Starting phenix.real_space_refine on Fri Jul 3 02:45:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lrv_63344/07_2026/9lrv_63344.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lrv_63344/07_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_63344/07_2026/9lrv_63344.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lrv_63344/07_2026/9lrv_63344.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lrv_63344/07_2026/9lrv_63344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lrv_63344/07_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.43, per 1000 atoms: 0.21 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: 0.73 Conformation dependent library (CDL) restraints added in 154.8 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: 1.24 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: 1.81 Time building geometry restraints manager: 0.98 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: 16070 1.08 - 2.15: 1532 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: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.760 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.920 ------------------------------------------------------------------------------- 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 : 0.694 5.375 18061 Z= 0.622 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 0.69415 / 0.62 (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 : 0.312 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: 0.9200 time to fit residues: 193.4612 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 : 0.304 ------------------------------------------------------------------------------- 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: 7.9990 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 = 0.3537 r_free = 0.3537 target = 0.086176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.054170 restraints weight = 28928.778| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 2.04 r_work: 0.2585 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1532 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= 0.161 Angle : 0.614 6.656 18061 Z= 0.367 Chirality : 0.043 0.208 2076 Planarity : 0.005 0.038 1287 Dihedral : 30.985 170.349 3954 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.90 % Allowed : 16.70 % Favored : 80.41 % 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 0.007 0.001 ARG B 96 TYR 0.009 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 0.00277 / 0.16 (12438) covalent geometry : angle 0.61416 / 0.37 (18061) hydrogen bonds : bond 0.06096 / 4.25 ( 643) hydrogen bonds : angle 3.18216 / 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 : 0.301 Fit side-chains REVERT: B 36 ARG cc_start: 0.8520 (mtp85) cc_final: 0.8079 (mtp85) REVERT: B 45 LYS cc_start: 0.8957 (mtpp) cc_final: 0.8484 (mttt) REVERT: B 94 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8425 (mp10) REVERT: B 96 ARG cc_start: 0.8275 (mmt90) cc_final: 0.7905 (tpp-160) REVERT: C 66 GLU cc_start: 0.8990 (tt0) cc_final: 0.8475 (tm-30) REVERT: C 106 GLN cc_start: 0.9278 (mm-40) cc_final: 0.8893 (mm110) REVERT: D 68 ASP cc_start: 0.9140 (t0) cc_final: 0.8866 (t0) REVERT: E 34 LYS cc_start: 0.8948 (tttm) cc_final: 0.8743 (ttpm) REVERT: E 40 ASP cc_start: 0.8893 (p0) cc_final: 0.8657 (p0) REVERT: G 73 ARG cc_start: 0.8682 (mtm110) cc_final: 0.8476 (ttp80) REVERT: G 97 LYS cc_start: 0.9344 (tppp) cc_final: 0.9140 (ttmp) REVERT: H 60 ARG cc_start: 0.8539 (mmm-85) cc_final: 0.8298 (mmm-85) REVERT: H 68 ASP cc_start: 0.8962 (t0) cc_final: 0.8654 (t0) outliers start: 17 outliers final: 5 residues processed: 165 average time/residue: 0.8320 time to fit residues: 145.1857 Evaluate side-chains 154 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 148 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 94 GLN 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: 3.9990 chunk 27 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 0 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3527 r_free = 0.3527 target = 0.084898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.053008 restraints weight = 29440.478| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 2.06 r_work: 0.2565 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12438 Z= 0.182 Angle : 0.580 6.290 18061 Z= 0.344 Chirality : 0.041 0.226 2076 Planarity : 0.004 0.044 1287 Dihedral : 31.257 172.565 3954 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.56 % Allowed : 19.76 % Favored : 77.68 % 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: 2.43 (0.30), residues: 726 helix: 2.38 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.91 (0.41), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 96 TYR 0.012 0.001 TYR D 40 PHE 0.013 0.001 PHE E 59 TRP 0.002 0.001 TRP A 71 HIS 0.004 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.18 (12438) covalent geometry : angle 0.57965 / 0.34 (18061) hydrogen bonds : bond 0.05629 / 3.93 ( 643) hydrogen bonds : angle 2.99988 / 2.17 ( 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 165 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.329 Fit side-chains REVERT: B 36 ARG cc_start: 0.8538 (mtp85) cc_final: 0.8041 (mtt90) REVERT: B 53 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8625 (mp0) REVERT: B 92 LYS cc_start: 0.9510 (OUTLIER) cc_final: 0.9207 (ttpt) REVERT: B 96 ARG cc_start: 0.8547 (mmt90) cc_final: 0.8301 (tpp-160) REVERT: C 66 GLU cc_start: 0.9000 (tt0) cc_final: 0.8443 (tm-30) REVERT: C 106 GLN cc_start: 0.9391 (mm-40) cc_final: 0.8812 (mm110) REVERT: D 68 ASP cc_start: 0.9237 (t0) cc_final: 0.8850 (t0) REVERT: D 85 LYS cc_start: 0.9385 (OUTLIER) cc_final: 0.8953 (mtmm) REVERT: E 58 GLU cc_start: 0.8811 (tt0) cc_final: 0.8580 (tm-30) REVERT: F 80 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8561 (mtmt) REVERT: G 73 ARG cc_start: 0.8659 (mtm110) cc_final: 0.8447 (ttp80) REVERT: H 60 ARG cc_start: 0.8554 (mmm-85) cc_final: 0.8311 (mmm-85) REVERT: H 68 ASP cc_start: 0.9084 (t0) cc_final: 0.8664 (t0) outliers start: 15 outliers final: 5 residues processed: 158 average time/residue: 0.8163 time to fit residues: 136.2201 Evaluate side-chains 151 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 143 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 D residue 85 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: 1.9990 chunk 57 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 77 optimal weight: 9.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3526 r_free = 0.3526 target = 0.084706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.052807 restraints weight = 29411.476| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 2.04 r_work: 0.2568 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12438 Z= 0.167 Angle : 0.566 6.076 18061 Z= 0.336 Chirality : 0.040 0.211 2076 Planarity : 0.004 0.038 1287 Dihedral : 31.268 171.055 3954 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.90 % Allowed : 20.61 % Favored : 76.49 % 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: 2.65 (0.30), residues: 726 helix: 2.54 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -0.84 (0.41), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 96 TYR 0.022 0.001 TYR D 40 PHE 0.008 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 0.00322 / 0.17 (12438) covalent geometry : angle 0.56573 / 0.34 (18061) hydrogen bonds : bond 0.04881 / 3.40 ( 643) hydrogen bonds : angle 2.89085 / 2.10 ( 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 173 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: B 45 LYS cc_start: 0.8964 (mtpp) cc_final: 0.8461 (mttt) REVERT: B 92 LYS cc_start: 0.9506 (OUTLIER) cc_final: 0.9188 (ttpt) REVERT: B 94 GLN cc_start: 0.8935 (mm-40) cc_final: 0.8599 (mm-40) REVERT: C 66 GLU cc_start: 0.8998 (tt0) cc_final: 0.8452 (tm-30) REVERT: C 106 GLN cc_start: 0.9395 (mm-40) cc_final: 0.9151 (mm-40) REVERT: D 68 ASP cc_start: 0.9251 (t0) cc_final: 0.8842 (t0) REVERT: D 85 LYS cc_start: 0.9366 (OUTLIER) cc_final: 0.8952 (mtmm) REVERT: E 44 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8299 (mm-40) REVERT: F 80 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8586 (mtmt) REVERT: G 73 ARG cc_start: 0.8723 (mtm110) cc_final: 0.8509 (ttp80) REVERT: H 35 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8017 (mm-30) REVERT: H 60 ARG cc_start: 0.8583 (mmm-85) cc_final: 0.8364 (mmm-85) REVERT: H 68 ASP cc_start: 0.9118 (t0) cc_final: 0.8740 (t0) outliers start: 17 outliers final: 5 residues processed: 163 average time/residue: 0.7477 time to fit residues: 129.0231 Evaluate side-chains 156 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 80 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 97 optimal weight: 20.0000 chunk 58 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 76 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 17 GLN G 43 GLN G 91 ASN H 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.085589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.053820 restraints weight = 29151.695| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 2.06 r_work: 0.2584 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12438 Z= 0.137 Angle : 0.538 5.944 18061 Z= 0.325 Chirality : 0.040 0.210 2076 Planarity : 0.004 0.048 1287 Dihedral : 31.216 170.668 3954 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 3.24 % Allowed : 20.78 % Favored : 75.98 % 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: 2.67 (0.21), residues: 548 sheet: None (None), residues: 0 loop : -0.76 (0.41), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 96 TYR 0.024 0.001 TYR D 40 PHE 0.012 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/Z covalent geometry : bond 0.00231 / 0.14 (12438) covalent geometry : angle 0.53772 / 0.33 (18061) hydrogen bonds : bond 0.04494 / 3.11 ( 643) hydrogen bonds : angle 2.76787 / 2.01 ( 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 177 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.186 Fit side-chains REVERT: B 36 ARG cc_start: 0.8486 (mtp85) cc_final: 0.8012 (mtp85) REVERT: B 45 LYS cc_start: 0.8891 (mtpp) cc_final: 0.8449 (mttp) REVERT: B 92 LYS cc_start: 0.9493 (ttmm) cc_final: 0.9159 (ttpt) REVERT: C 66 GLU cc_start: 0.8967 (tt0) cc_final: 0.8443 (tm-30) REVERT: D 68 ASP cc_start: 0.9231 (t0) cc_final: 0.8846 (t0) REVERT: D 85 LYS cc_start: 0.9370 (OUTLIER) cc_final: 0.8976 (mtmm) REVERT: E 44 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8290 (mm-40) REVERT: F 80 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8616 (mtmt) REVERT: G 73 ARG cc_start: 0.8763 (mtm110) cc_final: 0.8534 (ttp80) REVERT: G 94 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8673 (mm-30) REVERT: H 35 GLU cc_start: 0.8538 (mm-30) cc_final: 0.7962 (mm-30) REVERT: H 60 ARG cc_start: 0.8538 (mmm-85) cc_final: 0.8337 (mmm-85) REVERT: H 68 ASP cc_start: 0.9131 (t0) cc_final: 0.8771 (t0) outliers start: 19 outliers final: 6 residues processed: 163 average time/residue: 0.7118 time to fit residues: 122.7437 Evaluate side-chains 153 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 144 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 38 SER Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 80 LYS Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 58 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 5 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 97 optimal weight: 30.0000 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: 0.5980 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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 = 0.3543 r_free = 0.3543 target = 0.085470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.053259 restraints weight = 29693.490| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 2.01 r_work: 0.2571 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2406 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= 0.143 Angle : 0.541 5.933 18061 Z= 0.324 Chirality : 0.039 0.208 2076 Planarity : 0.004 0.042 1287 Dihedral : 31.240 169.502 3954 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.07 % Allowed : 22.32 % Favored : 74.62 % 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 : -0.66 (0.42), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 96 TYR 0.024 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 0.00254 / 0.14 (12438) covalent geometry : angle 0.54131 / 0.32 (18061) hydrogen bonds : bond 0.04377 / 3.05 ( 643) hydrogen bonds : angle 2.72980 / 1.98 ( 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 172 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: B 92 LYS cc_start: 0.9479 (ttmm) cc_final: 0.9152 (ttpt) REVERT: B 94 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.7828 (mp10) REVERT: C 66 GLU cc_start: 0.8949 (tt0) cc_final: 0.8417 (tm-30) REVERT: C 106 GLN cc_start: 0.9310 (mm-40) cc_final: 0.9041 (mm110) REVERT: D 68 ASP cc_start: 0.9218 (t0) cc_final: 0.8823 (t0) REVERT: D 85 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.8940 (mtmm) REVERT: E 44 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8300 (mm-40) REVERT: F 80 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8626 (mtmt) REVERT: G 73 ARG cc_start: 0.8765 (mtm110) cc_final: 0.8553 (ttp80) REVERT: G 94 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8651 (mm-30) REVERT: H 68 ASP cc_start: 0.9134 (t0) cc_final: 0.8775 (t0) REVERT: H 116 LYS cc_start: 0.9265 (ttpp) cc_final: 0.8970 (ptmm) REVERT: H 119 THR cc_start: 0.9382 (m) cc_final: 0.9098 (p) outliers start: 18 outliers final: 7 residues processed: 163 average time/residue: 0.7278 time to fit residues: 125.4645 Evaluate side-chains 160 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 149 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 12 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 61 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 0.0270 chunk 72 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.086032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.054005 restraints weight = 29799.558| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 1.98 r_work: 0.2584 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 12438 Z= 0.131 Angle : 0.535 5.788 18061 Z= 0.322 Chirality : 0.039 0.205 2076 Planarity : 0.004 0.045 1287 Dihedral : 31.216 169.273 3954 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.21 % Allowed : 24.19 % Favored : 73.59 % 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: 3.02 (0.30), residues: 726 helix: 2.79 (0.21), residues: 548 sheet: None (None), residues: 0 loop : -0.64 (0.42), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 96 TYR 0.024 0.001 TYR D 40 PHE 0.007 0.001 PHE B 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 0.00227 / 0.13 (12438) covalent geometry : angle 0.53472 / 0.32 (18061) hydrogen bonds : bond 0.04206 / 2.92 ( 643) hydrogen bonds : angle 2.69324 / 1.95 ( 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 173 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: B 45 LYS cc_start: 0.8907 (mtpp) cc_final: 0.8451 (mttp) REVERT: B 92 LYS cc_start: 0.9474 (ttmm) cc_final: 0.9111 (ttpt) REVERT: B 94 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.7778 (mp10) REVERT: C 66 GLU cc_start: 0.8909 (tt0) cc_final: 0.8436 (tm-30) REVERT: C 106 GLN cc_start: 0.9288 (mm-40) cc_final: 0.8928 (mm110) REVERT: D 68 ASP cc_start: 0.9202 (t0) cc_final: 0.8800 (t0) REVERT: D 85 LYS cc_start: 0.9349 (OUTLIER) cc_final: 0.8961 (mtmm) REVERT: E 44 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8321 (mm-40) REVERT: F 80 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8609 (mtmt) REVERT: G 73 ARG cc_start: 0.8788 (mtm110) cc_final: 0.8570 (ttp80) REVERT: G 94 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8619 (mm-30) REVERT: H 35 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8235 (tp30) REVERT: H 68 ASP cc_start: 0.9115 (t0) cc_final: 0.8756 (t0) REVERT: H 116 LYS cc_start: 0.9250 (ttpp) cc_final: 0.8982 (ptmm) REVERT: H 119 THR cc_start: 0.9377 (m) cc_final: 0.9101 (p) outliers start: 13 outliers final: 5 residues processed: 166 average time/residue: 0.7126 time to fit residues: 125.6883 Evaluate side-chains 160 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 THR 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 F residue 80 LYS 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: 10.9990 chunk 47 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 96 optimal weight: 20.0000 chunk 48 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 67 optimal weight: 0.7980 chunk 61 optimal weight: 10.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.085678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.053692 restraints weight = 29891.601| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 1.99 r_work: 0.2580 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2539 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= 0.145 Angle : 0.536 5.750 18061 Z= 0.320 Chirality : 0.038 0.205 2076 Planarity : 0.004 0.039 1287 Dihedral : 31.234 168.559 3954 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.90 % Allowed : 23.17 % 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: 3.03 (0.30), residues: 726 helix: 2.81 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -0.68 (0.41), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 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 0.006 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.15 (12438) covalent geometry : angle 0.53563 / 0.32 (18061) hydrogen bonds : bond 0.04229 / 2.95 ( 643) hydrogen bonds : angle 2.69676 / 1.96 ( 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 172 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: B 45 LYS cc_start: 0.8940 (mtpp) cc_final: 0.8443 (mttt) REVERT: B 92 LYS cc_start: 0.9475 (ttmm) cc_final: 0.9106 (ttpt) REVERT: B 94 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.7798 (mp10) REVERT: C 66 GLU cc_start: 0.8986 (tt0) cc_final: 0.8476 (tm-30) REVERT: C 73 ARG cc_start: 0.8787 (ttp80) cc_final: 0.8546 (ttp80) REVERT: C 78 THR cc_start: 0.9235 (p) cc_final: 0.8938 (t) REVERT: C 106 GLN cc_start: 0.9308 (mm-40) cc_final: 0.8913 (mm110) REVERT: D 68 ASP cc_start: 0.9234 (t0) cc_final: 0.8813 (t0) REVERT: D 85 LYS cc_start: 0.9349 (OUTLIER) cc_final: 0.8986 (mtmm) REVERT: E 44 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8350 (mm-40) REVERT: E 60 VAL cc_start: 0.8521 (p) cc_final: 0.8290 (p) REVERT: G 73 ARG cc_start: 0.8772 (mtm110) cc_final: 0.8551 (ttp80) REVERT: G 94 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8649 (mm-30) REVERT: H 35 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8001 (mm-30) REVERT: H 68 ASP cc_start: 0.9123 (t0) cc_final: 0.8749 (t0) REVERT: H 116 LYS cc_start: 0.9253 (ttpp) cc_final: 0.8969 (ptmm) REVERT: H 119 THR cc_start: 0.9378 (m) cc_final: 0.9104 (p) outliers start: 17 outliers final: 7 residues processed: 164 average time/residue: 0.7060 time to fit residues: 122.6134 Evaluate side-chains 161 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 151 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 Chi-restraints excluded: chain G residue 38 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 97 optimal weight: 20.0000 chunk 62 optimal weight: 2.9990 chunk 70 optimal weight: 40.0000 chunk 89 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 78 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.086133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.054045 restraints weight = 29573.089| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 1.97 r_work: 0.2591 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 12438 Z= 0.136 Angle : 0.541 6.415 18061 Z= 0.322 Chirality : 0.039 0.330 2076 Planarity : 0.004 0.043 1287 Dihedral : 31.217 168.274 3954 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.21 % Allowed : 24.36 % Favored : 73.42 % 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: 3.08 (0.30), residues: 726 helix: 2.84 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -0.65 (0.42), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 96 TYR 0.025 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/Z covalent geometry : bond 0.00245 / 0.14 (12438) covalent geometry : angle 0.54061 / 0.32 (18061) hydrogen bonds : bond 0.04104 / 2.86 ( 643) hydrogen bonds : angle 2.70233 / 1.96 ( 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 174 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 161 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: B 45 LYS cc_start: 0.8859 (mtpp) cc_final: 0.8373 (mttt) REVERT: B 92 LYS cc_start: 0.9476 (ttmm) cc_final: 0.9114 (ttpt) REVERT: B 94 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.7841 (mp10) REVERT: C 66 GLU cc_start: 0.8954 (tt0) cc_final: 0.8592 (tm-30) REVERT: C 78 THR cc_start: 0.9227 (p) cc_final: 0.8937 (t) REVERT: C 106 GLN cc_start: 0.9303 (mm-40) cc_final: 0.8902 (mm110) REVERT: D 68 ASP cc_start: 0.9216 (t0) cc_final: 0.8817 (t0) REVERT: D 85 LYS cc_start: 0.9361 (OUTLIER) cc_final: 0.9000 (mtmm) REVERT: E 44 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8343 (mm-40) REVERT: E 60 VAL cc_start: 0.8600 (OUTLIER) cc_final: 0.8396 (p) REVERT: G 73 ARG cc_start: 0.8797 (mtm110) cc_final: 0.8566 (ttp80) REVERT: G 94 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8639 (mm-30) REVERT: H 35 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8006 (mm-30) REVERT: H 68 ASP cc_start: 0.9127 (t0) cc_final: 0.8771 (t0) REVERT: H 105 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8461 (mm-30) REVERT: H 108 LYS cc_start: 0.8773 (ttmm) cc_final: 0.8367 (mtmp) REVERT: H 116 LYS cc_start: 0.9265 (ttpp) cc_final: 0.9000 (ptmm) REVERT: H 119 THR cc_start: 0.9382 (m) cc_final: 0.9109 (p) outliers start: 13 outliers final: 7 residues processed: 167 average time/residue: 0.7174 time to fit residues: 127.0846 Evaluate side-chains 165 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 154 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 E residue 60 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 50 LEU 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: 0.8980 chunk 45 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 71 optimal weight: 20.0000 chunk 75 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 33 optimal weight: 0.0270 chunk 97 optimal weight: 20.0000 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.085954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.053764 restraints weight = 29993.772| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 2.01 r_work: 0.2588 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12438 Z= 0.139 Angle : 0.536 6.656 18061 Z= 0.320 Chirality : 0.038 0.205 2076 Planarity : 0.004 0.039 1287 Dihedral : 31.220 167.794 3954 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.04 % Allowed : 24.36 % Favored : 73.59 % 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 (0.30), residues: 726 helix: 2.81 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -0.66 (0.41), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 96 TYR 0.024 0.001 TYR D 40 PHE 0.007 0.001 PHE B 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 0.00253 / 0.14 (12438) covalent geometry : angle 0.53627 / 0.32 (18061) hydrogen bonds : bond 0.04093 / 2.86 ( 643) hydrogen bonds : angle 2.70516 / 1.96 ( 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 : 0.310 Fit side-chains revert: symmetry clash REVERT: B 45 LYS cc_start: 0.8874 (mtpp) cc_final: 0.8393 (mttt) REVERT: B 92 LYS cc_start: 0.9475 (ttmm) cc_final: 0.9117 (ttpt) REVERT: B 94 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.7834 (mp10) REVERT: C 66 GLU cc_start: 0.9036 (tt0) cc_final: 0.8484 (tm-30) REVERT: C 78 THR cc_start: 0.9222 (p) cc_final: 0.8938 (t) REVERT: C 106 GLN cc_start: 0.9336 (mm-40) cc_final: 0.8967 (mm110) REVERT: D 68 ASP cc_start: 0.9218 (t0) cc_final: 0.8821 (t0) REVERT: D 85 LYS cc_start: 0.9358 (OUTLIER) cc_final: 0.8972 (mtmm) REVERT: E 44 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8349 (mm-40) REVERT: E 60 VAL cc_start: 0.8480 (p) cc_final: 0.8274 (p) REVERT: F 80 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8669 (mtmt) REVERT: G 73 ARG cc_start: 0.8771 (mtm110) cc_final: 0.8560 (ttp80) REVERT: G 94 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8661 (mm-30) REVERT: H 35 GLU cc_start: 0.8589 (mm-30) cc_final: 0.7992 (mm-30) REVERT: H 68 ASP cc_start: 0.9135 (t0) cc_final: 0.8780 (t0) REVERT: H 105 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8487 (mm-30) REVERT: H 108 LYS cc_start: 0.8774 (ttmm) cc_final: 0.8375 (mtmp) REVERT: H 116 LYS cc_start: 0.9263 (ttpp) cc_final: 0.8972 (ptmm) REVERT: H 119 THR cc_start: 0.9381 (m) cc_final: 0.9109 (p) outliers start: 12 outliers final: 6 residues processed: 162 average time/residue: 0.7335 time to fit residues: 125.7946 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 : 0.321 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 11 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 17 GLN G 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.086042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.053901 restraints weight = 29885.199| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 2.00 r_work: 0.2587 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2738 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= 0.144 Angle : 0.540 7.197 18061 Z= 0.322 Chirality : 0.038 0.200 2076 Planarity : 0.004 0.048 1287 Dihedral : 31.238 167.398 3954 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.04 % Allowed : 24.53 % Favored : 73.42 % 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: 3.05 (0.30), residues: 726 helix: 2.82 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -0.66 (0.41), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 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 0.006 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 (12438) covalent geometry : angle 0.53984 / 0.32 (18061) hydrogen bonds : bond 0.04085 / 2.86 ( 643) hydrogen bonds : angle 2.73312 / 1.98 ( 1679) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3638.12 seconds wall clock time: 62 minutes 36.41 seconds (3756.41 seconds total)