Starting phenix.real_space_refine on Wed Mar 4 01:45:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6skk_10226/03_2026/6skk_10226.cif Found real_map, /net/cci-nas-00/data/ceres_data/6skk_10226/03_2026/6skk_10226.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6skk_10226/03_2026/6skk_10226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6skk_10226/03_2026/6skk_10226.map" model { file = "/net/cci-nas-00/data/ceres_data/6skk_10226/03_2026/6skk_10226.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6skk_10226/03_2026/6skk_10226.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 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 78 5.16 5 C 6506 2.51 5 N 1806 2.21 5 O 1938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10328 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1724 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1716 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Conformer: "B" Number of residues, atoms: 220, 1716 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} bond proxies already assigned to first conformer: 1745 Chain: "B" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1716 Classifications: {'peptide': 220} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 202} Chain: "C" Number of atoms: 1724 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1716 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Conformer: "B" Number of residues, atoms: 220, 1716 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} bond proxies already assigned to first conformer: 1745 Chain: "D" Number of atoms: 1724 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1716 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Conformer: "B" Number of residues, atoms: 220, 1716 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} bond proxies already assigned to first conformer: 1745 Chain: "E" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1716 Classifications: {'peptide': 220} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 202} Chain: "F" Number of atoms: 1724 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1716 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Conformer: "B" Number of residues, atoms: 220, 1716 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} bond proxies already assigned to first conformer: 1745 Time building chain proxies: 3.90, per 1000 atoms: 0.38 Number of scatterers: 10328 At special positions: 0 Unit cell: (109.18, 117.66, 80.56, 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 78 16.00 O 1938 8.00 N 1806 7.00 C 6506 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 218 " distance=2.03 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 218 " distance=2.04 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 218 " distance=2.03 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 218 " distance=2.03 Simple disulfide: pdb=" SG CYS E 198 " - pdb=" SG CYS E 218 " distance=2.03 Simple disulfide: pdb=" SG CYS F 198 " - pdb=" SG CYS F 218 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 889.7 milliseconds 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2480 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 5 sheets defined 67.3% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 16 through 31 Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 62 through 84 Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 110 through 120 Processing helix chain 'A' and resid 125 through 145 Processing helix chain 'A' and resid 160 through 175 Processing helix chain 'A' and resid 178 through 193 removed outlier: 3.895A pdb=" N TRP A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 Processing helix chain 'A' and resid 210 through 218 Processing helix chain 'B' and resid 16 through 27 Processing helix chain 'B' and resid 35 through 44 Processing helix chain 'B' and resid 48 through 58 Processing helix chain 'B' and resid 62 through 84 Processing helix chain 'B' and resid 110 through 120 Processing helix chain 'B' and resid 125 through 145 Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.526A pdb=" N ILE B 153 " --> pdb=" O ILE B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 175 Processing helix chain 'B' and resid 178 through 190 removed outlier: 3.791A pdb=" N TRP B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU B 187 " --> pdb=" O ASN B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 206 removed outlier: 3.595A pdb=" N LEU B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 218 removed outlier: 3.803A pdb=" N CYS B 218 " --> pdb=" O MET B 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 31 Processing helix chain 'C' and resid 33 through 35 No H-bonds generated for 'chain 'C' and resid 33 through 35' Processing helix chain 'C' and resid 36 through 44 Processing helix chain 'C' and resid 48 through 58 Processing helix chain 'C' and resid 62 through 84 Processing helix chain 'C' and resid 100 through 105 removed outlier: 4.008A pdb=" N ALA C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 119 Processing helix chain 'C' and resid 125 through 145 Processing helix chain 'C' and resid 160 through 174 Processing helix chain 'C' and resid 179 through 193 removed outlier: 3.536A pdb=" N GLU C 187 " --> pdb=" O ASN C 183 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 204 Processing helix chain 'C' and resid 210 through 219 removed outlier: 3.871A pdb=" N CYS C 218 " --> pdb=" O MET C 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 30 removed outlier: 3.675A pdb=" N LEU D 20 " --> pdb=" O SER D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 44 Processing helix chain 'D' and resid 48 through 58 Processing helix chain 'D' and resid 62 through 83 Processing helix chain 'D' and resid 100 through 105 Processing helix chain 'D' and resid 110 through 118 removed outlier: 3.700A pdb=" N GLN D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 146 removed outlier: 3.602A pdb=" N ARG D 132 " --> pdb=" O GLU D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 174 Processing helix chain 'D' and resid 178 through 193 removed outlier: 4.766A pdb=" N LEU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N VAL D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 Processing helix chain 'D' and resid 210 through 218 Processing helix chain 'E' and resid 16 through 31 Processing helix chain 'E' and resid 35 through 44 Processing helix chain 'E' and resid 48 through 58 Processing helix chain 'E' and resid 62 through 84 Processing helix chain 'E' and resid 100 through 105 Processing helix chain 'E' and resid 110 through 120 Processing helix chain 'E' and resid 125 through 145 Processing helix chain 'E' and resid 149 through 153 Processing helix chain 'E' and resid 160 through 175 Processing helix chain 'E' and resid 178 through 189 removed outlier: 3.692A pdb=" N GLU E 187 " --> pdb=" O ASN E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 removed outlier: 3.905A pdb=" N ILE E 201 " --> pdb=" O ASP E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 218 removed outlier: 3.510A pdb=" N MET E 214 " --> pdb=" O THR E 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 31 removed outlier: 3.526A pdb=" N LEU F 20 " --> pdb=" O SER F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 44 Processing helix chain 'F' and resid 48 through 58 Processing helix chain 'F' and resid 62 through 84 Processing helix chain 'F' and resid 100 through 105 Processing helix chain 'F' and resid 110 through 119 Processing helix chain 'F' and resid 125 through 145 Processing helix chain 'F' and resid 160 through 176 Processing helix chain 'F' and resid 179 through 193 removed outlier: 4.362A pdb=" N LEU F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN F 193 " --> pdb=" O LEU F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 204 Processing helix chain 'F' and resid 210 through 219 removed outlier: 3.922A pdb=" N CYS F 218 " --> pdb=" O MET F 214 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4 Processing sheet with id=AA2, first strand: chain 'B' and resid 2 through 3 removed outlier: 3.669A pdb=" N VAL B 3 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL B 11 " --> pdb=" O VAL B 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 3 through 4 removed outlier: 3.600A pdb=" N VAL C 3 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL C 11 " --> pdb=" O VAL C 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'E' and resid 2 through 3 removed outlier: 3.664A pdb=" N VAL E 3 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL E 11 " --> pdb=" O VAL E 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 3 through 4 removed outlier: 3.541A pdb=" N VAL F 3 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL F 11 " --> pdb=" O VAL F 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 595 hydrogen bonds defined for protein. 1776 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: 1.61 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3219 1.34 - 1.46: 1521 1.46 - 1.58: 5676 1.58 - 1.70: 0 1.70 - 1.82: 144 Bond restraints: 10560 Sorted by residual: bond pdb=" N SER C 33 " pdb=" CA SER C 33 " ideal model delta sigma weight residual 1.453 1.487 -0.034 9.20e-03 1.18e+04 1.38e+01 bond pdb=" N SER B 33 " pdb=" CA SER B 33 " ideal model delta sigma weight residual 1.456 1.485 -0.029 8.70e-03 1.32e+04 1.13e+01 bond pdb=" N VAL B 36 " pdb=" CA VAL B 36 " ideal model delta sigma weight residual 1.461 1.498 -0.038 1.19e-02 7.06e+03 1.01e+01 bond pdb=" N VAL E 36 " pdb=" CA VAL E 36 " ideal model delta sigma weight residual 1.461 1.495 -0.035 1.19e-02 7.06e+03 8.41e+00 bond pdb=" N VAL D 36 " pdb=" CA VAL D 36 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.40e+00 ... (remaining 10555 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 13490 1.12 - 2.25: 655 2.25 - 3.37: 181 3.37 - 4.50: 28 4.50 - 5.62: 8 Bond angle restraints: 14362 Sorted by residual: angle pdb=" C ALA F 31 " pdb=" CA ALA F 31 " pdb=" CB ALA F 31 " ideal model delta sigma weight residual 116.54 110.92 5.62 1.15e+00 7.56e-01 2.39e+01 angle pdb=" CA GLY D 61 " pdb=" C GLY D 61 " pdb=" O GLY D 61 " ideal model delta sigma weight residual 122.78 117.66 5.12 1.20e+00 6.94e-01 1.82e+01 angle pdb=" CA ALA F 31 " pdb=" C ALA F 31 " pdb=" N PHE F 32 " ideal model delta sigma weight residual 119.52 116.58 2.94 7.90e-01 1.60e+00 1.38e+01 angle pdb=" CA SER B 33 " pdb=" C SER B 33 " pdb=" N PRO B 34 " ideal model delta sigma weight residual 117.68 120.29 -2.61 7.10e-01 1.98e+00 1.35e+01 angle pdb=" C ALA B 31 " pdb=" CA ALA B 31 " pdb=" CB ALA B 31 " ideal model delta sigma weight residual 116.63 112.60 4.03 1.16e+00 7.43e-01 1.21e+01 ... (remaining 14357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 6009 17.93 - 35.86: 400 35.86 - 53.79: 94 53.79 - 71.72: 11 71.72 - 89.65: 8 Dihedral angle restraints: 6522 sinusoidal: 2696 harmonic: 3826 Sorted by residual: dihedral pdb=" CB CYS B 198 " pdb=" SG CYS B 198 " pdb=" SG CYS B 218 " pdb=" CB CYS B 218 " ideal model delta sinusoidal sigma weight residual -86.00 -134.76 48.76 1 1.00e+01 1.00e-02 3.27e+01 dihedral pdb=" CB GLU B 28 " pdb=" CG GLU B 28 " pdb=" CD GLU B 28 " pdb=" OE1 GLU B 28 " ideal model delta sinusoidal sigma weight residual 0.00 89.65 -89.65 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU A 213 " pdb=" CG GLU A 213 " pdb=" CD GLU A 213 " pdb=" OE1 GLU A 213 " ideal model delta sinusoidal sigma weight residual 0.00 -89.55 89.55 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 6519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1131 0.036 - 0.072: 338 0.072 - 0.109: 110 0.109 - 0.145: 21 0.145 - 0.181: 6 Chirality restraints: 1606 Sorted by residual: chirality pdb=" CA VAL D 36 " pdb=" N VAL D 36 " pdb=" C VAL D 36 " pdb=" CB VAL D 36 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.19e-01 chirality pdb=" CA ILE B 37 " pdb=" N ILE B 37 " pdb=" C ILE B 37 " pdb=" CB ILE B 37 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.73e-01 chirality pdb=" CA VAL E 36 " pdb=" N VAL E 36 " pdb=" C VAL E 36 " pdb=" CB VAL E 36 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.36e-01 ... (remaining 1603 not shown) Planarity restraints: 1880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU E 28 " 0.023 2.00e-02 2.50e+03 4.64e-02 2.15e+01 pdb=" C GLU E 28 " -0.080 2.00e-02 2.50e+03 pdb=" O GLU E 28 " 0.030 2.00e-02 2.50e+03 pdb=" N GLU E 29 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 28 " -0.023 2.00e-02 2.50e+03 4.60e-02 2.12e+01 pdb=" C GLU A 28 " 0.080 2.00e-02 2.50e+03 pdb=" O GLU A 28 " -0.030 2.00e-02 2.50e+03 pdb=" N GLU A 29 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 28 " 0.020 2.00e-02 2.50e+03 3.99e-02 1.59e+01 pdb=" C GLU D 28 " -0.069 2.00e-02 2.50e+03 pdb=" O GLU D 28 " 0.026 2.00e-02 2.50e+03 pdb=" N GLU D 29 " 0.023 2.00e-02 2.50e+03 ... (remaining 1877 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 3241 2.83 - 3.35: 10396 3.35 - 3.87: 16612 3.87 - 4.38: 18319 4.38 - 4.90: 30470 Nonbonded interactions: 79038 Sorted by model distance: nonbonded pdb=" O THR C 54 " pdb=" OG1 THR C 58 " model vdw 2.319 3.040 nonbonded pdb=" O ILE F 115 " pdb=" OG1 THR F 119 " model vdw 2.327 3.040 nonbonded pdb=" O GLY D 156 " pdb=" ND2 ASN D 195 " model vdw 2.339 3.120 nonbonded pdb=" NE2 GLN E 155 " pdb=" O GLU E 159 " model vdw 2.351 3.120 nonbonded pdb=" OG SER B 102 " pdb=" OG1 THR B 107 " model vdw 2.357 3.040 ... (remaining 79033 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 17 or resid 19 through 220)) selection = (chain 'B' and (resid 1 through 17 or resid 19 through 220)) selection = (chain 'C' and (resid 1 through 17 or resid 19 through 220)) selection = (chain 'D' and (resid 1 through 17 or resid 19 through 220)) selection = (chain 'E' and (resid 1 through 17 or resid 19 through 220)) selection = (chain 'F' and (resid 1 through 17 or resid 19 through 220)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.290 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: 0.040 Set scattering table: 0.030 Process input model: 12.560 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 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 0.038 10566 Z= 0.226 Angle : 0.605 5.622 14374 Z= 0.393 Chirality : 0.041 0.181 1606 Planarity : 0.004 0.046 1880 Dihedral : 12.957 89.647 4024 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.18 % Allowed : 2.49 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % 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: -1.14 (0.21), residues: 1312 helix: -0.47 (0.16), residues: 862 sheet: -3.37 (0.46), residues: 54 loop : -0.61 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 100 TYR 0.014 0.001 TYR F 130 PHE 0.004 0.001 PHE F 40 TRP 0.006 0.001 TRP A 80 HIS 0.002 0.001 HIS D 62 Details of bonding type rmsd covalent geometry : bond 0.00348 (10560) covalent geometry : angle 0.60471 (14362) SS BOND : bond 0.00186 ( 6) SS BOND : angle 0.99376 ( 12) hydrogen bonds : bond 0.13164 ( 595) hydrogen bonds : angle 5.05550 ( 1776) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.6854 (mtp) cc_final: 0.6549 (mtp) REVERT: A 118 MET cc_start: 0.8323 (mtm) cc_final: 0.7783 (mtp) REVERT: A 144 MET cc_start: 0.8019 (ttp) cc_final: 0.7694 (ttt) REVERT: B 55 MET cc_start: 0.8091 (mtp) cc_final: 0.7777 (mtp) REVERT: B 144 MET cc_start: 0.7663 (ttt) cc_final: 0.7371 (ttm) REVERT: C 25 LYS cc_start: 0.8061 (mttt) cc_final: 0.7720 (mttm) REVERT: C 182 LYS cc_start: 0.8535 (ttmm) cc_final: 0.8128 (mtpp) REVERT: D 66 MET cc_start: 0.7990 (mmm) cc_final: 0.7469 (mmm) REVERT: D 118 MET cc_start: 0.8197 (mtm) cc_final: 0.7917 (mtp) REVERT: D 144 MET cc_start: 0.7953 (ttp) cc_final: 0.7064 (ttp) REVERT: D 203 LYS cc_start: 0.7344 (mmmt) cc_final: 0.7038 (tttm) REVERT: E 25 LYS cc_start: 0.8211 (mttt) cc_final: 0.7851 (mttm) REVERT: E 66 MET cc_start: 0.8959 (mmm) cc_final: 0.8700 (mmt) REVERT: F 12 HIS cc_start: 0.8107 (t70) cc_final: 0.7896 (t-90) REVERT: F 182 LYS cc_start: 0.8380 (ttmm) cc_final: 0.8155 (mtpt) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 0.1215 time to fit residues: 55.2691 Evaluate side-chains 243 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.0570 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.0010 chunk 55 optimal weight: 0.0870 overall best weight: 0.2682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN A 7 GLN A 183 ASN A 195 ASN B 9 GLN B 53 ASN B 179 GLN B 183 ASN B 219 GLN C 21 ASN C 219 GLN D 4 GLN D 12 HIS D 67 GLN D 95 GLN D 195 ASN E 9 GLN E 53 ASN E 219 GLN F 9 GLN F 21 ASN F 95 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.176193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.138488 restraints weight = 40754.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.141117 restraints weight = 18530.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.142944 restraints weight = 12973.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.145657 restraints weight = 8975.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.145923 restraints weight = 7496.270| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3684 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3684 r_free = 0.3684 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3683 r_free = 0.3683 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3683 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10566 Z= 0.127 Angle : 0.580 9.876 14374 Z= 0.297 Chirality : 0.042 0.164 1606 Planarity : 0.005 0.043 1880 Dihedral : 3.723 19.140 1410 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.51 % Allowed : 14.12 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % 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: 0.35 (0.23), residues: 1312 helix: 0.65 (0.18), residues: 868 sheet: -2.91 (0.53), residues: 54 loop : 0.06 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 97 TYR 0.015 0.001 TYR F 164 PHE 0.010 0.001 PHE C 40 TRP 0.028 0.001 TRP C 117 HIS 0.005 0.001 HIS C 12 Details of bonding type rmsd covalent geometry : bond 0.00275 (10560) covalent geometry : angle 0.58015 (14362) SS BOND : bond 0.00179 ( 6) SS BOND : angle 0.72856 ( 12) hydrogen bonds : bond 0.03993 ( 595) hydrogen bonds : angle 4.14215 ( 1776) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 269 time to evaluate : 0.362 Fit side-chains REVERT: A 100 ARG cc_start: 0.7230 (tpt-90) cc_final: 0.6712 (tpt90) REVERT: A 118 MET cc_start: 0.8482 (mtm) cc_final: 0.7980 (mtp) REVERT: A 182 LYS cc_start: 0.8962 (mtpp) cc_final: 0.8708 (mtpt) REVERT: A 214 MET cc_start: 0.8266 (mtp) cc_final: 0.7971 (mtt) REVERT: B 55 MET cc_start: 0.7911 (mtp) cc_final: 0.7682 (mtp) REVERT: B 179 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8196 (tm-30) REVERT: C 25 LYS cc_start: 0.8243 (mttt) cc_final: 0.7901 (mttm) REVERT: C 28 GLU cc_start: 0.6296 (mm-30) cc_final: 0.6060 (mm-30) REVERT: C 182 LYS cc_start: 0.8648 (ttmm) cc_final: 0.8148 (mtpt) REVERT: C 185 MET cc_start: 0.7132 (mtm) cc_final: 0.6918 (mtp) REVERT: C 214 MET cc_start: 0.8528 (tpp) cc_final: 0.8290 (tpt) REVERT: D 36 VAL cc_start: 0.7573 (m) cc_final: 0.7319 (t) REVERT: D 118 MET cc_start: 0.8405 (mtm) cc_final: 0.8003 (mtp) REVERT: D 133 TRP cc_start: 0.8307 (m-10) cc_final: 0.7954 (m-10) REVERT: D 144 MET cc_start: 0.7780 (ttp) cc_final: 0.7527 (ttp) REVERT: D 203 LYS cc_start: 0.7407 (mmmt) cc_final: 0.7011 (tttm) REVERT: E 114 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7850 (mp10) REVERT: E 117 TRP cc_start: 0.7946 (m-10) cc_final: 0.7692 (m-10) REVERT: E 144 MET cc_start: 0.7840 (ttt) cc_final: 0.7560 (ttm) REVERT: F 212 GLU cc_start: 0.7372 (tt0) cc_final: 0.6979 (tt0) outliers start: 15 outliers final: 9 residues processed: 275 average time/residue: 0.1197 time to fit residues: 43.2961 Evaluate side-chains 251 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 240 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain B residue 179 GLN Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain F residue 110 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 130 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 25 optimal weight: 0.0010 chunk 61 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 124 optimal weight: 0.5980 overall best weight: 1.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 HIS A 95 GLN A 195 ASN B 183 ASN D 195 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.175335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.140673 restraints weight = 32589.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.145645 restraints weight = 19848.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.146160 restraints weight = 12835.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.148456 restraints weight = 7894.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.150519 restraints weight = 6368.421| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3719 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3719 r_free = 0.3719 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3719 r_free = 0.3719 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10566 Z= 0.129 Angle : 0.564 7.617 14374 Z= 0.291 Chirality : 0.042 0.278 1606 Planarity : 0.005 0.051 1880 Dihedral : 3.777 18.737 1410 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.95 % Allowed : 15.99 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % 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: 0.76 (0.24), residues: 1312 helix: 0.92 (0.18), residues: 870 sheet: -2.60 (0.59), residues: 54 loop : 0.32 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 143 TYR 0.012 0.001 TYR F 130 PHE 0.014 0.001 PHE B 161 TRP 0.031 0.001 TRP C 117 HIS 0.006 0.001 HIS C 12 Details of bonding type rmsd covalent geometry : bond 0.00302 (10560) covalent geometry : angle 0.56408 (14362) SS BOND : bond 0.00279 ( 6) SS BOND : angle 0.78925 ( 12) hydrogen bonds : bond 0.03952 ( 595) hydrogen bonds : angle 4.13426 ( 1776) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 260 time to evaluate : 0.363 Fit side-chains REVERT: A 100 ARG cc_start: 0.7388 (tpt-90) cc_final: 0.7178 (tpt-90) REVERT: A 118 MET cc_start: 0.8357 (mtm) cc_final: 0.7902 (mtp) REVERT: B 55 MET cc_start: 0.8172 (mtp) cc_final: 0.7953 (mtp) REVERT: C 25 LYS cc_start: 0.8193 (mttt) cc_final: 0.7851 (mttm) REVERT: C 182 LYS cc_start: 0.8598 (ttmm) cc_final: 0.8250 (mtpt) REVERT: C 214 MET cc_start: 0.8444 (tpp) cc_final: 0.8203 (tpt) REVERT: D 118 MET cc_start: 0.8373 (mtm) cc_final: 0.7953 (mtp) REVERT: D 144 MET cc_start: 0.7821 (ttp) cc_final: 0.7162 (ttp) REVERT: D 149 SER cc_start: 0.8420 (OUTLIER) cc_final: 0.8169 (t) REVERT: D 203 LYS cc_start: 0.7360 (mmmt) cc_final: 0.6966 (tttm) REVERT: E 144 MET cc_start: 0.7691 (ttt) cc_final: 0.7485 (ttt) REVERT: E 151 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7532 (mm) REVERT: F 44 SER cc_start: 0.8881 (p) cc_final: 0.8646 (t) REVERT: F 215 MET cc_start: 0.7813 (ptp) cc_final: 0.7581 (mtm) outliers start: 20 outliers final: 10 residues processed: 267 average time/residue: 0.1167 time to fit residues: 41.3441 Evaluate side-chains 241 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 229 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain F residue 59 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 53 optimal weight: 0.0570 chunk 55 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 96 optimal weight: 0.0170 chunk 121 optimal weight: 8.9990 chunk 72 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 195 ASN ** E 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 21 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.176796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.133351 restraints weight = 34338.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.138841 restraints weight = 14866.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.141566 restraints weight = 8370.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.142004 restraints weight = 7354.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.142190 restraints weight = 6871.574| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3640 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3640 r_free = 0.3640 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3639 r_free = 0.3639 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10566 Z= 0.123 Angle : 0.576 8.875 14374 Z= 0.294 Chirality : 0.042 0.268 1606 Planarity : 0.005 0.049 1880 Dihedral : 3.806 19.830 1410 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.60 % Allowed : 17.67 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % 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 (0.24), residues: 1312 helix: 1.13 (0.18), residues: 882 sheet: -2.39 (0.63), residues: 54 loop : 0.32 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 162 TYR 0.010 0.001 TYR F 164 PHE 0.010 0.001 PHE F 168 TRP 0.040 0.001 TRP C 117 HIS 0.007 0.001 HIS C 12 Details of bonding type rmsd covalent geometry : bond 0.00271 (10560) covalent geometry : angle 0.57539 (14362) SS BOND : bond 0.00193 ( 6) SS BOND : angle 0.94273 ( 12) hydrogen bonds : bond 0.03793 ( 595) hydrogen bonds : angle 4.03157 ( 1776) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 248 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7368 (tpt-90) cc_final: 0.7140 (tpt-90) REVERT: A 118 MET cc_start: 0.8390 (mtm) cc_final: 0.7843 (mtp) REVERT: B 144 MET cc_start: 0.7870 (ttm) cc_final: 0.7668 (ttm) REVERT: C 25 LYS cc_start: 0.8183 (mttt) cc_final: 0.7853 (mttm) REVERT: C 100 ARG cc_start: 0.7807 (ptm160) cc_final: 0.7328 (ttp-110) REVERT: C 133 TRP cc_start: 0.7886 (m-10) cc_final: 0.6962 (m-10) REVERT: C 182 LYS cc_start: 0.8710 (ttmm) cc_final: 0.8256 (mtpp) REVERT: C 214 MET cc_start: 0.8616 (tpp) cc_final: 0.8338 (tpt) REVERT: D 118 MET cc_start: 0.8413 (mtm) cc_final: 0.7972 (mtp) REVERT: D 144 MET cc_start: 0.7892 (ttp) cc_final: 0.7587 (ttt) REVERT: D 145 TYR cc_start: 0.7527 (OUTLIER) cc_final: 0.7241 (m-80) REVERT: D 149 SER cc_start: 0.8406 (OUTLIER) cc_final: 0.8189 (t) REVERT: D 203 LYS cc_start: 0.7448 (mmmt) cc_final: 0.7034 (tttm) REVERT: E 39 MET cc_start: 0.7685 (tpp) cc_final: 0.7468 (tpp) REVERT: E 114 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7923 (mp10) REVERT: E 151 LEU cc_start: 0.7928 (mm) cc_final: 0.7562 (mm) REVERT: F 28 GLU cc_start: 0.6354 (mm-30) cc_final: 0.5872 (mm-30) REVERT: F 143 ARG cc_start: 0.8209 (mmm-85) cc_final: 0.7288 (mmm160) outliers start: 16 outliers final: 8 residues processed: 257 average time/residue: 0.1089 time to fit residues: 37.6550 Evaluate side-chains 234 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 223 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 145 TYR Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 189 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 60 optimal weight: 6.9990 chunk 86 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 127 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.171147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.128529 restraints weight = 28644.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.133993 restraints weight = 13083.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.134787 restraints weight = 7985.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.135221 restraints weight = 7221.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.135474 restraints weight = 6903.248| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3565 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3565 r_free = 0.3565 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3565 r_free = 0.3565 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3565 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10566 Z= 0.188 Angle : 0.635 10.158 14374 Z= 0.328 Chirality : 0.044 0.210 1606 Planarity : 0.005 0.049 1880 Dihedral : 4.028 18.965 1410 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.13 % Allowed : 17.94 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % 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: 0.87 (0.24), residues: 1312 helix: 0.98 (0.18), residues: 882 sheet: -2.34 (0.62), residues: 54 loop : 0.35 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 97 TYR 0.026 0.002 TYR A 169 PHE 0.013 0.002 PHE E 161 TRP 0.053 0.002 TRP C 117 HIS 0.005 0.001 HIS C 12 Details of bonding type rmsd covalent geometry : bond 0.00460 (10560) covalent geometry : angle 0.63409 (14362) SS BOND : bond 0.00453 ( 6) SS BOND : angle 1.10922 ( 12) hydrogen bonds : bond 0.04384 ( 595) hydrogen bonds : angle 4.34741 ( 1776) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 235 time to evaluate : 0.325 Fit side-chains REVERT: A 29 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7337 (mm-30) REVERT: A 100 ARG cc_start: 0.7399 (tpt-90) cc_final: 0.7136 (tpt-90) REVERT: A 118 MET cc_start: 0.8441 (mtm) cc_final: 0.7941 (mtp) REVERT: A 214 MET cc_start: 0.8340 (mtp) cc_final: 0.8035 (mtt) REVERT: B 98 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6693 (tm-30) REVERT: C 25 LYS cc_start: 0.8299 (mttt) cc_final: 0.7857 (mttm) REVERT: C 39 MET cc_start: 0.8490 (mmt) cc_final: 0.8150 (mmt) REVERT: C 100 ARG cc_start: 0.7860 (ptm160) cc_final: 0.7543 (ttp-110) REVERT: C 117 TRP cc_start: 0.8060 (m-90) cc_final: 0.7729 (m-90) REVERT: C 133 TRP cc_start: 0.8070 (m-10) cc_final: 0.7170 (m-10) REVERT: C 214 MET cc_start: 0.8689 (tpp) cc_final: 0.8405 (tpt) REVERT: D 100 ARG cc_start: 0.7440 (tpt-90) cc_final: 0.7117 (tpt-90) REVERT: D 117 TRP cc_start: 0.7426 (m-10) cc_final: 0.7196 (m-10) REVERT: D 118 MET cc_start: 0.8599 (mtm) cc_final: 0.8116 (mtp) REVERT: D 203 LYS cc_start: 0.7513 (mmmt) cc_final: 0.7108 (tttm) REVERT: E 114 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7783 (mp10) REVERT: E 151 LEU cc_start: 0.7979 (mm) cc_final: 0.7694 (mm) REVERT: F 143 ARG cc_start: 0.8263 (mmm-85) cc_final: 0.7348 (mmm160) outliers start: 22 outliers final: 15 residues processed: 249 average time/residue: 0.1089 time to fit residues: 36.3364 Evaluate side-chains 241 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 224 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain E residue 70 LYS Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 189 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 33 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 22 optimal weight: 0.0070 chunk 7 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.174664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.130460 restraints weight = 35349.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.135974 restraints weight = 15242.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.139538 restraints weight = 8501.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.139309 restraints weight = 7202.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.139605 restraints weight = 6756.944| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3605 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3605 r_free = 0.3605 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3605 r_free = 0.3605 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3605 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10566 Z= 0.125 Angle : 0.579 8.111 14374 Z= 0.298 Chirality : 0.042 0.218 1606 Planarity : 0.005 0.048 1880 Dihedral : 3.957 19.907 1410 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.69 % Allowed : 18.83 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.24), residues: 1312 helix: 1.15 (0.18), residues: 882 sheet: -2.15 (0.64), residues: 54 loop : 0.41 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 97 TYR 0.008 0.001 TYR D 169 PHE 0.012 0.001 PHE E 161 TRP 0.040 0.001 TRP C 117 HIS 0.005 0.001 HIS C 12 Details of bonding type rmsd covalent geometry : bond 0.00294 (10560) covalent geometry : angle 0.57848 (14362) SS BOND : bond 0.00289 ( 6) SS BOND : angle 1.08022 ( 12) hydrogen bonds : bond 0.03932 ( 595) hydrogen bonds : angle 4.10947 ( 1776) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 243 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7286 (tpt-90) cc_final: 0.7012 (tpt-90) REVERT: A 118 MET cc_start: 0.8353 (mtm) cc_final: 0.7890 (mtp) REVERT: C 100 ARG cc_start: 0.7814 (ptm160) cc_final: 0.7544 (ttp-110) REVERT: C 114 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7874 (mp10) REVERT: C 117 TRP cc_start: 0.8077 (m-90) cc_final: 0.7725 (m-90) REVERT: C 182 LYS cc_start: 0.8684 (mtpp) cc_final: 0.8460 (mtpt) REVERT: C 214 MET cc_start: 0.8599 (tpp) cc_final: 0.8308 (tpt) REVERT: D 118 MET cc_start: 0.8505 (mtm) cc_final: 0.8057 (mtp) REVERT: D 203 LYS cc_start: 0.7480 (mmmt) cc_final: 0.7065 (tttm) REVERT: E 114 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7797 (mp10) REVERT: E 144 MET cc_start: 0.7646 (ttt) cc_final: 0.7442 (ttm) REVERT: E 151 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7646 (mm) REVERT: F 28 GLU cc_start: 0.6662 (mm-30) cc_final: 0.5925 (mm-30) REVERT: F 143 ARG cc_start: 0.8207 (mmm-85) cc_final: 0.7268 (mmm160) outliers start: 17 outliers final: 11 residues processed: 252 average time/residue: 0.1062 time to fit residues: 36.0427 Evaluate side-chains 232 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 218 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 189 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 119 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 83 optimal weight: 0.3980 chunk 92 optimal weight: 0.9990 chunk 100 optimal weight: 0.0670 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 195 ASN ** F 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.176098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.140292 restraints weight = 30086.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.144348 restraints weight = 18790.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.144796 restraints weight = 13910.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.147416 restraints weight = 8309.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.149364 restraints weight = 6618.623| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10566 Z= 0.123 Angle : 0.597 10.950 14374 Z= 0.304 Chirality : 0.042 0.189 1606 Planarity : 0.005 0.049 1880 Dihedral : 3.908 20.005 1410 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.78 % Allowed : 19.18 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % 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: 1.27 (0.24), residues: 1312 helix: 1.28 (0.18), residues: 882 sheet: -1.94 (0.66), residues: 54 loop : 0.48 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 162 TYR 0.021 0.001 TYR D 169 PHE 0.012 0.001 PHE E 161 TRP 0.035 0.001 TRP C 117 HIS 0.005 0.000 HIS C 12 Details of bonding type rmsd covalent geometry : bond 0.00276 (10560) covalent geometry : angle 0.59657 (14362) SS BOND : bond 0.00267 ( 6) SS BOND : angle 1.05874 ( 12) hydrogen bonds : bond 0.03771 ( 595) hydrogen bonds : angle 4.03666 ( 1776) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 240 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7186 (tpt-90) cc_final: 0.6899 (tpt-90) REVERT: A 118 MET cc_start: 0.8324 (mtm) cc_final: 0.7860 (mtp) REVERT: B 98 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6557 (tm-30) REVERT: B 102 SER cc_start: 0.8298 (OUTLIER) cc_final: 0.7844 (m) REVERT: B 180 GLU cc_start: 0.7874 (mp0) cc_final: 0.7224 (tm-30) REVERT: C 100 ARG cc_start: 0.7730 (ptm160) cc_final: 0.7442 (ttp-110) REVERT: C 117 TRP cc_start: 0.8049 (m-90) cc_final: 0.7843 (m-90) REVERT: C 214 MET cc_start: 0.8353 (tpp) cc_final: 0.8128 (tpt) REVERT: D 100 ARG cc_start: 0.7410 (tpt-90) cc_final: 0.6760 (tpt90) REVERT: D 118 MET cc_start: 0.8405 (mtm) cc_final: 0.7961 (mtp) REVERT: D 143 ARG cc_start: 0.7845 (ttm170) cc_final: 0.6713 (tpt170) REVERT: D 203 LYS cc_start: 0.7313 (mmmt) cc_final: 0.6920 (tttm) REVERT: E 114 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7876 (mp10) REVERT: E 151 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7659 (mm) REVERT: F 28 GLU cc_start: 0.6629 (mm-30) cc_final: 0.6421 (mm-30) REVERT: F 143 ARG cc_start: 0.7962 (mmm-85) cc_final: 0.7478 (mmm160) outliers start: 18 outliers final: 9 residues processed: 251 average time/residue: 0.1074 time to fit residues: 36.3794 Evaluate side-chains 238 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 225 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 189 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 127 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 92 optimal weight: 0.0170 chunk 117 optimal weight: 7.9990 chunk 75 optimal weight: 0.2980 chunk 72 optimal weight: 7.9990 chunk 12 optimal weight: 0.6980 chunk 61 optimal weight: 10.0000 chunk 104 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 0.0970 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 114 GLN D 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.177585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.141343 restraints weight = 28321.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.146611 restraints weight = 16264.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.147216 restraints weight = 11039.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.148324 restraints weight = 7660.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.150718 restraints weight = 6660.580| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3739 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3739 r_free = 0.3739 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3739 r_free = 0.3739 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3739 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10566 Z= 0.123 Angle : 0.621 12.090 14374 Z= 0.314 Chirality : 0.042 0.167 1606 Planarity : 0.005 0.047 1880 Dihedral : 3.896 19.539 1410 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.60 % Allowed : 19.72 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % 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: 1.33 (0.24), residues: 1312 helix: 1.33 (0.18), residues: 880 sheet: -1.86 (0.65), residues: 54 loop : 0.49 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 97 TYR 0.008 0.001 TYR F 164 PHE 0.010 0.001 PHE E 161 TRP 0.033 0.001 TRP C 117 HIS 0.004 0.000 HIS C 12 Details of bonding type rmsd covalent geometry : bond 0.00276 (10560) covalent geometry : angle 0.62007 (14362) SS BOND : bond 0.00228 ( 6) SS BOND : angle 1.07321 ( 12) hydrogen bonds : bond 0.03666 ( 595) hydrogen bonds : angle 4.06310 ( 1776) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 239 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7255 (mm-30) REVERT: A 39 MET cc_start: 0.7218 (OUTLIER) cc_final: 0.6990 (tpp) REVERT: A 100 ARG cc_start: 0.7215 (tpt-90) cc_final: 0.6965 (tpt-90) REVERT: A 118 MET cc_start: 0.8340 (mtm) cc_final: 0.7854 (mtp) REVERT: A 203 LYS cc_start: 0.7202 (mmmt) cc_final: 0.6736 (tttm) REVERT: B 102 SER cc_start: 0.8303 (OUTLIER) cc_final: 0.7859 (m) REVERT: B 180 GLU cc_start: 0.7812 (mp0) cc_final: 0.7226 (tm-30) REVERT: C 25 LYS cc_start: 0.8135 (ttmt) cc_final: 0.7361 (ttpp) REVERT: C 28 GLU cc_start: 0.6466 (mm-30) cc_final: 0.6254 (mm-30) REVERT: C 100 ARG cc_start: 0.7642 (ptm160) cc_final: 0.7273 (ttp-110) REVERT: C 117 TRP cc_start: 0.8064 (m-90) cc_final: 0.7825 (m-90) REVERT: C 176 GLN cc_start: 0.7878 (tm-30) cc_final: 0.7551 (tm-30) REVERT: C 214 MET cc_start: 0.8429 (tpp) cc_final: 0.8214 (tpt) REVERT: D 99 PRO cc_start: 0.6418 (Cg_exo) cc_final: 0.5949 (Cg_endo) REVERT: D 118 MET cc_start: 0.8382 (mtm) cc_final: 0.7920 (mtp) REVERT: D 143 ARG cc_start: 0.7856 (ttm170) cc_final: 0.6729 (tpt170) REVERT: D 203 LYS cc_start: 0.7373 (mmmt) cc_final: 0.6952 (tttm) REVERT: E 114 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7865 (mp10) REVERT: E 151 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7666 (mm) REVERT: F 28 GLU cc_start: 0.6620 (mm-30) cc_final: 0.6418 (mm-30) REVERT: F 143 ARG cc_start: 0.7991 (mmm-85) cc_final: 0.7440 (mmm160) outliers start: 16 outliers final: 7 residues processed: 247 average time/residue: 0.1085 time to fit residues: 36.3580 Evaluate side-chains 238 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 227 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 189 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 116 optimal weight: 10.0000 chunk 14 optimal weight: 0.0030 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 52 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 overall best weight: 3.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.172106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.127815 restraints weight = 33848.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.133675 restraints weight = 14759.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.136063 restraints weight = 8328.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.136268 restraints weight = 7287.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.136472 restraints weight = 6734.402| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3569 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3569 r_free = 0.3569 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3569 r_free = 0.3569 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3569 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10566 Z= 0.196 Angle : 0.698 12.566 14374 Z= 0.355 Chirality : 0.045 0.177 1606 Planarity : 0.005 0.048 1880 Dihedral : 4.114 18.640 1410 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.42 % Allowed : 19.89 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % 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: 1.04 (0.24), residues: 1312 helix: 1.10 (0.18), residues: 880 sheet: -1.97 (0.64), residues: 54 loop : 0.40 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 162 TYR 0.027 0.002 TYR D 169 PHE 0.012 0.002 PHE D 40 TRP 0.024 0.002 TRP C 117 HIS 0.005 0.001 HIS C 12 Details of bonding type rmsd covalent geometry : bond 0.00477 (10560) covalent geometry : angle 0.69797 (14362) SS BOND : bond 0.00444 ( 6) SS BOND : angle 1.09541 ( 12) hydrogen bonds : bond 0.04395 ( 595) hydrogen bonds : angle 4.46337 ( 1776) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 236 time to evaluate : 0.354 Fit side-chains REVERT: A 29 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7269 (mm-30) REVERT: A 100 ARG cc_start: 0.7339 (tpt-90) cc_final: 0.6914 (tpt-90) REVERT: A 118 MET cc_start: 0.8349 (mtm) cc_final: 0.7846 (mtp) REVERT: B 98 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6626 (tm-30) REVERT: B 132 ARG cc_start: 0.8165 (mtp-110) cc_final: 0.7663 (mtt90) REVERT: B 180 GLU cc_start: 0.7982 (mp0) cc_final: 0.7279 (tm-30) REVERT: B 213 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8495 (mm-30) REVERT: C 25 LYS cc_start: 0.8130 (ttmt) cc_final: 0.7379 (ttpp) REVERT: C 117 TRP cc_start: 0.8199 (m-90) cc_final: 0.7853 (m-90) REVERT: C 133 TRP cc_start: 0.8021 (m-10) cc_final: 0.6943 (m100) REVERT: C 176 GLN cc_start: 0.7923 (tm-30) cc_final: 0.7576 (tm-30) REVERT: C 214 MET cc_start: 0.8689 (tpp) cc_final: 0.8389 (tpt) REVERT: D 39 MET cc_start: 0.7867 (tpp) cc_final: 0.7297 (tpp) REVERT: D 99 PRO cc_start: 0.6497 (Cg_exo) cc_final: 0.6055 (Cg_endo) REVERT: D 100 ARG cc_start: 0.7340 (tpt-90) cc_final: 0.6488 (tpt90) REVERT: D 118 MET cc_start: 0.8648 (mtm) cc_final: 0.8247 (mtp) REVERT: D 203 LYS cc_start: 0.7514 (mmmt) cc_final: 0.7080 (tttm) REVERT: E 114 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7875 (mp10) REVERT: E 151 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7734 (mm) REVERT: F 25 LYS cc_start: 0.8051 (ttmt) cc_final: 0.7379 (tmtt) REVERT: F 103 ASP cc_start: 0.6881 (t0) cc_final: 0.6226 (t0) REVERT: F 143 ARG cc_start: 0.8165 (mmm-85) cc_final: 0.7507 (mmm160) REVERT: F 182 LYS cc_start: 0.8273 (mtpt) cc_final: 0.8060 (mtpp) REVERT: F 215 MET cc_start: 0.7603 (ptp) cc_final: 0.7224 (mpp) outliers start: 14 outliers final: 10 residues processed: 244 average time/residue: 0.1192 time to fit residues: 38.4048 Evaluate side-chains 243 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 230 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 189 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 102 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 119 optimal weight: 0.0170 chunk 111 optimal weight: 0.4980 chunk 55 optimal weight: 0.8980 chunk 120 optimal weight: 0.2980 chunk 81 optimal weight: 3.9990 chunk 4 optimal weight: 0.0980 chunk 19 optimal weight: 0.9990 chunk 41 optimal weight: 20.0000 overall best weight: 0.3618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 9 GLN D 179 GLN ** F 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.177150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.133334 restraints weight = 24837.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.138122 restraints weight = 12588.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.141181 restraints weight = 8452.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.143115 restraints weight = 6711.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.144051 restraints weight = 5872.511| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3683 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3683 r_free = 0.3683 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3683 r_free = 0.3683 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3683 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10566 Z= 0.128 Angle : 0.654 13.000 14374 Z= 0.331 Chirality : 0.043 0.162 1606 Planarity : 0.005 0.046 1880 Dihedral : 4.002 19.190 1410 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.98 % Allowed : 20.34 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.24), residues: 1312 helix: 1.28 (0.18), residues: 878 sheet: -1.83 (0.65), residues: 54 loop : 0.44 (0.34), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 97 TYR 0.021 0.001 TYR D 169 PHE 0.010 0.001 PHE F 168 TRP 0.034 0.001 TRP C 117 HIS 0.004 0.001 HIS C 12 Details of bonding type rmsd covalent geometry : bond 0.00286 (10560) covalent geometry : angle 0.65390 (14362) SS BOND : bond 0.00557 ( 6) SS BOND : angle 1.15067 ( 12) hydrogen bonds : bond 0.03768 ( 595) hydrogen bonds : angle 4.21281 ( 1776) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 242 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7239 (mm-30) REVERT: A 100 ARG cc_start: 0.7250 (tpt-90) cc_final: 0.6899 (tpt-90) REVERT: A 103 ASP cc_start: 0.6512 (t0) cc_final: 0.6300 (t0) REVERT: A 118 MET cc_start: 0.8273 (mtm) cc_final: 0.7807 (mtp) REVERT: A 172 LEU cc_start: 0.8857 (tp) cc_final: 0.8325 (tt) REVERT: B 98 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6502 (tm-30) REVERT: B 102 SER cc_start: 0.8358 (OUTLIER) cc_final: 0.7873 (m) REVERT: B 132 ARG cc_start: 0.8159 (mtp-110) cc_final: 0.7757 (mtt90) REVERT: B 180 GLU cc_start: 0.7841 (mp0) cc_final: 0.7244 (tm-30) REVERT: C 25 LYS cc_start: 0.8087 (ttmt) cc_final: 0.7332 (ttpp) REVERT: C 28 GLU cc_start: 0.6676 (mm-30) cc_final: 0.6391 (mm-30) REVERT: C 117 TRP cc_start: 0.8067 (m-90) cc_final: 0.7818 (m-90) REVERT: C 143 ARG cc_start: 0.8047 (mmm-85) cc_final: 0.7524 (mmm160) REVERT: C 176 GLN cc_start: 0.7824 (tm-30) cc_final: 0.7218 (pt0) REVERT: C 214 MET cc_start: 0.8605 (tpp) cc_final: 0.8327 (tpt) REVERT: C 215 MET cc_start: 0.7341 (ptp) cc_final: 0.6974 (mpp) REVERT: D 28 GLU cc_start: 0.7426 (tt0) cc_final: 0.7208 (tt0) REVERT: D 39 MET cc_start: 0.7628 (tpp) cc_final: 0.7017 (tpp) REVERT: D 99 PRO cc_start: 0.6195 (Cg_exo) cc_final: 0.5791 (Cg_endo) REVERT: D 100 ARG cc_start: 0.7171 (tpt-90) cc_final: 0.6963 (tpt-90) REVERT: D 118 MET cc_start: 0.8428 (mtm) cc_final: 0.7991 (mtp) REVERT: D 203 LYS cc_start: 0.7418 (mmmt) cc_final: 0.6960 (tttm) REVERT: D 214 MET cc_start: 0.7465 (mtt) cc_final: 0.7227 (mtt) REVERT: E 114 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7822 (mp10) REVERT: E 151 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7811 (mm) REVERT: F 28 GLU cc_start: 0.6617 (mm-30) cc_final: 0.5864 (mm-30) REVERT: F 103 ASP cc_start: 0.6460 (t0) cc_final: 0.6002 (t0) REVERT: F 143 ARG cc_start: 0.8019 (mmm-85) cc_final: 0.7288 (mmm160) REVERT: F 212 GLU cc_start: 0.7360 (tt0) cc_final: 0.7153 (tt0) REVERT: F 215 MET cc_start: 0.7368 (ptp) cc_final: 0.7043 (mpp) outliers start: 9 outliers final: 4 residues processed: 248 average time/residue: 0.1179 time to fit residues: 38.7640 Evaluate side-chains 238 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 230 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 189 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 79 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 9 GLN ** F 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.176397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.133966 restraints weight = 29808.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.138612 restraints weight = 13623.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.140750 restraints weight = 8223.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.140754 restraints weight = 7579.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.141293 restraints weight = 7047.044| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10566 Z= 0.133 Angle : 0.665 13.071 14374 Z= 0.335 Chirality : 0.043 0.206 1606 Planarity : 0.005 0.047 1880 Dihedral : 3.959 18.921 1410 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.15 % Allowed : 19.63 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.24), residues: 1312 helix: 1.30 (0.18), residues: 878 sheet: -1.71 (0.65), residues: 54 loop : 0.44 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 162 TYR 0.008 0.001 TYR F 164 PHE 0.007 0.001 PHE E 161 TRP 0.028 0.001 TRP C 117 HIS 0.005 0.001 HIS C 12 Details of bonding type rmsd covalent geometry : bond 0.00315 (10560) covalent geometry : angle 0.66431 (14362) SS BOND : bond 0.00310 ( 6) SS BOND : angle 1.16092 ( 12) hydrogen bonds : bond 0.03823 ( 595) hydrogen bonds : angle 4.26369 ( 1776) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1770.86 seconds wall clock time: 31 minutes 9.44 seconds (1869.44 seconds total)