Starting phenix.real_space_refine on Thu Jul 2 16:50:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d3n_46540/07_2026/9d3n_46540.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d3n_46540/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9d3n_46540/07_2026/9d3n_46540.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d3n_46540/07_2026/9d3n_46540.map" model { file = "/net/cci-nas-00/data/ceres_data/9d3n_46540/07_2026/9d3n_46540.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d3n_46540/07_2026/9d3n_46540.cif" } 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): 0.00s 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: 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: 1.91, per 1000 atoms: 0.20 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: 0.77 Conformation dependent library (CDL) restraints added in 205.0 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: 1.19 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: 1.08 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: 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: 13704 1.94 - 3.88: 519 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 9.030 Find NCS groups from input model: 0.120 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:5.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.520 ------------------------------------------------------------------------------- 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 : 0.775 9.694 14246 Z= 0.651 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 0.77538 / 0.65 (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 : 0.156 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: 0.5174 time to fit residues: 58.9798 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 : 0.252 ------------------------------------------------------------------------------- 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 = 0.4716 r_free = 0.4716 target = 0.224065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.168569 restraints weight = 11421.559| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 1.45 r_work: 0.4039 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.0755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9947 Z= 0.157 Angle : 0.631 7.135 14246 Z= 0.375 Chirality : 0.045 0.205 1631 Planarity : 0.004 0.044 1138 Dihedral : 30.668 171.374 2834 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.39 % Allowed : 26.14 % 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: 0.61 (0.33), residues: 681 helix: 1.06 (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 0.020 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 0.00282 / 0.16 ( 9947) covalent geometry : angle 0.63141 / 0.38 (14246) hydrogen bonds : bond 0.04743 / 3.24 ( 613) hydrogen bonds : angle 3.54538 / 2.58 ( 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 122 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 79 LYS cc_start: 0.5191 (tptm) cc_final: 0.3857 (mptm) REVERT: E 73 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6960 (tt0) REVERT: H 59 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.8030 (mmm) outliers start: 25 outliers final: 9 residues processed: 107 average time/residue: 0.4991 time to fit residues: 56.9618 Evaluate side-chains 105 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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 59 MET 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: 3.9990 chunk 25 optimal weight: 1.9990 chunk 72 optimal weight: 20.0000 chunk 48 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 67 optimal weight: 50.0000 chunk 69 optimal weight: 20.0000 chunk 15 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 = 0.4682 r_free = 0.4682 target = 0.220632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.164021 restraints weight = 11440.335| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 1.45 r_work: 0.3986 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9947 Z= 0.200 Angle : 0.656 6.840 14246 Z= 0.381 Chirality : 0.046 0.199 1631 Planarity : 0.005 0.038 1138 Dihedral : 30.961 171.423 2834 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 5.26 % Allowed : 26.14 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.32), residues: 681 helix: 0.88 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -2.21 (0.44), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 40 TYR 0.014 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 0.00421 / 0.20 ( 9947) covalent geometry : angle 0.65562 / 0.38 (14246) hydrogen bonds : bond 0.05031 / 3.47 ( 613) hydrogen bonds : angle 3.51554 / 2.57 ( 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: 30 poor density : 100 time to evaluate : 0.166 Fit side-chains REVERT: A 69 ARG cc_start: 0.7500 (mtm180) cc_final: 0.7278 (ttp-110) REVERT: E 73 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.7002 (tt0) REVERT: H 71 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7726 (tm-30) outliers start: 30 outliers final: 18 residues processed: 115 average time/residue: 0.4794 time to fit residues: 58.6901 Evaluate side-chains 115 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 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 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 119 THR 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: 0.8980 chunk 38 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 79 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 72 optimal weight: 20.0000 chunk 74 optimal weight: 40.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 = 0.4688 r_free = 0.4688 target = 0.221359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.164518 restraints weight = 11424.344| |-----------------------------------------------------------------------------| r_work (start): 0.4168 rms_B_bonded: 1.48 r_work: 0.3999 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9947 Z= 0.174 Angle : 0.633 7.229 14246 Z= 0.368 Chirality : 0.044 0.199 1631 Planarity : 0.004 0.035 1138 Dihedral : 31.016 171.180 2834 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 5.96 % Allowed : 27.02 % Favored : 67.02 % 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: 0.51 (0.32), residues: 681 helix: 1.04 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -2.09 (0.44), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 40 TYR 0.013 0.002 TYR A 54 PHE 0.011 0.002 PHE A 67 HIS 0.002 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 ( 9947) covalent geometry : angle 0.63338 / 0.37 (14246) hydrogen bonds : bond 0.04641 / 3.20 ( 613) hydrogen bonds : angle 3.42363 / 2.51 ( 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 133 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 99 time to evaluate : 0.283 Fit side-chains REVERT: A 59 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.6675 (pm20) REVERT: A 69 ARG cc_start: 0.7469 (mtm180) cc_final: 0.7247 (ttp-110) REVERT: A 82 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8145 (tt) REVERT: C 91 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7669 (pm20) REVERT: D 118 VAL cc_start: 0.7488 (OUTLIER) cc_final: 0.7238 (t) REVERT: E 73 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.7000 (tt0) REVERT: G 92 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7082 (mm-30) REVERT: H 59 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7982 (mmm) REVERT: H 71 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7724 (tm-30) outliers start: 34 outliers final: 18 residues processed: 115 average time/residue: 0.5279 time to fit residues: 64.8313 Evaluate side-chains 122 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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 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 D residue 106 LEU Chi-restraints excluded: chain D residue 118 VAL 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 92 GLU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 59 MET Chi-restraints excluded: chain H residue 119 THR 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: 4.9990 chunk 13 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 68 optimal weight: 30.0000 chunk 17 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN C 68 ASN 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 = 0.4673 r_free = 0.4673 target = 0.219878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.162800 restraints weight = 11384.230| |-----------------------------------------------------------------------------| r_work (start): 0.4153 rms_B_bonded: 1.47 r_work: 0.3983 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9947 Z= 0.208 Angle : 0.662 6.815 14246 Z= 0.380 Chirality : 0.046 0.198 1631 Planarity : 0.004 0.035 1138 Dihedral : 31.167 170.915 2834 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 7.19 % Allowed : 27.19 % Favored : 65.61 % 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: 0.31 (0.31), residues: 681 helix: 0.89 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -2.10 (0.44), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 29 TYR 0.019 0.002 TYR G 50 PHE 0.012 0.002 PHE A 67 HIS 0.003 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.21 ( 9947) covalent geometry : angle 0.66223 / 0.38 (14246) hydrogen bonds : bond 0.04961 / 3.43 ( 613) hydrogen bonds : angle 3.47939 / 2.55 ( 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 144 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 103 time to evaluate : 0.248 Fit side-chains REVERT: A 65 LEU cc_start: 0.8417 (mt) cc_final: 0.8065 (tt) REVERT: A 82 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8124 (tt) REVERT: E 73 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.7015 (tt0) REVERT: E 125 GLN cc_start: 0.7763 (mm-40) cc_final: 0.7553 (mm-40) REVERT: G 92 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7204 (mm-30) REVERT: H 59 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7884 (mmm) REVERT: H 71 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7762 (tm-30) outliers start: 41 outliers final: 24 residues processed: 125 average time/residue: 0.5640 time to fit residues: 75.2945 Evaluate side-chains 127 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.288 ------------------------------------------------------------------------------- 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 82 LEU 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 90 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 45 THR 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 F residue 50 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 79 ILE 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 59 MET Chi-restraints excluded: chain H residue 78 SER 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: 4.9990 chunk 25 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 76 optimal weight: 40.0000 chunk 72 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 chunk 67 optimal weight: 50.0000 chunk 7 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.4682 r_free = 0.4682 target = 0.220915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.163933 restraints weight = 11490.433| |-----------------------------------------------------------------------------| r_work (start): 0.4157 rms_B_bonded: 1.46 r_work: 0.3996 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.1428 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= 0.169 Angle : 0.643 8.070 14246 Z= 0.369 Chirality : 0.045 0.199 1631 Planarity : 0.004 0.034 1138 Dihedral : 31.188 171.241 2834 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 6.14 % Allowed : 28.60 % Favored : 65.26 % 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: 0.53 (0.32), residues: 681 helix: 1.06 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -2.07 (0.44), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 69 TYR 0.013 0.002 TYR A 54 PHE 0.012 0.002 PHE A 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.17 ( 9947) covalent geometry : angle 0.64256 / 0.37 (14246) hydrogen bonds : bond 0.04631 / 3.20 ( 613) hydrogen bonds : angle 3.39733 / 2.49 ( 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 132 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 97 time to evaluate : 0.263 Fit side-chains REVERT: A 65 LEU cc_start: 0.8337 (mt) cc_final: 0.8007 (tt) REVERT: A 82 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8143 (tt) REVERT: E 73 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6991 (tt0) REVERT: E 90 MET cc_start: 0.7698 (mmp) cc_final: 0.7416 (mmt) REVERT: E 125 GLN cc_start: 0.7765 (mm-40) cc_final: 0.7523 (mm-40) REVERT: G 92 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7141 (mm-30) REVERT: H 59 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7873 (mmm) REVERT: H 71 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7729 (tm-30) outliers start: 35 outliers final: 25 residues processed: 117 average time/residue: 0.5069 time to fit residues: 63.4797 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 : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 82 LEU 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 59 MET 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 D residue 111 VAL Chi-restraints excluded: chain E residue 45 THR 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 F residue 30 THR 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 59 MET Chi-restraints excluded: chain H residue 78 SER 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: 4.9990 chunk 83 optimal weight: 40.0000 chunk 1 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.4690 r_free = 0.4690 target = 0.221452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.164913 restraints weight = 11443.561| |-----------------------------------------------------------------------------| r_work (start): 0.4158 rms_B_bonded: 1.45 r_work: 0.3996 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9947 Z= 0.170 Angle : 0.631 6.691 14246 Z= 0.364 Chirality : 0.045 0.199 1631 Planarity : 0.004 0.035 1138 Dihedral : 31.199 171.161 2834 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 6.49 % Allowed : 28.42 % 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: 0.66 (0.32), residues: 681 helix: 1.15 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -2.04 (0.44), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 69 TYR 0.013 0.002 TYR A 54 PHE 0.012 0.002 PHE A 67 HIS 0.002 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 ( 9947) covalent geometry : angle 0.63109 / 0.36 (14246) hydrogen bonds : bond 0.04606 / 3.19 ( 613) hydrogen bonds : angle 3.36049 / 2.46 ( 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 135 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 98 time to evaluate : 0.306 Fit side-chains REVERT: A 65 LEU cc_start: 0.8367 (mt) cc_final: 0.8041 (tt) REVERT: A 82 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8071 (tt) REVERT: E 73 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.7011 (tt0) REVERT: E 125 GLN cc_start: 0.7725 (mm-40) cc_final: 0.7506 (mm-40) REVERT: G 92 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7133 (mm-30) REVERT: H 59 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7970 (mmm) outliers start: 37 outliers final: 25 residues processed: 116 average time/residue: 0.5664 time to fit residues: 69.9995 Evaluate side-chains 126 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 82 LEU 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 E residue 45 THR Chi-restraints excluded: chain E residue 58 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 30 THR 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 79 ILE 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 59 MET Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 93 GLU 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: 0.6980 chunk 5 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.4616 r_free = 0.4616 target = 0.217278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.157603 restraints weight = 11485.668| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 1.52 r_work: 0.3879 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.1507 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= 0.146 Angle : 0.622 9.182 14246 Z= 0.360 Chirality : 0.044 0.202 1631 Planarity : 0.004 0.036 1138 Dihedral : 31.197 171.415 2834 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.74 % Allowed : 31.23 % 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: 1.01 (0.32), residues: 681 helix: 1.40 (0.23), residues: 524 sheet: None (None), residues: 0 loop : -1.84 (0.46), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 69 TYR 0.017 0.002 TYR D 42 PHE 0.015 0.002 PHE A 67 HIS 0.002 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.15 ( 9947) covalent geometry : angle 0.62193 / 0.36 (14246) hydrogen bonds : bond 0.04393 / 3.03 ( 613) hydrogen bonds : angle 3.26074 / 2.38 ( 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 130 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8309 (mt) cc_final: 0.7942 (tt) REVERT: D 121 TYR cc_start: 0.7255 (t80) cc_final: 0.6954 (t80) REVERT: E 73 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6942 (tt0) REVERT: E 90 MET cc_start: 0.7618 (mmp) cc_final: 0.7338 (mmt) REVERT: E 125 GLN cc_start: 0.7885 (mm-40) cc_final: 0.7598 (mm-40) REVERT: G 92 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7128 (mm-30) REVERT: H 59 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7844 (mmm) outliers start: 27 outliers final: 22 residues processed: 118 average time/residue: 0.5594 time to fit residues: 70.6157 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 : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS 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 90 THR Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 111 VAL 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 92 GLU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 59 MET Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 93 GLU 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: 5.9990 chunk 78 optimal weight: 30.0000 chunk 59 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 69 optimal weight: 20.0000 chunk 64 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN B 93 GLN D 67 ASN F 27 GLN G 68 ASN H 47 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.217122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.157220 restraints weight = 11507.246| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 1.54 r_work: 0.3871 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.1592 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= 0.159 Angle : 0.623 8.534 14246 Z= 0.360 Chirality : 0.044 0.201 1631 Planarity : 0.004 0.034 1138 Dihedral : 31.204 171.488 2834 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 5.09 % Allowed : 31.40 % Favored : 63.51 % 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: 0.98 (0.32), residues: 681 helix: 1.36 (0.23), residues: 532 sheet: None (None), residues: 0 loop : -1.93 (0.46), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 69 TYR 0.012 0.002 TYR A 54 PHE 0.014 0.002 PHE A 67 HIS 0.002 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 ( 9947) covalent geometry : angle 0.62337 / 0.36 (14246) hydrogen bonds : bond 0.04393 / 3.03 ( 613) hydrogen bonds : angle 3.23796 / 2.37 ( 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: 29 poor density : 94 time to evaluate : 0.172 Fit side-chains REVERT: A 65 LEU cc_start: 0.8320 (mt) cc_final: 0.7949 (tt) REVERT: B 52 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6961 (tp30) REVERT: B 74 GLU cc_start: 0.7240 (tp30) cc_final: 0.7002 (tt0) REVERT: B 93 GLN cc_start: 0.7126 (OUTLIER) cc_final: 0.6652 (pp30) REVERT: D 121 TYR cc_start: 0.7259 (t80) cc_final: 0.6968 (t80) REVERT: E 73 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6966 (tt0) REVERT: E 90 MET cc_start: 0.7767 (mmp) cc_final: 0.7456 (mmt) REVERT: E 125 GLN cc_start: 0.7888 (mm-40) cc_final: 0.7594 (mm-40) REVERT: G 92 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7131 (mm-30) REVERT: H 59 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7848 (mmm) REVERT: H 71 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7718 (tm-30) outliers start: 29 outliers final: 19 residues processed: 111 average time/residue: 0.5672 time to fit residues: 67.1889 Evaluate side-chains 116 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 52 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 111 VAL 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 87 SER Chi-restraints excluded: chain F residue 30 THR 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 59 MET Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 93 GLU 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: 0.8980 chunk 80 optimal weight: 20.0000 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 73 optimal weight: 30.0000 chunk 12 optimal weight: 0.7980 chunk 72 optimal weight: 20.0000 chunk 41 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 11 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4634 r_free = 0.4634 target = 0.219090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.159777 restraints weight = 11545.143| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 1.54 r_work: 0.3898 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9947 Z= 0.137 Angle : 0.611 8.423 14246 Z= 0.353 Chirality : 0.043 0.205 1631 Planarity : 0.004 0.035 1138 Dihedral : 31.196 171.745 2834 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.51 % Allowed : 32.81 % 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: 1.37 (0.33), residues: 681 helix: 1.62 (0.23), residues: 530 sheet: None (None), residues: 0 loop : -1.65 (0.48), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 92 TYR 0.014 0.002 TYR H 40 PHE 0.020 0.001 PHE A 67 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.14 ( 9947) covalent geometry : angle 0.61148 / 0.35 (14246) hydrogen bonds : bond 0.04131 / 2.83 ( 613) hydrogen bonds : angle 3.11708 / 2.28 ( 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 118 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.261 Fit side-chains REVERT: A 65 LEU cc_start: 0.8323 (mt) cc_final: 0.7921 (tt) REVERT: B 74 GLU cc_start: 0.7234 (tp30) cc_final: 0.6987 (tt0) REVERT: B 93 GLN cc_start: 0.7016 (OUTLIER) cc_final: 0.6711 (pp30) REVERT: D 121 TYR cc_start: 0.7297 (t80) cc_final: 0.7025 (t80) REVERT: E 73 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6935 (tt0) REVERT: E 90 MET cc_start: 0.7743 (mmp) cc_final: 0.7434 (mmt) REVERT: E 125 GLN cc_start: 0.7849 (mm-40) cc_final: 0.7512 (mm110) REVERT: H 71 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7753 (tm-30) outliers start: 20 outliers final: 14 residues processed: 108 average time/residue: 0.5752 time to fit residues: 66.2842 Evaluate side-chains 110 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 111 VAL 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 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 78 SER Chi-restraints excluded: chain H residue 93 GLU 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: 3.9990 chunk 16 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 83 optimal weight: 40.0000 chunk 72 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 = 0.4617 r_free = 0.4617 target = 0.217195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.156929 restraints weight = 11408.349| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 1.53 r_work: 0.3865 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9947 Z= 0.182 Angle : 0.637 8.328 14246 Z= 0.365 Chirality : 0.044 0.202 1631 Planarity : 0.004 0.062 1138 Dihedral : 31.206 171.536 2834 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.68 % Allowed : 32.28 % 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: 1.15 (0.32), residues: 681 helix: 1.45 (0.23), residues: 530 sheet: None (None), residues: 0 loop : -1.71 (0.47), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 92 TYR 0.013 0.002 TYR H 42 PHE 0.012 0.002 PHE A 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.18 ( 9947) covalent geometry : angle 0.63715 / 0.36 (14246) hydrogen bonds : bond 0.04489 / 3.10 ( 613) hydrogen bonds : angle 3.25489 / 2.39 ( 1587) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2619.23 seconds wall clock time: 45 minutes 22.45 seconds (2722.45 seconds total)