Starting phenix.real_space_refine on Thu Jul 2 23:25:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d3s_46546/07_2026/9d3s_46546.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d3s_46546/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9d3s_46546/07_2026/9d3s_46546.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d3s_46546/07_2026/9d3s_46546.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9d3s_46546/07_2026/9d3s_46546.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d3s_46546/07_2026/9d3s_46546.map" } 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): 0.00s 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: 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: 1.77, per 1000 atoms: 0.16 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: 0.81 Conformation dependent library (CDL) restraints added in 209.9 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: 1.03 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: 1.80 Time building geometry restraints manager: 1.04 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: 0.510 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 9.330 Find NCS groups from input model: 0.080 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: 0.000 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.060 ------------------------------------------------------------------------------- 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 : 1.070 73.848 16759 Z= 0.752 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 1.06987 / 0.75 (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 : 0.279 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 103 average time/residue: 0.1086 time to fit residues: 14.8075 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 : 0.249 ------------------------------------------------------------------------------- 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: 8.9990 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 = 0.4473 r_free = 0.4473 target = 0.203003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.159084 restraints weight = 14476.320| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 1.27 r_work: 0.3865 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3739 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.0529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 11631 Z= 0.143 Angle : 0.615 7.129 16759 Z= 0.370 Chirality : 0.044 0.234 1908 Planarity : 0.005 0.061 1272 Dihedral : 30.736 129.128 3498 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.60 % Allowed : 25.20 % Favored : 72.20 % 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: 1.29 (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 0.017 0.001 TYR E 54 PHE 0.026 0.002 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.14 (11631) covalent geometry : angle 0.61531 / 0.37 (16759) hydrogen bonds : bond 0.04787 / 3.30 ( 688) hydrogen bonds : angle 3.31454 / 2.33 ( 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: 16 poor density : 111 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: C 41 GLU cc_start: 0.7388 (mm-30) cc_final: 0.7046 (mt-10) outliers start: 16 outliers final: 13 residues processed: 121 average time/residue: 0.1153 time to fit residues: 18.2582 Evaluate side-chains 115 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.194 ------------------------------------------------------------------------------- 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 82 THR 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 Chi-restraints excluded: chain H residue 106 LEU 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: 0.7980 chunk 49 optimal weight: 0.7980 chunk 66 optimal weight: 8.9990 chunk 83 optimal weight: 30.0000 chunk 82 optimal weight: 40.0000 chunk 50 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 chunk 7 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN E 125 GLN H 67 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.203278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.157041 restraints weight = 14392.042| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 1.33 r_work: 0.3841 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3714 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.0760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11631 Z= 0.140 Angle : 0.600 9.161 16759 Z= 0.359 Chirality : 0.043 0.221 1908 Planarity : 0.004 0.059 1272 Dihedral : 30.862 129.865 3495 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.11 % Allowed : 26.50 % Favored : 71.38 % 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: 1.59 (0.31), residues: 732 helix: 1.66 (0.23), residues: 542 sheet: None (None), residues: 0 loop : -0.65 (0.42), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 52 TYR 0.019 0.001 TYR E 54 PHE 0.020 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.14 (11631) covalent geometry : angle 0.60017 / 0.36 (16759) hydrogen bonds : bond 0.04514 / 3.12 ( 688) hydrogen bonds : angle 3.15050 / 2.22 ( 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 124 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: C 41 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7096 (mt-10) REVERT: H 42 TYR cc_start: 0.7329 (OUTLIER) cc_final: 0.6465 (m-80) outliers start: 13 outliers final: 11 residues processed: 116 average time/residue: 0.1308 time to fit residues: 20.1001 Evaluate side-chains 114 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 B residue 84 MET 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 42 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 48 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 71 optimal weight: 30.0000 chunk 9 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 85 optimal weight: 30.0000 chunk 2 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN C 68 ASN E 125 GLN H 82 HIS H 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.201204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.154598 restraints weight = 14348.265| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 1.31 r_work: 0.3800 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3673 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.0933 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= 0.158 Angle : 0.614 7.426 16759 Z= 0.362 Chirality : 0.044 0.217 1908 Planarity : 0.005 0.060 1272 Dihedral : 30.976 129.209 3495 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.07 % Allowed : 25.53 % 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: 1.52 (0.31), residues: 732 helix: 1.61 (0.23), residues: 542 sheet: None (None), residues: 0 loop : -0.68 (0.43), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 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 0.00291 / 0.16 (11631) covalent geometry : angle 0.61390 / 0.36 (16759) hydrogen bonds : bond 0.04796 / 3.34 ( 688) hydrogen bonds : angle 3.16561 / 2.23 ( 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 132 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: C 41 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7164 (mt-10) REVERT: H 42 TYR cc_start: 0.7394 (OUTLIER) cc_final: 0.6655 (m-80) outliers start: 25 outliers final: 19 residues processed: 122 average time/residue: 0.1219 time to fit residues: 19.9248 Evaluate side-chains 121 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 GLN 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 84 ASN 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: 1.9990 chunk 30 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 80 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 H 82 HIS H 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.201742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.155017 restraints weight = 14326.507| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 1.34 r_work: 0.3817 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3686 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.1017 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 : 0.601 7.013 16759 Z= 0.354 Chirality : 0.043 0.222 1908 Planarity : 0.004 0.043 1272 Dihedral : 31.018 129.582 3495 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % 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: 1.71 (0.31), residues: 732 helix: 1.75 (0.23), residues: 542 sheet: None (None), residues: 0 loop : -0.64 (0.43), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 52 TYR 0.011 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 0.00251 / 0.14 (11631) covalent geometry : angle 0.60132 / 0.35 (16759) hydrogen bonds : bond 0.04461 / 3.10 ( 688) hydrogen bonds : angle 3.07423 / 2.16 ( 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 136 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: C 41 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7134 (mt-10) REVERT: H 42 TYR cc_start: 0.7379 (OUTLIER) cc_final: 0.6635 (m-80) outliers start: 27 outliers final: 20 residues processed: 120 average time/residue: 0.1305 time to fit residues: 20.6906 Evaluate side-chains 126 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 GLN 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 89 ASN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 52 THR 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 62 MET Chi-restraints excluded: chain H residue 85 LYS 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: 0.9990 chunk 81 optimal weight: 30.0000 chunk 83 optimal weight: 30.0000 chunk 46 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 2 optimal weight: 0.3980 chunk 72 optimal weight: 50.0000 chunk 7 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN G 73 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 = 0.4451 r_free = 0.4451 target = 0.202089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.155864 restraints weight = 14289.516| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 1.31 r_work: 0.3818 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3689 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.1075 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= 0.144 Angle : 0.598 7.015 16759 Z= 0.352 Chirality : 0.043 0.221 1908 Planarity : 0.004 0.042 1272 Dihedral : 31.029 129.459 3495 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.07 % Allowed : 27.32 % Favored : 68.62 % 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: 1.76 (0.31), residues: 732 helix: 1.79 (0.23), residues: 543 sheet: None (None), residues: 0 loop : -0.62 (0.43), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 52 TYR 0.008 0.001 TYR B 51 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 0.00259 / 0.14 (11631) covalent geometry : angle 0.59772 / 0.35 (16759) hydrogen bonds : bond 0.04440 / 3.08 ( 688) hydrogen bonds : angle 3.04668 / 2.14 ( 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 137 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: C 41 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7202 (mt-10) REVERT: E 82 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.6875 (tt) REVERT: H 42 TYR cc_start: 0.7384 (OUTLIER) cc_final: 0.6643 (m-80) REVERT: H 84 ASN cc_start: 0.7781 (OUTLIER) cc_final: 0.7562 (t0) outliers start: 25 outliers final: 19 residues processed: 124 average time/residue: 0.1413 time to fit residues: 23.1869 Evaluate side-chains 131 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 39 optimal weight: 0.9990 chunk 74 optimal weight: 30.0000 chunk 67 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 = 0.4425 r_free = 0.4425 target = 0.199480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.153003 restraints weight = 14204.703| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 1.31 r_work: 0.3784 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3654 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11631 Z= 0.194 Angle : 0.643 7.805 16759 Z= 0.372 Chirality : 0.045 0.210 1908 Planarity : 0.004 0.043 1272 Dihedral : 31.051 128.902 3495 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.23 % Allowed : 26.83 % Favored : 68.94 % 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: 1.34 (0.31), residues: 732 helix: 1.49 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -0.80 (0.43), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 35 TYR 0.010 0.002 TYR G 57 PHE 0.020 0.002 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.19 (11631) covalent geometry : angle 0.64251 / 0.37 (16759) hydrogen bonds : bond 0.05096 / 3.54 ( 688) hydrogen bonds : angle 3.21685 / 2.27 ( 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 137 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.290 Fit side-chains REVERT: C 41 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7323 (mt-10) REVERT: E 82 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7227 (tt) REVERT: H 42 TYR cc_start: 0.7483 (OUTLIER) cc_final: 0.6753 (m-80) outliers start: 26 outliers final: 18 residues processed: 126 average time/residue: 0.1282 time to fit residues: 21.6118 Evaluate side-chains 128 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 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 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 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: 2.9990 chunk 29 optimal weight: 0.9990 chunk 73 optimal weight: 30.0000 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 G 73 ASN H 67 ASN 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 = 0.4461 r_free = 0.4461 target = 0.202137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.155291 restraints weight = 14290.747| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 1.33 r_work: 0.3823 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3691 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.1232 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= 0.135 Angle : 0.606 7.024 16759 Z= 0.354 Chirality : 0.044 0.228 1908 Planarity : 0.004 0.043 1272 Dihedral : 31.075 129.496 3495 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.90 % Allowed : 27.48 % Favored : 68.62 % 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: 1.76 (0.31), residues: 732 helix: 1.81 (0.23), residues: 542 sheet: None (None), residues: 0 loop : -0.68 (0.43), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 35 TYR 0.008 0.001 TYR B 51 PHE 0.022 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.14 (11631) covalent geometry : angle 0.60560 / 0.35 (16759) hydrogen bonds : bond 0.04324 / 2.99 ( 688) hydrogen bonds : angle 3.01143 / 2.12 ( 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 128 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.217 Fit side-chains REVERT: C 41 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7291 (mt-10) REVERT: E 82 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7129 (tt) REVERT: H 42 TYR cc_start: 0.7431 (OUTLIER) cc_final: 0.6747 (m-80) outliers start: 24 outliers final: 19 residues processed: 115 average time/residue: 0.1203 time to fit residues: 18.4848 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 : 0.289 ------------------------------------------------------------------------------- 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 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 96 THR Chi-restraints excluded: chain H residue 42 TYR 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: 5.9990 chunk 79 optimal weight: 20.0000 chunk 37 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 87 optimal weight: 20.0000 chunk 16 optimal weight: 0.0570 chunk 90 optimal weight: 20.0000 chunk 85 optimal weight: 30.0000 chunk 66 optimal weight: 8.9990 chunk 77 optimal weight: 30.0000 chunk 45 optimal weight: 1.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.200851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.154342 restraints weight = 14067.211| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 1.30 r_work: 0.3798 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3669 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11631 Z= 0.166 Angle : 0.629 7.468 16759 Z= 0.364 Chirality : 0.044 0.215 1908 Planarity : 0.004 0.042 1272 Dihedral : 31.059 129.097 3495 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.39 % Allowed : 27.32 % Favored : 68.29 % 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: 1.61 (0.31), residues: 732 helix: 1.70 (0.23), residues: 542 sheet: None (None), residues: 0 loop : -0.73 (0.42), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 35 TYR 0.008 0.001 TYR G 57 PHE 0.020 0.002 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.17 (11631) covalent geometry : angle 0.62903 / 0.36 (16759) hydrogen bonds : bond 0.04692 / 3.25 ( 688) hydrogen bonds : angle 3.10115 / 2.19 ( 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 137 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.270 Fit side-chains REVERT: B 95 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.6747 (ptp90) REVERT: C 41 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7292 (mt-10) REVERT: E 82 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7133 (tt) REVERT: H 42 TYR cc_start: 0.7482 (OUTLIER) cc_final: 0.6803 (m-80) outliers start: 27 outliers final: 23 residues processed: 125 average time/residue: 0.1327 time to fit residues: 22.0156 Evaluate side-chains 135 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.289 ------------------------------------------------------------------------------- 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 76 GLN 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 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 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 106 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 3.9990 chunk 79 optimal weight: 20.0000 chunk 40 optimal weight: 0.9980 chunk 75 optimal weight: 30.0000 chunk 57 optimal weight: 10.0000 chunk 72 optimal weight: 50.0000 chunk 36 optimal weight: 0.3980 chunk 34 optimal weight: 0.5980 chunk 26 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- 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 ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4453 r_free = 0.4453 target = 0.201288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.156947 restraints weight = 14372.576| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 1.26 r_work: 0.3837 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3709 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.1361 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= 0.145 Angle : 0.619 7.732 16759 Z= 0.359 Chirality : 0.044 0.227 1908 Planarity : 0.004 0.042 1272 Dihedral : 31.074 129.306 3495 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.23 % Allowed : 27.48 % Favored : 68.29 % 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: 1.75 (0.31), residues: 732 helix: 1.81 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.70 (0.42), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 35 TYR 0.012 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 0.00266 / 0.14 (11631) covalent geometry : angle 0.61927 / 0.36 (16759) hydrogen bonds : bond 0.04407 / 3.05 ( 688) hydrogen bonds : angle 3.03156 / 2.13 ( 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 134 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.303 Fit side-chains REVERT: B 95 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.6730 (ptp90) REVERT: C 41 GLU cc_start: 0.7519 (mm-30) cc_final: 0.7286 (mt-10) REVERT: E 82 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7099 (tt) REVERT: H 42 TYR cc_start: 0.7563 (OUTLIER) cc_final: 0.6909 (m-80) outliers start: 26 outliers final: 21 residues processed: 122 average time/residue: 0.1238 time to fit residues: 19.8490 Evaluate side-chains 129 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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 76 GLN 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 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 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 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: 4.9990 chunk 6 optimal weight: 0.8980 chunk 26 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 81 optimal weight: 30.0000 chunk 53 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.199910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.155140 restraints weight = 14383.204| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 1.27 r_work: 0.3814 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3685 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11631 Z= 0.166 Angle : 0.636 7.941 16759 Z= 0.366 Chirality : 0.045 0.225 1908 Planarity : 0.004 0.042 1272 Dihedral : 31.077 128.929 3495 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 4.23 % Allowed : 27.64 % Favored : 68.13 % 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: 1.54 (0.31), residues: 732 helix: 1.65 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.76 (0.42), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 35 TYR 0.009 0.001 TYR G 57 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 0.00324 / 0.17 (11631) covalent geometry : angle 0.63622 / 0.37 (16759) hydrogen bonds : bond 0.04773 / 3.31 ( 688) hydrogen bonds : angle 3.12186 / 2.20 ( 1744) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2779.00 seconds wall clock time: 48 minutes 2.89 seconds (2882.89 seconds total)