-30) REVERT: G 97 LYS cc_start: 0.9332 (tppp) cc_final: 0.9081 (ttmp) REVERT: H 36 THR cc_start: 0.9136 (OUTLIER) cc_final: 0.8917 (t) REVERT: H 60 ARG cc_start: 0.8568 (mmm-85) cc_final: 0.8254 (mmm-85) REVERT: H 68 ASP cc_start: 0.9181 (t0) cc_final: 0.8834 (t0) REVERT: H 116 LYS cc_start: 0.9324 (OUTLIER) cc_final: 0.9022 (ttpp) REVERT: H 119 THR cc_start: 0.9403 (m) cc_final: 0.9131 (p) outliers start: 17 outliers final: 4 residues processed: 168 average time/residue: 0.8293 time to fit residues: 147.2139 Evaluate side-chains 162 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 152 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 94 GLN Chi-restraints excluded: chain C residue 58 GLU 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 H residue 36 THR Chi-restraints excluded: chain H residue 116 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 78 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 96 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 GLN G 91 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.083031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.050930 restraints weight = 29607.256| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 2.07 r_work: 0.2511 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 12438 Z= 0.253 Angle : 0.554 5.970 18061 Z= 0.331 Chirality : 0.034 0.155 2076 Planarity : 0.004 0.042 1287 Dihedral : 31.139 170.439 3954 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.24 % Allowed : 24.19 % Favored : 72.57 % 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: 2.83 (0.31), residues: 726 helix: 2.68 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -0.83 (0.41), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 37 TYR 0.024 0.001 TYR D 40 PHE 0.007 0.002 PHE F 62 TRP 0.006 0.001 TRP A 71 HIS 0.006 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00581 (12438) covalent geometry : angle 0.55425 (18061) hydrogen bonds : bond 0.04270 ( 643) hydrogen bonds : angle 2.86934 ( 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 168 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: B 45 LYS cc_start: 0.9003 (mtpp) cc_final: 0.8508 (mttt) REVERT: B 92 LYS cc_start: 0.9491 (ttmm) cc_final: 0.9150 (ttpt) REVERT: B 94 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8100 (mp10) REVERT: C 58 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8411 (tt0) REVERT: C 66 GLU cc_start: 0.9015 (tt0) cc_final: 0.8498 (tm-30) REVERT: C 106 GLN cc_start: 0.9405 (mm-40) cc_final: 0.9173 (mm-40) REVERT: D 68 ASP cc_start: 0.9263 (t0) cc_final: 0.8906 (t0) REVERT: D 85 LYS cc_start: 0.9333 (OUTLIER) cc_final: 0.8956 (mtmm) REVERT: D 113 GLU cc_start: 0.9221 (OUTLIER) cc_final: 0.8675 (mp0) REVERT: G 74 ASP cc_start: 0.8691 (m-30) cc_final: 0.8411 (m-30) REVERT: G 75 ASN cc_start: 0.8950 (OUTLIER) cc_final: 0.8524 (t0) REVERT: H 35 GLU cc_start: 0.8819 (mm-30) cc_final: 0.7980 (mm-30) REVERT: H 36 THR cc_start: 0.9151 (OUTLIER) cc_final: 0.8811 (t) REVERT: H 47 GLN cc_start: 0.8846 (mt0) cc_final: 0.8616 (mt0) REVERT: H 60 ARG cc_start: 0.8509 (mmm-85) cc_final: 0.8161 (mmm-85) REVERT: H 68 ASP cc_start: 0.9164 (t0) cc_final: 0.8766 (t0) REVERT: H 116 LYS cc_start: 0.9303 (OUTLIER) cc_final: 0.9059 (ttpp) REVERT: H 119 THR cc_start: 0.9408 (m) cc_final: 0.9138 (p) outliers start: 19 outliers final: 5 residues processed: 158 average time/residue: 0.9025 time to fit residues: 150.1291 Evaluate side-chains 157 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 94 GLN Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 116 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 97 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.083309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.051354 restraints weight = 29194.711| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 2.08 r_work: 0.2539 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12438 Z= 0.211 Angle : 0.550 10.908 18061 Z= 0.326 Chirality : 0.033 0.132 2076 Planarity : 0.004 0.050 1287 Dihedral : 31.094 171.043 3954 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.07 % Allowed : 23.85 % Favored : 73.08 % 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: 2.81 (0.30), residues: 726 helix: 2.66 (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 0.011 0.001 ARG C 37 TYR 0.026 0.001 TYR D 40 PHE 0.007 0.001 PHE F 62 TRP 0.004 0.001 TRP A 71 HIS 0.006 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00484 (12438) covalent geometry : angle 0.54981 (18061) hydrogen bonds : bond 0.04010 ( 643) hydrogen bonds : angle 2.82332 ( 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 167 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: B 45 LYS cc_start: 0.9004 (mtpp) cc_final: 0.8528 (mttt) REVERT: B 92 LYS cc_start: 0.9522 (ttmm) cc_final: 0.9173 (ttpt) REVERT: B 94 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8157 (mp10) REVERT: C 58 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8421 (tt0) REVERT: C 66 GLU cc_start: 0.9038 (tt0) cc_final: 0.8544 (tm-30) REVERT: C 78 THR cc_start: 0.9322 (p) cc_final: 0.9022 (t) REVERT: C 106 GLN cc_start: 0.9430 (mm-40) cc_final: 0.9219 (mm-40) REVERT: D 68 ASP cc_start: 0.9265 (t0) cc_final: 0.8908 (t0) REVERT: D 85 LYS cc_start: 0.9365 (OUTLIER) cc_final: 0.9020 (mtmm) REVERT: G 74 ASP cc_start: 0.8684 (m-30) cc_final: 0.8403 (m-30) REVERT: G 75 ASN cc_start: 0.9019 (OUTLIER) cc_final: 0.8610 (t0) REVERT: H 47 GLN cc_start: 0.8902 (mt0) cc_final: 0.8667 (mt0) REVERT: H 68 ASP cc_start: 0.9207 (t0) cc_final: 0.8838 (t0) REVERT: H 116 LYS cc_start: 0.9333 (OUTLIER) cc_final: 0.9013 (ttpp) REVERT: H 119 THR cc_start: 0.9413 (m) cc_final: 0.9143 (p) outliers start: 18 outliers final: 9 residues processed: 154 average time/residue: 0.8236 time to fit residues: 133.6178 Evaluate side-chains 162 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.288 ------------------------------------------------------------------------------- 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 C residue 58 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 38 LYS Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain H residue 116 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 63 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 97 optimal weight: 7.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.084197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.052444 restraints weight = 29558.502| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 2.09 r_work: 0.2571 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 12438 Z= 0.156 Angle : 0.535 8.127 18061 Z= 0.320 Chirality : 0.032 0.133 2076 Planarity : 0.004 0.052 1287 Dihedral : 31.025 171.831 3954 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.04 % Allowed : 25.38 % Favored : 72.57 % 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: 2.90 (0.30), residues: 726 helix: 2.71 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -0.70 (0.41), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 37 TYR 0.024 0.001 TYR D 40 PHE 0.008 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 covalent geometry : bond 0.00350 (12438) covalent geometry : angle 0.53471 (18061) hydrogen bonds : bond 0.03709 ( 643) hydrogen bonds : angle 2.76831 ( 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 168 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: B 45 LYS cc_start: 0.8985 (mtpp) cc_final: 0.8522 (mttt) REVERT: B 92 LYS cc_start: 0.9515 (ttmm) cc_final: 0.9160 (ttpt) REVERT: B 94 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8123 (mp10) REVERT: C 58 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8437 (tt0) REVERT: C 66 GLU cc_start: 0.9029 (tt0) cc_final: 0.8667 (tm-30) REVERT: C 78 THR cc_start: 0.9299 (p) cc_final: 0.9013 (t) REVERT: C 106 GLN cc_start: 0.9413 (mm-40) cc_final: 0.9151 (mm110) REVERT: D 68 ASP cc_start: 0.9256 (t0) cc_final: 0.8879 (t0) REVERT: D 85 LYS cc_start: 0.9364 (OUTLIER) cc_final: 0.9018 (mtmm) REVERT: G 74 ASP cc_start: 0.8676 (m-30) cc_final: 0.8424 (m-30) REVERT: H 35 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8104 (mm-30) REVERT: H 47 GLN cc_start: 0.8888 (mt0) cc_final: 0.8656 (mt0) REVERT: H 60 ARG cc_start: 0.8541 (mmm-85) cc_final: 0.8324 (mmm-85) REVERT: H 68 ASP cc_start: 0.9164 (t0) cc_final: 0.8815 (t0) REVERT: H 116 LYS cc_start: 0.9323 (OUTLIER) cc_final: 0.9019 (ttpp) REVERT: H 119 THR cc_start: 0.9400 (m) cc_final: 0.9128 (p) outliers start: 12 outliers final: 5 residues processed: 158 average time/residue: 0.8587 time to fit residues: 143.0870 Evaluate side-chains 161 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 152 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 C residue 58 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain H residue 116 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 54 optimal weight: 0.0370 chunk 11 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 chunk 7 optimal weight: 0.0030 chunk 60 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 overall best weight: 0.4868 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.085324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.053049 restraints weight = 29824.716| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 2.03 r_work: 0.2575 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12438 Z= 0.146 Angle : 0.532 10.893 18061 Z= 0.316 Chirality : 0.031 0.195 2076 Planarity : 0.004 0.043 1287 Dihedral : 30.896 172.405 3954 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.70 % Allowed : 25.72 % Favored : 72.57 % 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: 2.97 (0.30), residues: 726 helix: 2.75 (0.21), residues: 548 sheet: None (None), residues: 0 loop : -0.63 (0.42), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 37 TYR 0.024 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 covalent geometry : bond 0.00320 (12438) covalent geometry : angle 0.53151 (18061) hydrogen bonds : bond 0.03455 ( 643) hydrogen bonds : angle 2.71435 ( 1679) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4089.68 seconds wall clock time: 70 minutes 11.74 seconds (4211.74 seconds total)