Starting phenix.real_space_refine on Wed Aug 5 17:11:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d3s_46546/08_2026/9d3s_46546.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d3s_46546/08_2026/9d3s_46546.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d3s_46546/08_2026/9d3s_46546.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d3s_46546/08_2026/9d3s_46546.map" model { file = "/net/cci-nas-00/data/ceres_data/9d3s_46546/08_2026/9d3s_46546.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d3s_46546/08_2026/9d3s_46546.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.038 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 246 5.49 5 S 14 5.16 5 C 6102 2.51 5 N 2053 2.21 5 O 2524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10939 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 788 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 92} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 641 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 806 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 730 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 805 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 786 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "H" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 713 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 2530 Classifications: {'DNA': 123} Link IDs: {'rna3p': 122} Chain: "J" Number of atoms: 2513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 2513 Classifications: {'DNA': 123} Link IDs: {'rna3p': 122} Time building chain proxies: 2.30, per 1000 atoms: 0.21 Number of scatterers: 10939 At special positions: 0 Unit cell: (116.875, 76.67, 118.745, 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 14 16.00 P 246 15.00 O 2524 8.00 N 2053 7.00 C 6102 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: 0.77 Conformation dependent library (CDL) restraints added in 225.6 milliseconds 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1392 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 9 sheets defined 71.1% alpha, 2.7% beta 118 base pairs and 224 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.057A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.932A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 88 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 57 through 84 removed outlier: 3.953A pdb=" N ASN D 63 " --> pdb=" O MET D 59 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER D 64 " --> pdb=" O GLY D 60 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.507A pdb=" N GLU E 94 " --> pdb=" O MET E 90 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL E 101 " --> pdb=" O GLU E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.634A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 18 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 72 removed outlier: 3.537A pdb=" N ALA G 53 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA G 66 " --> pdb=" O ILE G 62 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA G 70 " --> pdb=" O ALA G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 47 removed outlier: 3.513A pdb=" N LYS H 43 " --> pdb=" O VAL H 39 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS H 46 " --> pdb=" O TYR H 42 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.642A pdb=" N ARG H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA H 81 " --> pdb=" O ALA H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.674A pdb=" N THR H 96 " --> pdb=" O ARG H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 123 removed outlier: 3.822A pdb=" N SER H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.131A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.514A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.903A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.822A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.135A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 380 hydrogen bonds defined for protein. 1128 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 308 hydrogen bonds 616 hydrogen bond angles 0 basepair planarities 118 basepair parallelities 224 stacking parallelities Total time for adding SS restraints: 2.05 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.21: 7 1.21 - 1.48: 7316 1.48 - 1.75: 4281 1.75 - 2.02: 26 2.02 - 2.29: 1 Bond restraints: 11631 Sorted by residual: bond pdb=" N PRO C 48 " pdb=" CD PRO C 48 " ideal model delta sigma weight residual 1.473 2.288 -0.815 1.40e-02 5.10e+03 3.39e+03 bond pdb=" CB PRO C 26 " pdb=" CG PRO C 26 " ideal model delta sigma weight residual 1.492 0.946 0.546 5.00e-02 4.00e+02 1.19e+02 bond pdb=" CG PRO C 26 " pdb=" CD PRO C 26 " ideal model delta sigma weight residual 1.503 1.160 0.343 3.40e-02 8.65e+02 1.02e+02 bond pdb=" CG PRO C 48 " pdb=" CD PRO C 48 " ideal model delta sigma weight residual 1.503 1.364 0.139 3.40e-02 8.65e+02 1.67e+01 bond pdb=" C3' DG J 63 " pdb=" C2' DG J 63 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 ... (remaining 11626 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.77: 16754 14.77 - 29.54: 3 29.54 - 44.31: 1 44.31 - 59.08: 0 59.08 - 73.85: 1 Bond angle restraints: 16759 Sorted by residual: angle pdb=" CA PRO C 48 " pdb=" N PRO C 48 " pdb=" CD PRO C 48 " ideal model delta sigma weight residual 112.00 76.02 35.98 1.40e+00 5.10e-01 6.61e+02 angle pdb=" CB PRO C 26 " pdb=" CG PRO C 26 " pdb=" CD PRO C 26 " ideal model delta sigma weight residual 106.10 179.95 -73.85 3.20e+00 9.77e-02 5.33e+02 angle pdb=" N PRO C 48 " pdb=" CD PRO C 48 " pdb=" CG PRO C 48 " ideal model delta sigma weight residual 103.20 75.80 27.40 1.50e+00 4.44e-01 3.34e+02 angle pdb=" N PRO C 26 " pdb=" CD PRO C 26 " pdb=" CG PRO C 26 " ideal model delta sigma weight residual 103.20 79.88 23.32 1.50e+00 4.44e-01 2.42e+02 angle pdb=" CA PRO C 26 " pdb=" CB PRO C 26 " pdb=" CG PRO C 26 " ideal model delta sigma weight residual 104.50 76.89 27.61 1.90e+00 2.77e-01 2.11e+02 ... (remaining 16754 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.50: 4527 26.50 - 53.00: 1490 53.00 - 79.50: 314 79.50 - 106.00: 11 106.00 - 132.50: 1 Dihedral angle restraints: 6343 sinusoidal: 4181 harmonic: 2162 Sorted by residual: dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 87.50 132.50 1 3.50e+01 8.16e-04 1.31e+01 dihedral pdb=" CB GLU C 41 " pdb=" CG GLU C 41 " pdb=" CD GLU C 41 " pdb=" OE1 GLU C 41 " ideal model delta sinusoidal sigma weight residual 0.00 89.44 -89.44 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU E 97 " pdb=" CG GLU E 97 " pdb=" CD GLU E 97 " pdb=" OE1 GLU E 97 " ideal model delta sinusoidal sigma weight residual 0.00 87.38 -87.38 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 6340 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1331 0.044 - 0.088: 452 0.088 - 0.132: 118 0.132 - 0.175: 6 0.175 - 0.219: 1 Chirality restraints: 1908 Sorted by residual: chirality pdb=" CB ILE H 94 " pdb=" CA ILE H 94 " pdb=" CG1 ILE H 94 " pdb=" CG2 ILE H 94 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA PRO C 26 " pdb=" N PRO C 26 " pdb=" C PRO C 26 " pdb=" CB PRO C 26 " both_signs ideal model delta sigma weight residual False 2.72 2.88 -0.16 2.00e-01 2.50e+01 6.71e-01 chirality pdb=" C3' DT I -67 " pdb=" C4' DT I -67 " pdb=" O3' DT I -67 " pdb=" C2' DT I -67 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.38e-01 ... (remaining 1905 not shown) Planarity restraints: 1272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 47 " 0.196 5.00e-02 4.00e+02 2.15e-01 7.42e+01 pdb=" N PRO C 48 " -0.364 5.00e-02 4.00e+02 pdb=" CA PRO C 48 " 0.092 5.00e-02 4.00e+02 pdb=" CD PRO C 48 " 0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 25 " 0.062 5.00e-02 4.00e+02 8.49e-02 1.15e+01 pdb=" N PRO C 26 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO C 26 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 26 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 17 " 0.027 2.00e-02 2.50e+03 1.31e-02 4.29e+00 pdb=" N1 DT I 17 " -0.026 2.00e-02 2.50e+03 pdb=" C2 DT I 17 " -0.006 2.00e-02 2.50e+03 pdb=" O2 DT I 17 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DT I 17 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DT I 17 " 0.003 2.00e-02 2.50e+03 pdb=" O4 DT I 17 " 0.013 2.00e-02 2.50e+03 pdb=" C5 DT I 17 " -0.000 2.00e-02 2.50e+03 pdb=" C7 DT I 17 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DT I 17 " -0.000 2.00e-02 2.50e+03 ... (remaining 1269 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 30 2.51 - 3.11: 7334 3.11 - 3.71: 19465 3.71 - 4.30: 27755 4.30 - 4.90: 40587 Nonbonded interactions: 95171 Sorted by model distance: nonbonded pdb=" OE1 GLU E 73 " pdb=" ND2 ASN F 25 " model vdw 1.917 3.120 nonbonded pdb=" CD PRO C 48 " pdb=" N VAL C 49 " model vdw 2.025 3.520 nonbonded pdb=" OG1 THR B 73 " pdb=" OD2 ASP B 85 " model vdw 2.179 3.040 nonbonded pdb=" NH2 ARG C 20 " pdb=" O SER D 124 " model vdw 2.197 3.120 nonbonded pdb=" N GLU A 59 " pdb=" OE1 GLU A 59 " model vdw 2.231 3.120 ... (remaining 95166 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 39 through 133 or (resid 134 and (name N or name CA or nam \ e C or name O or name CB )))) selection = (chain 'E' and (resid 39 through 41 or (resid 42 and (name N or name CA or name \ C or name O or name CB )) or resid 43 through 134)) } ncs_group { reference = (chain 'B' and resid 24 through 102) selection = (chain 'F' and (resid 24 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = (chain 'C' and resid 17 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 33 through 123) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.500 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.210 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 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 : 0.012 0.815 11631 Z= 0.771 Angle : 1.074 73.848 16759 Z= 0.757 Chirality : 0.045 0.219 1908 Planarity : 0.008 0.215 1272 Dihedral : 28.495 132.498 4951 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.33 % Allowed : 26.67 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.31), residues: 732 helix: 1.05 (0.23), residues: 537 sheet: None (None), residues: 0 loop : -1.05 (0.42), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 52 TYR 0.035 0.002 TYR G 50 PHE 0.026 0.003 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.01168 / 0.77 (11631) covalent geometry : angle 1.07438 / 0.76 (16759) hydrogen bonds : bond 0.10515 / 6.52 ( 688) hydrogen bonds : angle 4.59694 / 3.17 ( 1744) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 102 time to evaluate : 0.297 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 103 average time/residue: 0.1329 time to fit residues: 18.1173 Evaluate side-chains 103 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 30.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 HIS H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.203030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.158970 restraints weight = 14464.255| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 1.28 r_work: 0.3864 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3739 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.0536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 11631 Z= 0.144 Angle : 0.627 7.196 16759 Z= 0.373 Chirality : 0.045 0.236 1908 Planarity : 0.005 0.064 1272 Dihedral : 30.678 129.415 3498 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.44 % Allowed : 25.20 % Favored : 72.36 % 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: 1.30 (0.31), residues: 732 helix: 1.48 (0.23), residues: 541 sheet: None (None), residues: 0 loop : -0.87 (0.42), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 52 TYR 0.016 0.001 TYR E 54 PHE 0.025 0.002 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.14 (11631) covalent geometry : angle 0.62707 / 0.37 (16759) hydrogen bonds : bond 0.04762 / 3.28 ( 688) hydrogen bonds : angle 3.30730 / 2.32 ( 1744) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: C 41 GLU cc_start: 0.7400 (mm-30) cc_final: 0.7054 (mt-10) outliers start: 15 outliers final: 12 residues processed: 121 average time/residue: 0.1183 time to fit residues: 18.8024 Evaluate side-chains 115 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 84 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 34 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 66 optimal weight: 8.9990 chunk 83 optimal weight: 30.0000 chunk 82 optimal weight: 30.0000 chunk 50 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 chunk 7 optimal weight: 0.6980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN F 25 ASN H 67 ASN H 82 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.200199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.155643 restraints weight = 14568.507| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 1.27 r_work: 0.3828 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3702 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.0774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11631 Z= 0.169 Angle : 0.641 9.499 16759 Z= 0.376 Chirality : 0.045 0.218 1908 Planarity : 0.005 0.061 1272 Dihedral : 30.800 129.577 3495 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.76 % Allowed : 26.18 % Favored : 71.06 % 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: 1.26 (0.31), residues: 732 helix: 1.43 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.83 (0.42), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 52 TYR 0.020 0.002 TYR E 54 PHE 0.021 0.002 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.17 (11631) covalent geometry : angle 0.64074 / 0.38 (16759) hydrogen bonds : bond 0.04980 / 3.46 ( 688) hydrogen bonds : angle 3.28938 / 2.32 ( 1744) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: C 41 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7114 (mt-10) REVERT: H 42 TYR cc_start: 0.7499 (OUTLIER) cc_final: 0.6630 (m-80) outliers start: 17 outliers final: 14 residues processed: 122 average time/residue: 0.1252 time to fit residues: 20.0620 Evaluate side-chains 118 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 48 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 71 optimal weight: 30.0000 chunk 9 optimal weight: 0.9980 chunk 54 optimal weight: 0.4980 chunk 85 optimal weight: 30.0000 chunk 2 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN E 125 GLN H 67 ASN H 82 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.202325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.155771 restraints weight = 14442.233| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 1.34 r_work: 0.3823 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3694 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.0829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11631 Z= 0.137 Angle : 0.615 6.948 16759 Z= 0.362 Chirality : 0.045 0.232 1908 Planarity : 0.004 0.065 1272 Dihedral : 30.847 129.846 3495 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.58 % Allowed : 26.02 % Favored : 70.41 % 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: 1.55 (0.31), residues: 732 helix: 1.64 (0.23), residues: 542 sheet: None (None), residues: 0 loop : -0.72 (0.42), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 52 TYR 0.012 0.001 TYR E 54 PHE 0.021 0.002 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.14 (11631) covalent geometry : angle 0.61517 / 0.36 (16759) hydrogen bonds : bond 0.04539 / 3.15 ( 688) hydrogen bonds : angle 3.15358 / 2.22 ( 1744) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: C 41 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7120 (mt-10) REVERT: H 42 TYR cc_start: 0.7396 (OUTLIER) cc_final: 0.6503 (m-80) outliers start: 22 outliers final: 17 residues processed: 120 average time/residue: 0.1234 time to fit residues: 19.8682 Evaluate side-chains 120 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 56 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 80 optimal weight: 20.0000 chunk 49 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.202250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.155735 restraints weight = 14335.106| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 1.33 r_work: 0.3822 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3693 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11631 Z= 0.139 Angle : 0.610 6.829 16759 Z= 0.357 Chirality : 0.044 0.225 1908 Planarity : 0.004 0.045 1272 Dihedral : 30.905 129.723 3495 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.39 % Allowed : 25.53 % Favored : 70.08 % 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: 1.76 (0.31), residues: 732 helix: 1.81 (0.23), residues: 543 sheet: None (None), residues: 0 loop : -0.67 (0.43), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 52 TYR 0.022 0.001 TYR E 54 PHE 0.020 0.002 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.14 (11631) covalent geometry : angle 0.61014 / 0.36 (16759) hydrogen bonds : bond 0.04436 / 3.08 ( 688) hydrogen bonds : angle 3.05414 / 2.15 ( 1744) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: C 41 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7143 (mt-10) REVERT: E 82 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.6878 (tt) REVERT: H 42 TYR cc_start: 0.7412 (OUTLIER) cc_final: 0.6679 (m-80) outliers start: 27 outliers final: 19 residues processed: 125 average time/residue: 0.1241 time to fit residues: 20.6778 Evaluate side-chains 125 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 31 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 81 optimal weight: 30.0000 chunk 83 optimal weight: 30.0000 chunk 46 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 72 optimal weight: 50.0000 chunk 7 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN E 125 GLN F 25 ASN G 104 GLN H 82 HIS H 84 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.200025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.153289 restraints weight = 14305.300| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 1.31 r_work: 0.3786 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3655 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11631 Z= 0.183 Angle : 0.649 7.612 16759 Z= 0.374 Chirality : 0.045 0.215 1908 Planarity : 0.005 0.084 1272 Dihedral : 30.945 129.132 3495 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.39 % Allowed : 25.85 % Favored : 69.76 % 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: 1.38 (0.31), residues: 732 helix: 1.52 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -0.78 (0.43), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 52 TYR 0.015 0.002 TYR E 54 PHE 0.018 0.002 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.18 (11631) covalent geometry : angle 0.64855 / 0.37 (16759) hydrogen bonds : bond 0.05051 / 3.52 ( 688) hydrogen bonds : angle 3.20973 / 2.27 ( 1744) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.174 Fit side-chains revert: symmetry clash REVERT: C 41 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7265 (mt-10) REVERT: E 82 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7045 (tt) REVERT: H 42 TYR cc_start: 0.7460 (OUTLIER) cc_final: 0.6672 (m-80) REVERT: H 84 ASN cc_start: 0.7941 (OUTLIER) cc_final: 0.7690 (t0) outliers start: 27 outliers final: 19 residues processed: 126 average time/residue: 0.1130 time to fit residues: 19.0636 Evaluate side-chains 130 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 74 optimal weight: 30.0000 chunk 67 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN E 125 GLN F 25 ASN G 38 ASN G 73 ASN G 104 GLN H 67 ASN H 82 HIS H 84 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.200864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.154516 restraints weight = 14180.332| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 1.30 r_work: 0.3800 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3671 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11631 Z= 0.154 Angle : 0.630 7.487 16759 Z= 0.364 Chirality : 0.045 0.224 1908 Planarity : 0.004 0.055 1272 Dihedral : 30.980 129.441 3495 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.55 % Allowed : 25.69 % Favored : 69.76 % 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: 1.48 (0.31), residues: 732 helix: 1.60 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -0.77 (0.43), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 52 TYR 0.017 0.001 TYR E 54 PHE 0.020 0.002 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.15 (11631) covalent geometry : angle 0.62969 / 0.36 (16759) hydrogen bonds : bond 0.04654 / 3.24 ( 688) hydrogen bonds : angle 3.12146 / 2.20 ( 1744) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.242 Fit side-chains REVERT: B 95 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.6696 (ptp90) REVERT: C 41 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7377 (mt-10) REVERT: E 82 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7182 (tt) REVERT: H 42 TYR cc_start: 0.7464 (OUTLIER) cc_final: 0.6710 (m-80) outliers start: 28 outliers final: 22 residues processed: 122 average time/residue: 0.1151 time to fit residues: 18.7150 Evaluate side-chains 130 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 30.0000 chunk 2 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 73 optimal weight: 40.0000 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 41 optimal weight: 0.8980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN G 38 ASN H 82 HIS H 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.201288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.154938 restraints weight = 14222.722| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 1.30 r_work: 0.3808 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3679 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11631 Z= 0.148 Angle : 0.627 7.383 16759 Z= 0.362 Chirality : 0.044 0.224 1908 Planarity : 0.004 0.047 1272 Dihedral : 30.982 129.487 3495 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.23 % Allowed : 26.34 % Favored : 69.43 % 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: 1.57 (0.31), residues: 732 helix: 1.67 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -0.75 (0.43), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 52 TYR 0.017 0.001 TYR E 54 PHE 0.020 0.002 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.15 (11631) covalent geometry : angle 0.62654 / 0.36 (16759) hydrogen bonds : bond 0.04531 / 3.15 ( 688) hydrogen bonds : angle 3.07937 / 2.17 ( 1744) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.203 Fit side-chains REVERT: B 95 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.6684 (ptp90) REVERT: C 41 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7378 (mt-10) REVERT: E 82 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7105 (tt) REVERT: H 42 TYR cc_start: 0.7483 (OUTLIER) cc_final: 0.6748 (m-80) outliers start: 26 outliers final: 22 residues processed: 121 average time/residue: 0.1164 time to fit residues: 18.7917 Evaluate side-chains 127 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 35 optimal weight: 4.9990 chunk 79 optimal weight: 20.0000 chunk 37 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 87 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 chunk 90 optimal weight: 20.0000 chunk 85 optimal weight: 30.0000 chunk 66 optimal weight: 3.9990 chunk 77 optimal weight: 30.0000 chunk 45 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN F 25 ASN G 104 GLN H 82 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.199201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.152743 restraints weight = 14107.674| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 1.29 r_work: 0.3778 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3646 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11631 Z= 0.192 Angle : 0.665 7.901 16759 Z= 0.380 Chirality : 0.046 0.214 1908 Planarity : 0.004 0.041 1272 Dihedral : 30.992 129.050 3495 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.72 % Allowed : 26.02 % Favored : 69.27 % 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: 1.24 (0.31), residues: 732 helix: 1.43 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.89 (0.42), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 52 TYR 0.018 0.002 TYR E 54 PHE 0.018 0.002 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.19 (11631) covalent geometry : angle 0.66450 / 0.38 (16759) hydrogen bonds : bond 0.05092 / 3.54 ( 688) hydrogen bonds : angle 3.22927 / 2.28 ( 1744) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.241 Fit side-chains REVERT: B 95 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.6825 (ptp90) REVERT: C 41 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7370 (mt-10) REVERT: H 42 TYR cc_start: 0.7542 (OUTLIER) cc_final: 0.6830 (m-80) outliers start: 29 outliers final: 25 residues processed: 126 average time/residue: 0.1142 time to fit residues: 19.2931 Evaluate side-chains 137 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 0.8980 chunk 79 optimal weight: 20.0000 chunk 40 optimal weight: 0.0970 chunk 75 optimal weight: 30.0000 chunk 57 optimal weight: 9.9990 chunk 72 optimal weight: 50.0000 chunk 36 optimal weight: 0.5980 chunk 34 optimal weight: 0.4980 chunk 26 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN G 38 ASN H 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.202001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.157259 restraints weight = 14361.387| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 1.33 r_work: 0.3835 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3705 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11631 Z= 0.136 Angle : 0.629 8.172 16759 Z= 0.362 Chirality : 0.044 0.228 1908 Planarity : 0.004 0.041 1272 Dihedral : 31.002 129.652 3495 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.25 % Allowed : 27.48 % Favored : 69.27 % 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: 1.74 (0.31), residues: 732 helix: 1.82 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.78 (0.42), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 52 TYR 0.015 0.001 TYR E 54 PHE 0.022 0.002 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.14 (11631) covalent geometry : angle 0.62915 / 0.36 (16759) hydrogen bonds : bond 0.04296 / 2.97 ( 688) hydrogen bonds : angle 3.00381 / 2.11 ( 1744) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.195 Fit side-chains REVERT: C 41 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7281 (mt-10) REVERT: H 42 TYR cc_start: 0.7632 (OUTLIER) cc_final: 0.6977 (m-80) outliers start: 20 outliers final: 19 residues processed: 118 average time/residue: 0.1230 time to fit residues: 19.0094 Evaluate side-chains 125 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 71 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 14 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 81 optimal weight: 40.0000 chunk 53 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN G 38 ASN H 82 HIS H 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.201541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.157145 restraints weight = 14357.355| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 1.26 r_work: 0.3839 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3713 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11631 Z= 0.143 Angle : 0.623 8.022 16759 Z= 0.359 Chirality : 0.044 0.215 1908 Planarity : 0.004 0.041 1272 Dihedral : 30.958 129.182 3495 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.74 % Allowed : 27.15 % Favored : 69.11 % 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: 1.81 (0.31), residues: 732 helix: 1.88 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.77 (0.42), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 52 TYR 0.008 0.001 TYR H 40 PHE 0.020 0.002 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.14 (11631) covalent geometry : angle 0.62322 / 0.36 (16759) hydrogen bonds : bond 0.04396 / 3.03 ( 688) hydrogen bonds : angle 2.98979 / 2.11 ( 1744) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2723.73 seconds wall clock time: 47 minutes 0.11 seconds (2820.11 seconds total)