Starting phenix.real_space_refine on Wed Aug 5 09:57:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d3n_46540/08_2026/9d3n_46540.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d3n_46540/08_2026/9d3n_46540.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9d3n_46540/08_2026/9d3n_46540.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d3n_46540/08_2026/9d3n_46540.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9d3n_46540/08_2026/9d3n_46540.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d3n_46540/08_2026/9d3n_46540.map" } resolution = 3.0 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= 0.002 sd= 0.035 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 192 5.49 5 S 14 5.16 5 C 5305 2.51 5 N 1754 2.21 5 O 2136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 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: 9401 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 732 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "B" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 626 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 695 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 87} 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: "D" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 689 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 86} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 726 Classifications: {'peptide': 90} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 87} 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: "F" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 626 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 687 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 87} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 684 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "I" Number of atoms: 1974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1974 Classifications: {'DNA': 96} Link IDs: {'rna3p': 95} Chain: "J" Number of atoms: 1962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1962 Classifications: {'DNA': 96} Link IDs: {'rna3p': 95} Time building chain proxies: 1.58, per 1000 atoms: 0.17 Number of scatterers: 9401 At special positions: 0 Unit cell: (116.875, 81.345, 115.94, 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 192 15.00 O 2136 8.00 N 1754 7.00 C 5305 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: 0.68 Conformation dependent library (CDL) restraints added in 201.1 milliseconds 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1290 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 8 sheets defined 75.5% alpha, 2.9% beta 92 base pairs and 161 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.187A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.557A pdb=" N GLU A 94 " --> pdb=" O MET A 90 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.601A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLU B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.613A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.904A pdb=" N ASN D 67 " --> pdb=" O ASN D 63 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU D 71 " --> pdb=" O ASN D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.550A pdb=" N THR D 122 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 87 through 114 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: 3.539A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 18 through 22 removed outlier: 3.520A pdb=" N GLY G 22 " --> pdb=" O SER G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.623A pdb=" N GLY G 67 " --> pdb=" O LEU G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 88 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.618A pdb=" N TYR H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 84 removed outlier: 3.524A pdb=" N SER H 64 " --> pdb=" O GLY H 60 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU H 71 " --> pdb=" O ASN H 67 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA H 81 " --> pdb=" O ALA H 77 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N HIS H 82 " --> pdb=" O SER H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.578A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 122 removed outlier: 3.695A pdb=" N HIS H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL H 111 " --> pdb=" O ALA H 107 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR H 115 " --> pdb=" O VAL H 111 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL H 118 " --> pdb=" O GLY H 114 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.036A 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: 6.839A 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: 7.412A 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 100 through 102 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.971A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 370 hydrogen bonds defined for protein. 1101 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 243 hydrogen bonds 486 hydrogen bond angles 0 basepair planarities 92 basepair parallelities 161 stacking parallelities Total time for adding SS restraints: 1.41 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2385 1.34 - 1.46: 2996 1.46 - 1.58: 4158 1.58 - 1.70: 382 1.70 - 1.82: 26 Bond restraints: 9947 Sorted by residual: bond pdb=" C3' DG I -11 " pdb=" C2' DG I -11 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.19e+01 bond pdb=" C3' DG I 32 " pdb=" C2' DG I 32 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C3' DA I -30 " pdb=" C2' DA I -30 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.93e+00 bond pdb=" C3' DC I -19 " pdb=" C2' DC I -19 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.81e+00 bond pdb=" C3' DG I 21 " pdb=" C2' DG I 21 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.31e+00 ... (remaining 9942 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 13701 1.94 - 3.88: 522 3.88 - 5.82: 19 5.82 - 7.75: 3 7.75 - 9.69: 1 Bond angle restraints: 14246 Sorted by residual: angle pdb=" O4' DA I 8 " pdb=" C4' DA I 8 " pdb=" C3' DA I 8 " ideal model delta sigma weight residual 106.00 103.25 2.75 6.00e-01 2.78e+00 2.10e+01 angle pdb=" N3 DT J 30 " pdb=" C4 DT J 30 " pdb=" O4 DT J 30 " ideal model delta sigma weight residual 119.90 122.62 -2.72 6.00e-01 2.78e+00 2.06e+01 angle pdb=" N3 DT I 44 " pdb=" C4 DT I 44 " pdb=" O4 DT I 44 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.87e+01 angle pdb=" O4 DT J 30 " pdb=" C4 DT J 30 " pdb=" C5 DT J 30 " ideal model delta sigma weight residual 124.90 121.89 3.01 7.00e-01 2.04e+00 1.85e+01 angle pdb=" N3 DT J -6 " pdb=" C4 DT J -6 " pdb=" O4 DT J -6 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 ... (remaining 14241 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.87: 4396 34.87 - 69.74: 1033 69.74 - 104.61: 21 104.61 - 139.48: 1 139.48 - 174.35: 1 Dihedral angle restraints: 5452 sinusoidal: 3445 harmonic: 2007 Sorted by residual: dihedral pdb=" CA LYS B 59 " pdb=" C LYS B 59 " pdb=" N VAL B 60 " pdb=" CA VAL B 60 " ideal model delta harmonic sigma weight residual 180.00 156.53 23.47 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" C4' DA J -17 " pdb=" C3' DA J -17 " pdb=" O3' DA J -17 " pdb=" P DG J -16 " ideal model delta sinusoidal sigma weight residual -140.00 34.35 -174.35 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA LEU G 63 " pdb=" C LEU G 63 " pdb=" N GLU G 64 " pdb=" CA GLU G 64 " ideal model delta harmonic sigma weight residual 180.00 161.22 18.78 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 5449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 802 0.028 - 0.056: 532 0.056 - 0.084: 181 0.084 - 0.112: 94 0.112 - 0.140: 22 Chirality restraints: 1631 Sorted by residual: chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA LEU A 65 " pdb=" N LEU A 65 " pdb=" C LEU A 65 " pdb=" CB LEU A 65 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" C3' DG I 31 " pdb=" C4' DG I 31 " pdb=" O3' DG I 31 " pdb=" C2' DG I 31 " both_signs ideal model delta sigma weight residual False -2.73 -2.60 -0.14 2.00e-01 2.50e+01 4.57e-01 ... (remaining 1628 not shown) Planarity restraints: 1138 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT I 17 " 0.025 2.00e-02 2.50e+03 1.26e-02 3.97e+00 pdb=" N1 DT I 17 " -0.027 2.00e-02 2.50e+03 pdb=" C2 DT I 17 " -0.003 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 " 0.010 2.00e-02 2.50e+03 pdb=" C5 DT I 17 " 0.001 2.00e-02 2.50e+03 pdb=" C7 DT I 17 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DT I 17 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 120 " 0.031 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO A 121 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 121 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 121 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 102 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO H 103 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO H 103 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO H 103 " -0.022 5.00e-02 4.00e+02 ... (remaining 1135 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 329 2.70 - 3.25: 8363 3.25 - 3.80: 17638 3.80 - 4.35: 22149 4.35 - 4.90: 32575 Nonbonded interactions: 81054 Sorted by model distance: nonbonded pdb=" OD2 ASP D 68 " pdb=" OH TYR F 98 " model vdw 2.145 3.040 nonbonded pdb=" OD1 ASP B 85 " pdb=" OH TYR D 83 " model vdw 2.165 3.040 nonbonded pdb=" OD2 ASP E 106 " pdb=" NH2 ARG E 131 " model vdw 2.248 3.120 nonbonded pdb=" O GLU C 64 " pdb=" ND2 ASN C 68 " model vdw 2.254 3.120 nonbonded pdb=" N GLU C 91 " pdb=" OE1 GLU C 91 " model vdw 2.258 3.120 ... (remaining 81049 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 44 through 51 or (resid 52 and (name N or name CA or name \ C or name O or name CB )) or resid 53 through 133)) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 18 through 28 or (resid 29 and (name N or name CA or name \ C or name O or name CB )) or resid 30 through 106)) selection = (chain 'G' and resid 18 through 106) } ncs_group { reference = (chain 'D' and resid 36 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: 0.640 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.890 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 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 : 0.005 0.039 9947 Z= 0.481 Angle : 0.781 9.694 14246 Z= 0.656 Chirality : 0.044 0.140 1631 Planarity : 0.004 0.048 1138 Dihedral : 28.299 174.351 4162 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.35 % Allowed : 25.96 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.32), residues: 681 helix: 0.54 (0.23), residues: 526 sheet: None (None), residues: 0 loop : -2.01 (0.45), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 92 TYR 0.022 0.002 TYR C 50 PHE 0.017 0.002 PHE D 65 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.48 ( 9947) covalent geometry : angle 0.78135 / 0.66 (14246) hydrogen bonds : bond 0.11970 / 7.91 ( 613) hydrogen bonds : angle 4.93826 / 3.61 ( 1587) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 106 time to evaluate : 0.236 Fit side-chains REVERT: A 79 LYS cc_start: 0.5179 (tptm) cc_final: 0.3874 (mptm) REVERT: E 90 MET cc_start: 0.7834 (mmp) cc_final: 0.7477 (mmt) REVERT: H 62 MET cc_start: 0.7507 (mtp) cc_final: 0.7198 (mtt) outliers start: 2 outliers final: 0 residues processed: 107 average time/residue: 0.5462 time to fit residues: 62.2067 Evaluate side-chains 92 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 30.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN B 27 GLN E 113 HIS F 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.224093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.168750 restraints weight = 11447.902| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 1.45 r_work: 0.4042 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.0795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9947 Z= 0.155 Angle : 0.644 7.239 14246 Z= 0.379 Chirality : 0.045 0.205 1631 Planarity : 0.005 0.044 1138 Dihedral : 30.618 171.623 2834 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.56 % Allowed : 25.96 % Favored : 69.47 % 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: 0.63 (0.33), residues: 681 helix: 1.08 (0.23), residues: 529 sheet: None (None), residues: 0 loop : -1.85 (0.46), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 55 TYR 0.021 0.002 TYR H 42 PHE 0.012 0.002 PHE D 65 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.16 ( 9947) covalent geometry : angle 0.64357 / 0.38 (14246) hydrogen bonds : bond 0.04640 / 3.18 ( 613) hydrogen bonds : angle 3.50557 / 2.55 ( 1587) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: A 79 LYS cc_start: 0.5207 (tptm) cc_final: 0.3853 (mptm) REVERT: C 61 GLU cc_start: 0.7003 (tm-30) cc_final: 0.6787 (tm-30) REVERT: E 73 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6962 (tt0) outliers start: 26 outliers final: 9 residues processed: 108 average time/residue: 0.5748 time to fit residues: 66.0275 Evaluate side-chains 104 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 7 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 72 optimal weight: 20.0000 chunk 48 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 67 optimal weight: 50.0000 chunk 69 optimal weight: 20.0000 chunk 15 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN F 27 GLN G 68 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.221231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.164595 restraints weight = 11403.924| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 1.46 r_work: 0.4003 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9947 Z= 0.193 Angle : 0.658 6.540 14246 Z= 0.380 Chirality : 0.045 0.205 1631 Planarity : 0.004 0.041 1138 Dihedral : 30.840 171.831 2834 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.91 % Allowed : 26.32 % Favored : 68.77 % 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: 0.40 (0.32), residues: 681 helix: 0.97 (0.23), residues: 528 sheet: None (None), residues: 0 loop : -2.17 (0.44), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 72 TYR 0.018 0.002 TYR H 42 PHE 0.010 0.002 PHE E 67 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.19 ( 9947) covalent geometry : angle 0.65844 / 0.38 (14246) hydrogen bonds : bond 0.04880 / 3.37 ( 613) hydrogen bonds : angle 3.48669 / 2.55 ( 1587) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.252 Fit side-chains REVERT: A 69 ARG cc_start: 0.7472 (mtm180) cc_final: 0.7180 (ttp-110) REVERT: D 59 MET cc_start: 0.6725 (OUTLIER) cc_final: 0.6488 (tpt) REVERT: E 73 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6999 (tt0) outliers start: 28 outliers final: 19 residues processed: 116 average time/residue: 0.5691 time to fit residues: 70.3059 Evaluate side-chains 117 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 79 optimal weight: 20.0000 chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 72 optimal weight: 20.0000 chunk 74 optimal weight: 30.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN D 109 HIS F 27 GLN G 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.222664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.166665 restraints weight = 11458.308| |-----------------------------------------------------------------------------| r_work (start): 0.4187 rms_B_bonded: 1.45 r_work: 0.4023 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9947 Z= 0.156 Angle : 0.634 7.471 14246 Z= 0.366 Chirality : 0.044 0.208 1631 Planarity : 0.004 0.035 1138 Dihedral : 30.871 171.802 2834 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 5.44 % Allowed : 27.37 % Favored : 67.19 % 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: 0.85 (0.32), residues: 681 helix: 1.28 (0.23), residues: 524 sheet: None (None), residues: 0 loop : -1.87 (0.45), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 72 TYR 0.012 0.002 TYR A 54 PHE 0.011 0.002 PHE A 67 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.16 ( 9947) covalent geometry : angle 0.63408 / 0.37 (14246) hydrogen bonds : bond 0.04470 / 3.07 ( 613) hydrogen bonds : angle 3.34964 / 2.44 ( 1587) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.256 Fit side-chains REVERT: A 59 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.6717 (pm20) REVERT: A 69 ARG cc_start: 0.7522 (mtm180) cc_final: 0.7287 (ttp-110) REVERT: A 82 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8105 (tt) REVERT: C 91 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7738 (pm20) REVERT: E 73 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6953 (tt0) outliers start: 31 outliers final: 16 residues processed: 111 average time/residue: 0.5083 time to fit residues: 60.1536 Evaluate side-chains 115 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 118 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 50.0000 chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 68 optimal weight: 30.0000 chunk 17 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN G 68 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.223259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.167125 restraints weight = 11388.056| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 1.45 r_work: 0.4026 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9947 Z= 0.150 Angle : 0.617 7.339 14246 Z= 0.359 Chirality : 0.044 0.210 1631 Planarity : 0.004 0.037 1138 Dihedral : 30.891 171.670 2834 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 5.09 % Allowed : 27.72 % Favored : 67.19 % 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: 1.09 (0.33), residues: 681 helix: 1.40 (0.23), residues: 530 sheet: None (None), residues: 0 loop : -1.71 (0.48), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 72 TYR 0.013 0.002 TYR G 50 PHE 0.013 0.002 PHE A 67 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.15 ( 9947) covalent geometry : angle 0.61713 / 0.36 (14246) hydrogen bonds : bond 0.04422 / 3.05 ( 613) hydrogen bonds : angle 3.26022 / 2.38 ( 1587) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 69 ARG cc_start: 0.7526 (mtm180) cc_final: 0.7244 (ttp-110) REVERT: A 82 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8133 (tt) REVERT: C 91 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7665 (pm20) REVERT: E 69 ARG cc_start: 0.7156 (OUTLIER) cc_final: 0.6871 (mtm180) REVERT: E 73 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6923 (tt0) REVERT: E 125 GLN cc_start: 0.7706 (mm-40) cc_final: 0.7481 (mm-40) REVERT: H 71 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7678 (tm-30) outliers start: 29 outliers final: 18 residues processed: 113 average time/residue: 0.5325 time to fit residues: 63.8940 Evaluate side-chains 117 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 47 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 76 optimal weight: 40.0000 chunk 72 optimal weight: 20.0000 chunk 16 optimal weight: 0.7980 chunk 67 optimal weight: 50.0000 chunk 7 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN G 68 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.222068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.165514 restraints weight = 11533.110| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 1.47 r_work: 0.4006 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9947 Z= 0.169 Angle : 0.632 7.795 14246 Z= 0.364 Chirality : 0.045 0.209 1631 Planarity : 0.004 0.035 1138 Dihedral : 31.001 171.807 2834 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 6.32 % Allowed : 27.72 % Favored : 65.96 % 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: 0.91 (0.32), residues: 681 helix: 1.28 (0.23), residues: 534 sheet: None (None), residues: 0 loop : -1.88 (0.47), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 72 TYR 0.013 0.002 TYR A 54 PHE 0.013 0.002 PHE A 67 HIS 0.002 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.17 ( 9947) covalent geometry : angle 0.63241 / 0.36 (14246) hydrogen bonds : bond 0.04521 / 3.11 ( 613) hydrogen bonds : angle 3.27689 / 2.40 ( 1587) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 97 time to evaluate : 0.215 Fit side-chains REVERT: A 59 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.6608 (pm20) REVERT: A 65 LEU cc_start: 0.8404 (mt) cc_final: 0.8085 (tt) REVERT: B 93 GLN cc_start: 0.7264 (pp30) cc_final: 0.7060 (pp30) REVERT: E 73 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6992 (tt0) REVERT: E 90 MET cc_start: 0.7667 (mmp) cc_final: 0.7456 (mmt) REVERT: E 125 GLN cc_start: 0.7768 (mm-40) cc_final: 0.7523 (mm-40) REVERT: G 92 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7062 (mm-30) REVERT: H 71 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7713 (tm-30) outliers start: 36 outliers final: 22 residues processed: 116 average time/residue: 0.5042 time to fit residues: 62.2156 Evaluate side-chains 119 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 3 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 83 optimal weight: 50.0000 chunk 1 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 44 optimal weight: 0.0970 chunk 36 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 0.3980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN G 68 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.218896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.159487 restraints weight = 11478.086| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 1.53 r_work: 0.3892 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9947 Z= 0.137 Angle : 0.616 7.879 14246 Z= 0.356 Chirality : 0.043 0.213 1631 Planarity : 0.004 0.033 1138 Dihedral : 31.004 171.999 2834 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.91 % Allowed : 30.00 % Favored : 65.09 % 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: 1.32 (0.33), residues: 681 helix: 1.57 (0.23), residues: 530 sheet: None (None), residues: 0 loop : -1.61 (0.48), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 39 TYR 0.013 0.002 TYR A 54 PHE 0.018 0.002 PHE A 67 HIS 0.002 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.14 ( 9947) covalent geometry : angle 0.61631 / 0.36 (14246) hydrogen bonds : bond 0.04176 / 2.85 ( 613) hydrogen bonds : angle 3.16148 / 2.31 ( 1587) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.173 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8271 (mt) cc_final: 0.7863 (tt) REVERT: B 74 GLU cc_start: 0.7229 (tp30) cc_final: 0.6977 (tt0) REVERT: D 121 TYR cc_start: 0.7266 (t80) cc_final: 0.6981 (t80) REVERT: E 73 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6919 (tt0) REVERT: E 90 MET cc_start: 0.7764 (mmp) cc_final: 0.7472 (mmt) REVERT: E 125 GLN cc_start: 0.7912 (mm-40) cc_final: 0.7595 (mm-40) REVERT: H 71 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7692 (tm-30) outliers start: 28 outliers final: 22 residues processed: 116 average time/residue: 0.4635 time to fit residues: 57.3891 Evaluate side-chains 117 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 57 optimal weight: 0.3980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN B 93 GLN F 27 GLN G 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.218168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.158413 restraints weight = 11506.575| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 1.54 r_work: 0.3881 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9947 Z= 0.153 Angle : 0.621 7.748 14246 Z= 0.357 Chirality : 0.044 0.212 1631 Planarity : 0.004 0.042 1138 Dihedral : 31.030 171.823 2834 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 5.09 % Allowed : 30.70 % Favored : 64.21 % 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: 1.28 (0.33), residues: 681 helix: 1.54 (0.23), residues: 534 sheet: None (None), residues: 0 loop : -1.71 (0.48), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 72 TYR 0.012 0.002 TYR A 54 PHE 0.013 0.002 PHE A 67 HIS 0.002 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 ( 9947) covalent geometry : angle 0.62091 / 0.36 (14246) hydrogen bonds : bond 0.04234 / 2.90 ( 613) hydrogen bonds : angle 3.15904 / 2.31 ( 1587) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.267 Fit side-chains REVERT: A 65 LEU cc_start: 0.8314 (mt) cc_final: 0.7898 (tt) REVERT: B 93 GLN cc_start: 0.7011 (OUTLIER) cc_final: 0.6729 (pp30) REVERT: C 91 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7815 (pm20) REVERT: D 121 TYR cc_start: 0.7300 (t80) cc_final: 0.7021 (t80) REVERT: E 73 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6940 (tt0) REVERT: E 125 GLN cc_start: 0.7863 (mm-40) cc_final: 0.7582 (mm-40) REVERT: H 71 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7734 (tm-30) outliers start: 29 outliers final: 20 residues processed: 112 average time/residue: 0.4536 time to fit residues: 54.1567 Evaluate side-chains 119 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 16 optimal weight: 2.9990 chunk 78 optimal weight: 30.0000 chunk 59 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 69 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN B 93 GLN C 24 GLN D 109 HIS F 27 GLN G 68 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.218365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.158604 restraints weight = 11468.520| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 1.54 r_work: 0.3882 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9947 Z= 0.150 Angle : 0.622 8.721 14246 Z= 0.357 Chirality : 0.043 0.213 1631 Planarity : 0.004 0.040 1138 Dihedral : 31.045 171.875 2834 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 4.74 % Allowed : 31.05 % Favored : 64.21 % 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: 1.40 (0.33), residues: 681 helix: 1.63 (0.23), residues: 530 sheet: None (None), residues: 0 loop : -1.58 (0.48), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 72 TYR 0.012 0.002 TYR H 121 PHE 0.013 0.001 PHE A 67 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.15 ( 9947) covalent geometry : angle 0.62246 / 0.36 (14246) hydrogen bonds : bond 0.04167 / 2.86 ( 613) hydrogen bonds : angle 3.13867 / 2.30 ( 1587) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.144 Fit side-chains REVERT: A 65 LEU cc_start: 0.8310 (mt) cc_final: 0.7893 (tt) REVERT: B 74 GLU cc_start: 0.7206 (tp30) cc_final: 0.6995 (tt0) REVERT: B 93 GLN cc_start: 0.7009 (OUTLIER) cc_final: 0.6713 (pp30) REVERT: C 91 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7659 (pm20) REVERT: D 121 TYR cc_start: 0.7303 (t80) cc_final: 0.7020 (t80) REVERT: E 73 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6941 (tt0) REVERT: E 90 MET cc_start: 0.7687 (mmp) cc_final: 0.7434 (mmt) REVERT: E 125 GLN cc_start: 0.7850 (mm-40) cc_final: 0.7587 (mm-40) REVERT: H 71 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7747 (tm-30) outliers start: 27 outliers final: 22 residues processed: 110 average time/residue: 0.4428 time to fit residues: 51.9329 Evaluate side-chains 120 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 20 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 80 optimal weight: 20.0000 chunk 36 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 73 optimal weight: 30.0000 chunk 12 optimal weight: 0.7980 chunk 72 optimal weight: 20.0000 chunk 41 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN G 68 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.219523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.160083 restraints weight = 11496.573| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 1.54 r_work: 0.3900 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9947 Z= 0.133 Angle : 0.608 8.803 14246 Z= 0.350 Chirality : 0.043 0.216 1631 Planarity : 0.004 0.043 1138 Dihedral : 31.032 172.031 2834 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.16 % Allowed : 32.81 % Favored : 64.04 % 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: 1.56 (0.33), residues: 681 helix: 1.74 (0.23), residues: 534 sheet: None (None), residues: 0 loop : -1.61 (0.48), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 72 TYR 0.012 0.002 TYR H 40 PHE 0.015 0.001 PHE A 67 HIS 0.002 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.13 ( 9947) covalent geometry : angle 0.60770 / 0.35 (14246) hydrogen bonds : bond 0.04007 / 2.73 ( 613) hydrogen bonds : angle 3.05010 / 2.23 ( 1587) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.244 Fit side-chains REVERT: A 65 LEU cc_start: 0.8292 (mt) cc_final: 0.7862 (tt) REVERT: B 74 GLU cc_start: 0.7238 (tp30) cc_final: 0.6995 (tt0) REVERT: C 91 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7613 (pm20) REVERT: D 121 TYR cc_start: 0.7283 (t80) cc_final: 0.7001 (t80) REVERT: E 73 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6931 (tt0) REVERT: E 90 MET cc_start: 0.7651 (mmp) cc_final: 0.7388 (mmt) REVERT: H 71 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7738 (tm-30) outliers start: 18 outliers final: 12 residues processed: 103 average time/residue: 0.5334 time to fit residues: 58.3275 Evaluate side-chains 108 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 36 optimal weight: 1.9990 chunk 16 optimal weight: 0.0970 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 83 optimal weight: 40.0000 chunk 72 optimal weight: 20.0000 chunk 50 optimal weight: 0.0010 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 0.1980 chunk 19 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN F 27 GLN G 68 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.220982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.161862 restraints weight = 11455.234| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 1.53 r_work: 0.3923 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 9947 Z= 0.130 Angle : 0.609 8.920 14246 Z= 0.351 Chirality : 0.043 0.218 1631 Planarity : 0.004 0.043 1138 Dihedral : 31.009 172.108 2834 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.46 % Allowed : 33.86 % Favored : 63.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.33), residues: 681 helix: 1.88 (0.23), residues: 534 sheet: None (None), residues: 0 loop : -1.58 (0.48), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 72 TYR 0.016 0.002 TYR D 40 PHE 0.017 0.001 PHE A 67 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.13 ( 9947) covalent geometry : angle 0.60938 / 0.35 (14246) hydrogen bonds : bond 0.03926 / 2.67 ( 613) hydrogen bonds : angle 2.97689 / 2.17 ( 1587) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2292.15 seconds wall clock time: 39 minutes 41.76 seconds (2381.76 seconds total)