Starting phenix.real_space_refine on Thu Oct 22 23:28:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/33ch_59343/10_2026/33ch_59343.cif Found real_map, /net/cci-nas-00/data/ceres_data/33ch_59343/10_2026/33ch_59343.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/33ch_59343/10_2026/33ch_59343.map" default_real_map = "/net/cci-nas-00/data/ceres_data/33ch_59343/10_2026/33ch_59343.map" model { file = "/net/cci-nas-00/data/ceres_data/33ch_59343/10_2026/33ch_59343.cif" } default_model = "/net/cci-nas-00/data/ceres_data/33ch_59343/10_2026/33ch_59343.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 4197 2.51 5 N 1154 2.21 5 O 1304 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6682 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2256 Classifications: {'peptide': 277} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 264} Chain: "B" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 837 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 94} Chain: "C" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 80 Classifications: {'peptide': 10} Modifications used: {'COO': 1} Link IDs: {'TRANS': 9} Chain: "F" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Chain: "G" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "D" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 853 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 103} Chain: "E" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 907 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 1.51, per 1000 atoms: 0.23 Number of scatterers: 6682 At special positions: 0 Unit cell: (68.9892, 100.275, 129.956, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 27 16.00 O 1304 8.00 N 1154 7.00 C 4197 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 164 " distance=2.04 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 259 " distance=2.03 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 80 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 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: 0.48 Conformation dependent library (CDL) restraints added in 344.3 milliseconds 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1552 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 18 sheets defined 13.7% alpha, 49.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 51 through 55 removed outlier: 3.550A pdb=" N GLN A 54 " --> pdb=" O TRP A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 85 Processing helix chain 'A' and resid 137 through 150 Processing helix chain 'A' and resid 151 through 161 removed outlier: 3.512A pdb=" N TYR A 159 " --> pdb=" O GLN A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 253 through 255 No H-bonds generated for 'chain 'A' and resid 253 through 255' Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.677A pdb=" N THR G 32 " --> pdb=" O VAL G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 65 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.894A pdb=" N ILE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 66 No H-bonds generated for 'chain 'E' and resid 64 through 66' Processing helix chain 'E' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 47 removed outlier: 6.744A pdb=" N GLY A 26 " --> pdb=" O PHE A 33 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ARG A 35 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA A 24 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASP A 37 " --> pdb=" O PHE A 22 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N PHE A 22 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N GLU A 19 " --> pdb=" O ARG A 14 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ARG A 14 " --> pdb=" O GLU A 19 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N HIS A 114 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 124 " --> pdb=" O TYR A 116 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N TYR A 118 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ASP A 122 " --> pdb=" O TYR A 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 189 through 193 removed outlier: 5.693A pdb=" N PHE A 241 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 189 through 193 removed outlier: 5.693A pdb=" N PHE A 241 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 223 Processing sheet with id=AA5, first strand: chain 'B' and resid 6 through 11 removed outlier: 5.461A pdb=" N PHE B 62 " --> pdb=" O GLY B 29 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 6 through 11 removed outlier: 5.461A pdb=" N PHE B 62 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER B 55 " --> pdb=" O TYR B 63 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 44 through 45 Processing sheet with id=AA8, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.582A pdb=" N THR F 22 " --> pdb=" O SER F 7 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.186A pdb=" N GLN F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AB2, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.495A pdb=" N ILE G 34 " --> pdb=" O ARG G 50 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ARG G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.772A pdb=" N TYR G 108 " --> pdb=" O ARG G 98 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N PHE G 100 " --> pdb=" O MET G 106 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N MET G 106 " --> pdb=" O PHE G 100 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 4 through 7 removed outlier: 6.158A pdb=" N THR D 69 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 9.989A pdb=" N GLN D 27 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 9.480A pdb=" N SER D 67 " --> pdb=" O GLN D 27 " (cutoff:3.500A) removed outlier: 12.101A pdb=" N ILE D 29 " --> pdb=" O SER D 65 " (cutoff:3.500A) removed outlier: 11.880A pdb=" N SER D 65 " --> pdb=" O ILE D 29 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 10 through 14 removed outlier: 6.146A pdb=" N LEU D 11 " --> pdb=" O GLU D 107 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS D 109 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ALA D 13 " --> pdb=" O LYS D 109 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 10 through 14 removed outlier: 6.146A pdb=" N LEU D 11 " --> pdb=" O GLU D 107 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS D 109 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ALA D 13 " --> pdb=" O LYS D 109 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB8, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.228A pdb=" N TRP E 35 " --> pdb=" O GLU E 51 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU E 51 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TRP E 37 " --> pdb=" O ILE E 49 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.946A pdb=" N TYR E 107 " --> pdb=" O ARG E 98 " (cutoff:3.500A) 327 hydrogen bonds defined for protein. 819 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.01 Time building geometry restraints manager: 0.66 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: 2175 1.34 - 1.46: 1707 1.46 - 1.58: 2921 1.58 - 1.70: 0 1.70 - 1.81: 38 Bond restraints: 6841 Sorted by residual: bond pdb=" CA TYR G 60 " pdb=" C TYR G 60 " ideal model delta sigma weight residual 1.522 1.482 0.040 1.23e-02 6.61e+03 1.08e+01 bond pdb=" N LYS A 268 " pdb=" CA LYS A 268 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.30e-02 5.92e+03 6.07e+00 bond pdb=" N GLY C 1 " pdb=" CA GLY C 1 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 5.86e+00 bond pdb=" C LYS A 268 " pdb=" N PRO A 269 " ideal model delta sigma weight residual 1.332 1.352 -0.020 1.12e-02 7.97e+03 3.29e+00 bond pdb=" N ASP F 1 " pdb=" CA ASP F 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 ... (remaining 6836 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 9080 1.51 - 3.02: 159 3.02 - 4.53: 42 4.53 - 6.04: 4 6.04 - 7.55: 1 Bond angle restraints: 9286 Sorted by residual: angle pdb=" C TYR G 60 " pdb=" CA TYR G 60 " pdb=" CB TYR G 60 " ideal model delta sigma weight residual 109.79 102.24 7.55 2.05e+00 2.38e-01 1.36e+01 angle pdb=" N ASP G 61 " pdb=" CA ASP G 61 " pdb=" C ASP G 61 " ideal model delta sigma weight residual 109.42 104.12 5.30 1.48e+00 4.57e-01 1.28e+01 angle pdb=" CA PRO A 269 " pdb=" C PRO A 269 " pdb=" O PRO A 269 " ideal model delta sigma weight residual 121.27 118.22 3.05 1.05e+00 9.07e-01 8.46e+00 angle pdb=" CA LYS B 48 " pdb=" CB LYS B 48 " pdb=" CG LYS B 48 " ideal model delta sigma weight residual 114.10 119.84 -5.74 2.00e+00 2.50e-01 8.25e+00 angle pdb=" CB LYS B 48 " pdb=" CG LYS B 48 " pdb=" CD LYS B 48 " ideal model delta sigma weight residual 111.30 116.51 -5.21 2.30e+00 1.89e-01 5.13e+00 ... (remaining 9281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 3629 17.79 - 35.58: 294 35.58 - 53.38: 83 53.38 - 71.17: 26 71.17 - 88.96: 14 Dihedral angle restraints: 4046 sinusoidal: 1616 harmonic: 2430 Sorted by residual: dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual 93.00 52.46 40.54 1 1.00e+01 1.00e-02 2.30e+01 dihedral pdb=" CB CYS G 22 " pdb=" SG CYS G 22 " pdb=" SG CYS G 96 " pdb=" CB CYS G 96 " ideal model delta sinusoidal sigma weight residual 93.00 59.44 33.56 1 1.00e+01 1.00e-02 1.60e+01 dihedral pdb=" CA TRP E 35 " pdb=" C TRP E 35 " pdb=" N ASN E 36 " pdb=" CA ASN E 36 " ideal model delta harmonic sigma weight residual -180.00 -162.97 -17.03 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 4043 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 781 0.045 - 0.090: 135 0.090 - 0.136: 66 0.136 - 0.181: 2 0.181 - 0.226: 1 Chirality restraints: 985 Sorted by residual: chirality pdb=" CA ASP G 61 " pdb=" N ASP G 61 " pdb=" C ASP G 61 " pdb=" CB ASP G 61 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA LYS A 268 " pdb=" N LYS A 268 " pdb=" C LYS A 268 " pdb=" CB LYS A 268 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CA VAL E 38 " pdb=" N VAL E 38 " pdb=" C VAL E 38 " pdb=" CB VAL E 38 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 982 not shown) Planarity restraints: 1198 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN E 40 " 0.023 5.00e-02 4.00e+02 3.46e-02 1.91e+00 pdb=" N PRO E 41 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO E 41 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 41 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP F 56 " 0.007 2.00e-02 2.50e+03 1.34e-02 1.80e+00 pdb=" CG ASP F 56 " -0.023 2.00e-02 2.50e+03 pdb=" OD1 ASP F 56 " 0.008 2.00e-02 2.50e+03 pdb=" OD2 ASP F 56 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR G 23 " -0.021 5.00e-02 4.00e+02 3.22e-02 1.65e+00 pdb=" N PRO G 24 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO G 24 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO G 24 " -0.018 5.00e-02 4.00e+02 ... (remaining 1195 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 923 2.76 - 3.30: 6098 3.30 - 3.83: 11637 3.83 - 4.37: 14769 4.37 - 4.90: 24473 Nonbonded interactions: 57900 Sorted by model distance: nonbonded pdb=" OG1 THR B 73 " pdb=" OD1 ASP B 76 " model vdw 2.227 3.040 nonbonded pdb=" O TRP A 60 " pdb=" OG1 THR A 64 " model vdw 2.284 3.040 nonbonded pdb=" OG SER D 12 " pdb=" OE1 GLU D 107 " model vdw 2.293 3.040 nonbonded pdb=" OE2 GLU A 154 " pdb=" OG SER E 55 " model vdw 2.302 3.040 nonbonded pdb=" O ASN D 30 " pdb=" OD1 ASN D 31 " model vdw 2.305 3.040 ... (remaining 57895 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.320 Find NCS groups from input model: 0.050 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:5.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 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 : 0.003 0.049 6848 Z= 0.158 Angle : 0.557 7.548 9300 Z= 0.301 Chirality : 0.043 0.226 985 Planarity : 0.004 0.035 1198 Dihedral : 15.751 88.959 2473 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.00 % Allowed : 12.00 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 0.86 (0.30), residues: 827 helix: -0.05 (0.58), residues: 79 sheet: 0.80 (0.27), residues: 377 loop : 0.66 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 75 TYR 0.017 0.001 TYR G 60 PHE 0.012 0.002 PHE B 56 TRP 0.013 0.001 TRP G 99 HIS 0.004 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.16 ( 6841) covalent geometry : angle 0.55610 / 0.30 ( 9286) SS BOND : bond 0.00452 / 0.22 ( 7) SS BOND : angle 0.84996 / 0.56 ( 14) hydrogen bonds : bond 0.18646 / 13.03 ( 285) hydrogen bonds : angle 7.92220 / 5.69 ( 819) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.237 Fit side-chains REVERT: A 98 MET cc_start: 0.8093 (tmm) cc_final: 0.7876 (tmm) REVERT: B 94 LYS cc_start: 0.8667 (mttp) cc_final: 0.8102 (mmtm) REVERT: F 107 LYS cc_start: 0.8028 (ttpp) cc_final: 0.7547 (tttm) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.6803 time to fit residues: 84.2823 Evaluate side-chains 110 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74] chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 HIS A 86 ASN A 114 HIS A 180 GLN A 188 HIS B 31 HIS B 89 GLN F 3 GLN G 5 GLN D 31 ASN D 53 ASN D 89 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.170257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.130724 restraints weight = 6183.930| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.74 r_work: 0.3298 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6848 Z= 0.170 Angle : 0.597 7.153 9300 Z= 0.325 Chirality : 0.046 0.163 985 Planarity : 0.005 0.037 1198 Dihedral : 5.166 23.966 924 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.03 % Allowed : 11.17 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.16 (0.30), residues: 827 helix: 1.26 (0.59), residues: 75 sheet: 0.87 (0.26), residues: 375 loop : 0.75 (0.34), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 75 TYR 0.014 0.002 TYR D 49 PHE 0.016 0.002 PHE E 79 TRP 0.017 0.002 TRP A 244 HIS 0.004 0.001 HIS G 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 ( 6841) covalent geometry : angle 0.59591 / 0.32 ( 9286) SS BOND : bond 0.00771 / 0.33 ( 7) SS BOND : angle 1.18367 / 0.76 ( 14) hydrogen bonds : bond 0.04807 / 3.21 ( 285) hydrogen bonds : angle 5.47082 / 3.91 ( 819) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.265 Fit side-chains REVERT: A 183 ASP cc_start: 0.7161 (m-30) cc_final: 0.6849 (m-30) REVERT: D 22 THR cc_start: 0.7594 (OUTLIER) cc_final: 0.7372 (p) outliers start: 22 outliers final: 9 residues processed: 125 average time/residue: 0.6357 time to fit residues: 82.9531 Evaluate side-chains 122 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain G residue 27 PHE Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 89 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: [72, 19, 11, 41, 27, 5, 50, 48, 35, 42, 24] chunk 72 optimal weight: 0.8980 chunk 19 optimal weight: 0.0000 chunk 11 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 ASN A 188 HIS G 43 GLN D 24 GLN D 31 ASN D 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.171949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.132595 restraints weight = 6155.472| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.67 r_work: 0.3314 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 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 0.032 6848 Z= 0.126 Angle : 0.534 6.024 9300 Z= 0.291 Chirality : 0.044 0.155 985 Planarity : 0.004 0.035 1198 Dihedral : 4.866 23.863 924 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.07 % Allowed : 13.52 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.30), residues: 827 helix: 1.67 (0.61), residues: 75 sheet: 1.00 (0.27), residues: 365 loop : 0.70 (0.34), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 76 TYR 0.013 0.001 TYR D 49 PHE 0.015 0.002 PHE E 79 TRP 0.014 0.001 TRP A 244 HIS 0.003 0.001 HIS A 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 ( 6841) covalent geometry : angle 0.53255 / 0.29 ( 9286) SS BOND : bond 0.00507 / 0.23 ( 7) SS BOND : angle 0.98828 / 0.64 ( 14) hydrogen bonds : bond 0.04046 / 2.67 ( 285) hydrogen bonds : angle 5.01681 / 3.58 ( 819) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.164 Fit side-chains REVERT: A 108 ARG cc_start: 0.7118 (mmm160) cc_final: 0.6844 (mmm160) REVERT: A 128 GLU cc_start: 0.7745 (tp30) cc_final: 0.7015 (mp0) REVERT: A 183 ASP cc_start: 0.7168 (m-30) cc_final: 0.6866 (m-30) REVERT: B 47 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8195 (mt-10) REVERT: B 94 LYS cc_start: 0.8771 (mttp) cc_final: 0.8211 (mmtm) REVERT: G 43 GLN cc_start: 0.8051 (mt0) cc_final: 0.7776 (mt0) REVERT: D 24 GLN cc_start: 0.7293 (OUTLIER) cc_final: 0.6609 (mm-40) REVERT: D 102 GLN cc_start: 0.7496 (pp30) cc_final: 0.7265 (pp30) outliers start: 15 outliers final: 6 residues processed: 124 average time/residue: 0.6590 time to fit residues: 85.0932 Evaluate side-chains 120 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain G residue 27 PHE Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: [53, 19, 63, 3, 51, 20, 27, 77, 67, 9, 50] chunk 53 optimal weight: 0.7980 chunk 19 optimal weight: 20.0000 chunk 63 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 27 optimal weight: 0.0980 chunk 77 optimal weight: 0.0870 chunk 67 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS D 31 ASN D 89 GLN E 61 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.172417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.133544 restraints weight = 6234.556| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.70 r_work: 0.3335 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6848 Z= 0.116 Angle : 0.514 5.552 9300 Z= 0.281 Chirality : 0.043 0.153 985 Planarity : 0.004 0.034 1198 Dihedral : 4.738 23.736 924 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.79 % Allowed : 15.17 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.30), residues: 827 helix: 1.76 (0.60), residues: 75 sheet: 1.04 (0.27), residues: 365 loop : 0.71 (0.34), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 76 TYR 0.012 0.001 TYR D 49 PHE 0.014 0.002 PHE E 79 TRP 0.012 0.001 TRP A 244 HIS 0.002 0.001 HIS A 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 ( 6841) covalent geometry : angle 0.51337 / 0.28 ( 9286) SS BOND : bond 0.00470 / 0.22 ( 7) SS BOND : angle 0.94219 / 0.62 ( 14) hydrogen bonds : bond 0.03777 / 2.48 ( 285) hydrogen bonds : angle 4.84616 / 3.45 ( 819) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.251 Fit side-chains REVERT: A 108 ARG cc_start: 0.7147 (mmm160) cc_final: 0.6924 (mmm160) REVERT: A 128 GLU cc_start: 0.7690 (tp30) cc_final: 0.6952 (mp0) REVERT: A 183 ASP cc_start: 0.7115 (m-30) cc_final: 0.6828 (m-30) REVERT: B 47 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8165 (mt-10) REVERT: B 94 LYS cc_start: 0.8758 (mttp) cc_final: 0.8197 (mmtm) REVERT: G 40 ARG cc_start: 0.7549 (mtp85) cc_final: 0.7327 (mtp85) REVERT: G 43 GLN cc_start: 0.8020 (mt0) cc_final: 0.7770 (mt0) REVERT: G 46 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7040 (mt-10) REVERT: D 24 GLN cc_start: 0.7387 (OUTLIER) cc_final: 0.6663 (mm-40) REVERT: D 102 GLN cc_start: 0.7462 (pp30) cc_final: 0.7180 (pp30) outliers start: 13 outliers final: 4 residues processed: 119 average time/residue: 0.6920 time to fit residues: 85.6907 Evaluate side-chains 116 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 109 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain G residue 27 PHE Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain D residue 24 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: [73, 65, 12, 1, 41, 60, 74, 2, 75, 18, 21] chunk 73 optimal weight: 0.8980 chunk 65 optimal weight: 0.0370 chunk 12 optimal weight: 0.2980 chunk 1 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS D 24 GLN D 31 ASN D 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.172645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.132397 restraints weight = 6387.712| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.99 r_work: 0.3315 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6848 Z= 0.115 Angle : 0.506 5.459 9300 Z= 0.276 Chirality : 0.043 0.147 985 Planarity : 0.004 0.034 1198 Dihedral : 4.677 23.285 924 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.21 % Allowed : 14.76 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.43 (0.30), residues: 827 helix: 1.77 (0.60), residues: 75 sheet: 1.19 (0.27), residues: 360 loop : 0.69 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 76 TYR 0.012 0.001 TYR D 49 PHE 0.015 0.002 PHE E 79 TRP 0.012 0.001 TRP A 244 HIS 0.003 0.001 HIS A 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 6841) covalent geometry : angle 0.50578 / 0.28 ( 9286) SS BOND : bond 0.00516 / 0.22 ( 7) SS BOND : angle 0.80453 / 0.50 ( 14) hydrogen bonds : bond 0.03695 / 2.43 ( 285) hydrogen bonds : angle 4.72970 / 3.37 ( 819) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.290 Fit side-chains REVERT: A 108 ARG cc_start: 0.7150 (mmm160) cc_final: 0.6940 (mmm160) REVERT: A 128 GLU cc_start: 0.7774 (tp30) cc_final: 0.7003 (mp0) REVERT: A 183 ASP cc_start: 0.7212 (m-30) cc_final: 0.6912 (m-30) REVERT: B 94 LYS cc_start: 0.8889 (mttp) cc_final: 0.8342 (mmtm) REVERT: G 43 GLN cc_start: 0.8048 (mt0) cc_final: 0.7820 (mt0) REVERT: G 46 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7134 (mt-10) REVERT: D 24 GLN cc_start: 0.7391 (OUTLIER) cc_final: 0.6627 (mm-40) REVERT: D 102 GLN cc_start: 0.7486 (pp30) cc_final: 0.7148 (pp30) outliers start: 16 outliers final: 10 residues processed: 126 average time/residue: 0.6630 time to fit residues: 87.0672 Evaluate side-chains 124 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain G residue 27 PHE Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 66 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: [15, 48, 58, 39, 78, 13, 24, 32, 17, 59, 16] chunk 15 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 17 optimal weight: 0.0060 chunk 59 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS D 31 ASN D 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.172265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.131922 restraints weight = 6329.939| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.98 r_work: 0.3309 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6848 Z= 0.126 Angle : 0.523 5.628 9300 Z= 0.284 Chirality : 0.043 0.151 985 Planarity : 0.004 0.034 1198 Dihedral : 4.712 23.305 924 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.07 % Allowed : 15.31 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.46 (0.30), residues: 827 helix: 1.73 (0.60), residues: 75 sheet: 1.24 (0.27), residues: 359 loop : 0.68 (0.33), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 76 TYR 0.012 0.001 TYR D 49 PHE 0.015 0.002 PHE E 79 TRP 0.012 0.001 TRP A 244 HIS 0.003 0.001 HIS A 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 ( 6841) covalent geometry : angle 0.52219 / 0.28 ( 9286) SS BOND : bond 0.00518 / 0.24 ( 7) SS BOND : angle 0.96777 / 0.65 ( 14) hydrogen bonds : bond 0.03768 / 2.48 ( 285) hydrogen bonds : angle 4.72245 / 3.37 ( 819) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.260 Fit side-chains REVERT: A 108 ARG cc_start: 0.7149 (mmm160) cc_final: 0.6949 (mmm160) REVERT: A 183 ASP cc_start: 0.7205 (m-30) cc_final: 0.6998 (m-30) REVERT: B 47 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8296 (mt-10) REVERT: B 94 LYS cc_start: 0.8881 (mttp) cc_final: 0.8348 (mmtm) REVERT: G 43 GLN cc_start: 0.8071 (mt0) cc_final: 0.7818 (mt0) REVERT: G 46 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7138 (mt-10) REVERT: D 24 GLN cc_start: 0.7410 (OUTLIER) cc_final: 0.7131 (mt0) REVERT: D 102 GLN cc_start: 0.7509 (pp30) cc_final: 0.7201 (pp30) outliers start: 15 outliers final: 9 residues processed: 121 average time/residue: 0.6543 time to fit residues: 82.7033 Evaluate side-chains 122 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain G residue 27 PHE Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 66 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: [19, 12, 70, 3, 32, 40, 38, 78, 2, 63, 26] chunk 19 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 3 optimal weight: 0.3980 chunk 32 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 63 optimal weight: 0.0470 chunk 26 optimal weight: 10.0000 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS D 24 GLN D 31 ASN D 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.172400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.132230 restraints weight = 6320.487| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.98 r_work: 0.3314 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6848 Z= 0.122 Angle : 0.519 5.515 9300 Z= 0.282 Chirality : 0.043 0.151 985 Planarity : 0.004 0.034 1198 Dihedral : 4.696 23.307 924 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.34 % Allowed : 15.59 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.45 (0.30), residues: 827 helix: 1.72 (0.60), residues: 75 sheet: 1.27 (0.27), residues: 358 loop : 0.64 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 40 TYR 0.012 0.001 TYR D 49 PHE 0.015 0.002 PHE E 79 TRP 0.012 0.001 TRP A 244 HIS 0.003 0.001 HIS A 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 6841) covalent geometry : angle 0.51825 / 0.28 ( 9286) SS BOND : bond 0.00548 / 0.24 ( 7) SS BOND : angle 0.85445 / 0.52 ( 14) hydrogen bonds : bond 0.03727 / 2.45 ( 285) hydrogen bonds : angle 4.69903 / 3.35 ( 819) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.292 Fit side-chains REVERT: A 108 ARG cc_start: 0.7133 (mmm160) cc_final: 0.6928 (mmm160) REVERT: A 183 ASP cc_start: 0.7219 (m-30) cc_final: 0.7013 (m-30) REVERT: B 94 LYS cc_start: 0.8883 (mttp) cc_final: 0.8345 (mmtm) REVERT: B 99 MET cc_start: 0.5861 (mtm) cc_final: 0.5652 (mtm) REVERT: G 43 GLN cc_start: 0.8057 (mt0) cc_final: 0.7793 (mt0) REVERT: G 46 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7138 (mt-10) REVERT: D 24 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.6684 (mm-40) REVERT: D 102 GLN cc_start: 0.7488 (pp30) cc_final: 0.7143 (pp30) outliers start: 17 outliers final: 10 residues processed: 122 average time/residue: 0.6569 time to fit residues: 83.5021 Evaluate side-chains 124 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain G residue 27 PHE Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 66 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: [10, 41, 68, 5, 4, 19, 6, 44, 3, 60, 1] chunk 10 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 4 optimal weight: 0.0980 chunk 19 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 3 optimal weight: 0.1980 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS D 31 ASN D 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.172579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.132311 restraints weight = 6325.622| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.98 r_work: 0.3313 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6848 Z= 0.123 Angle : 0.526 6.738 9300 Z= 0.284 Chirality : 0.043 0.149 985 Planarity : 0.004 0.051 1198 Dihedral : 4.682 23.175 924 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.34 % Allowed : 16.41 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.30), residues: 827 helix: 1.73 (0.59), residues: 75 sheet: 1.29 (0.27), residues: 358 loop : 0.67 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 40 TYR 0.012 0.001 TYR D 49 PHE 0.015 0.002 PHE E 79 TRP 0.012 0.001 TRP A 244 HIS 0.003 0.001 HIS A 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 6841) covalent geometry : angle 0.52525 / 0.28 ( 9286) SS BOND : bond 0.00530 / 0.24 ( 7) SS BOND : angle 0.89731 / 0.60 ( 14) hydrogen bonds : bond 0.03708 / 2.44 ( 285) hydrogen bonds : angle 4.68233 / 3.34 ( 819) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.267 Fit side-chains REVERT: A 108 ARG cc_start: 0.7143 (mmm160) cc_final: 0.6939 (mmm160) REVERT: A 128 GLU cc_start: 0.7803 (tp30) cc_final: 0.7016 (mp0) REVERT: A 183 ASP cc_start: 0.7226 (m-30) cc_final: 0.7022 (m-30) REVERT: B 47 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8242 (mt-10) REVERT: B 94 LYS cc_start: 0.8889 (mttp) cc_final: 0.8349 (mmtm) REVERT: G 43 GLN cc_start: 0.8063 (mt0) cc_final: 0.7774 (mt0) REVERT: G 46 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7136 (mt-10) REVERT: D 24 GLN cc_start: 0.7394 (OUTLIER) cc_final: 0.7085 (mt0) REVERT: D 102 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.7134 (pp30) outliers start: 17 outliers final: 9 residues processed: 125 average time/residue: 0.6257 time to fit residues: 81.5740 Evaluate side-chains 124 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain G residue 27 PHE Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 102 GLN Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 66 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: [57, 68, 8, 36, 9, 25, 15, 18, 40, 39, 59] chunk 57 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 15 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS D 24 GLN D 31 ASN D 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.168846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.129653 restraints weight = 6285.288| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.74 r_work: 0.3278 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 6848 Z= 0.210 Angle : 0.627 7.432 9300 Z= 0.338 Chirality : 0.046 0.155 985 Planarity : 0.005 0.059 1198 Dihedral : 5.257 24.224 924 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.93 % Allowed : 16.97 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.36 (0.30), residues: 827 helix: 1.39 (0.59), residues: 75 sheet: 1.09 (0.27), residues: 378 loop : 0.76 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 40 TYR 0.014 0.002 TYR D 49 PHE 0.021 0.003 PHE E 79 TRP 0.013 0.002 TRP A 244 HIS 0.004 0.001 HIS G 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.21 ( 6841) covalent geometry : angle 0.62586 / 0.34 ( 9286) SS BOND : bond 0.00824 / 0.35 ( 7) SS BOND : angle 1.17705 / 0.71 ( 14) hydrogen bonds : bond 0.04518 / 3.00 ( 285) hydrogen bonds : angle 5.01779 / 3.60 ( 819) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.212 Fit side-chains REVERT: A 108 ARG cc_start: 0.7194 (mmm160) cc_final: 0.6644 (mtp-110) REVERT: A 128 GLU cc_start: 0.7775 (tp30) cc_final: 0.7015 (mp0) REVERT: A 183 ASP cc_start: 0.7081 (m-30) cc_final: 0.6858 (m-30) REVERT: B 47 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8204 (mt-10) REVERT: F 42 LYS cc_start: 0.8281 (mmtm) cc_final: 0.7986 (mmtp) REVERT: G 46 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7119 (mt-10) REVERT: D 24 GLN cc_start: 0.7423 (OUTLIER) cc_final: 0.6597 (mm-40) REVERT: D 102 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.7229 (pp30) outliers start: 14 outliers final: 9 residues processed: 121 average time/residue: 0.6614 time to fit residues: 83.3656 Evaluate side-chains 121 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain G residue 27 PHE Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 102 GLN Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 66 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: [74, 39, 6, 17, 24, 30, 72, 31, 62, 37, 29] chunk 74 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 37 optimal weight: 0.0670 chunk 29 optimal weight: 0.6980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS D 24 GLN D 31 ASN D 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.171805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.132274 restraints weight = 6190.604| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.74 r_work: 0.3324 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6848 Z= 0.126 Angle : 0.551 7.627 9300 Z= 0.298 Chirality : 0.043 0.152 985 Planarity : 0.004 0.034 1198 Dihedral : 4.922 23.847 924 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.79 % Allowed : 16.97 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.39 (0.30), residues: 827 helix: 1.66 (0.60), residues: 75 sheet: 1.22 (0.27), residues: 359 loop : 0.62 (0.33), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 40 TYR 0.012 0.001 TYR D 49 PHE 0.015 0.002 PHE E 79 TRP 0.014 0.001 TRP A 244 HIS 0.002 0.001 HIS A 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 ( 6841) covalent geometry : angle 0.54994 / 0.30 ( 9286) SS BOND : bond 0.00607 / 0.25 ( 7) SS BOND : angle 0.88194 / 0.54 ( 14) hydrogen bonds : bond 0.03831 / 2.53 ( 285) hydrogen bonds : angle 4.78255 / 3.43 ( 819) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.201 Fit side-chains REVERT: A 108 ARG cc_start: 0.7067 (mmm160) cc_final: 0.6573 (mtp-110) REVERT: A 128 GLU cc_start: 0.7699 (tp30) cc_final: 0.6905 (mp0) REVERT: A 183 ASP cc_start: 0.7021 (m-30) cc_final: 0.6802 (m-30) REVERT: B 94 LYS cc_start: 0.8762 (mttp) cc_final: 0.8205 (mmtm) REVERT: G 46 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7048 (mt-10) REVERT: D 24 GLN cc_start: 0.7372 (OUTLIER) cc_final: 0.6572 (mm-40) REVERT: D 102 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.7071 (pp30) outliers start: 13 outliers final: 8 residues processed: 122 average time/residue: 0.6385 time to fit residues: 81.2148 Evaluate side-chains 124 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain G residue 27 PHE Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 102 GLN Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 66 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: [8, 36, 64, 27, 16, 22, 21, 35, 80, 55, 59] chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 27 optimal weight: 0.0570 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 55 optimal weight: 0.0970 chunk 59 optimal weight: 2.9990 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS D 24 GLN D 31 ASN D 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.171009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.131450 restraints weight = 6169.868| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.74 r_work: 0.3314 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6848 Z= 0.146 Angle : 0.572 7.277 9300 Z= 0.309 Chirality : 0.044 0.151 985 Planarity : 0.005 0.057 1198 Dihedral : 4.978 23.924 924 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.93 % Allowed : 17.38 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.36 (0.30), residues: 827 helix: 1.58 (0.59), residues: 75 sheet: 1.12 (0.27), residues: 366 loop : 0.69 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 40 TYR 0.013 0.001 TYR D 49 PHE 0.016 0.002 PHE E 79 TRP 0.013 0.002 TRP A 244 HIS 0.003 0.001 HIS A 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 ( 6841) covalent geometry : angle 0.57087 / 0.31 ( 9286) SS BOND : bond 0.00669 / 0.29 ( 7) SS BOND : angle 1.06659 / 0.65 ( 14) hydrogen bonds : bond 0.03957 / 2.61 ( 285) hydrogen bonds : angle 4.79383 / 3.44 ( 819) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3250.86 seconds wall clock time: 55 minutes 51.32 seconds (3351.32 seconds total)