Starting phenix.real_space_refine on Mon Jul 28 02:55:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6skk_10226/07_2025/6skk_10226.cif Found real_map, /net/cci-nas-00/data/ceres_data/6skk_10226/07_2025/6skk_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_10226/07_2025/6skk_10226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6skk_10226/07_2025/6skk_10226.map" model { file = "/net/cci-nas-00/data/ceres_data/6skk_10226/07_2025/6skk_10226.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6skk_10226/07_2025/6skk_10226.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.89, per 1000 atoms: 0.86 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: 2.36 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.06 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: 2.68 Time building geometry restraints manager: 2.84 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: 0.02 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: 0.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 29.270 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.410 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.006 0.001 TRP A 80 HIS 0.002 0.001 HIS D 62 PHE 0.004 0.001 PHE F 40 TYR 0.014 0.001 TYR F 130 ARG 0.004 0.000 ARG C 100 Details of bonding type rmsd hydrogen bonds : bond 0.13164 ( 595) hydrogen bonds : angle 5.05550 ( 1776) SS BOND : bond 0.00186 ( 6) SS BOND : angle 0.99376 ( 12) covalent geometry : bond 0.00348 (10560) covalent geometry : angle 0.60471 (14362) *********************** 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 : 1.163 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: 0.2811 time to fit residues: 127.5912 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 : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 55 optimal weight: 0.0870 chunk 34 optimal weight: 0.0030 chunk 67 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 62 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 119 optimal weight: 0.1980 overall best weight: 1.4572 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.174582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.139006 restraints weight = 26684.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.143640 restraints weight = 15693.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.143982 restraints weight = 11850.990| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3666 r_free = 0.3666 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3666 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10566 Z= 0.137 Angle : 0.593 9.911 14374 Z= 0.304 Chirality : 0.043 0.165 1606 Planarity : 0.005 0.044 1880 Dihedral : 3.795 18.399 1410 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.69 % Allowed : 14.30 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.23), residues: 1312 helix: 0.56 (0.18), residues: 868 sheet: -2.97 (0.52), residues: 54 loop : 0.07 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 117 HIS 0.006 0.001 HIS C 12 PHE 0.009 0.001 PHE C 40 TYR 0.016 0.002 TYR F 130 ARG 0.004 0.001 ARG B 97 Details of bonding type rmsd hydrogen bonds : bond 0.04208 ( 595) hydrogen bonds : angle 4.25408 ( 1776) SS BOND : bond 0.00297 ( 6) SS BOND : angle 0.70908 ( 12) covalent geometry : bond 0.00319 (10560) covalent geometry : angle 0.59249 (14362) *********************** 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 278 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 261 time to evaluate : 1.171 Fit side-chains revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7263 (tpt-90) cc_final: 0.6858 (tpt90) REVERT: A 118 MET cc_start: 0.8473 (mtm) cc_final: 0.7981 (mtp) REVERT: A 182 LYS cc_start: 0.8972 (mtpp) cc_final: 0.8731 (mtpt) REVERT: A 214 MET cc_start: 0.8116 (mtp) cc_final: 0.7869 (mtt) REVERT: B 55 MET cc_start: 0.8246 (mtp) cc_final: 0.7920 (mtp) REVERT: B 144 MET cc_start: 0.7712 (ttt) cc_final: 0.7453 (ttm) REVERT: C 25 LYS cc_start: 0.8227 (mttt) cc_final: 0.7879 (mttm) REVERT: C 28 GLU cc_start: 0.6409 (mm-30) cc_final: 0.6110 (mm-30) REVERT: C 66 MET cc_start: 0.8596 (mmm) cc_final: 0.8221 (mmt) REVERT: C 182 LYS cc_start: 0.8647 (ttmm) cc_final: 0.8192 (mtpt) REVERT: C 185 MET cc_start: 0.7077 (mtm) cc_final: 0.6863 (mtp) REVERT: C 214 MET cc_start: 0.8459 (tpp) cc_final: 0.8194 (tpt) REVERT: D 118 MET cc_start: 0.8396 (mtm) cc_final: 0.7957 (mtp) REVERT: D 144 MET cc_start: 0.7647 (ttp) cc_final: 0.7350 (ttp) REVERT: D 203 LYS cc_start: 0.7386 (mmmt) cc_final: 0.7032 (tttm) REVERT: E 114 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7969 (mp10) REVERT: E 117 TRP cc_start: 0.8053 (m-10) cc_final: 0.7831 (m-10) REVERT: F 25 LYS cc_start: 0.8358 (mttt) cc_final: 0.8005 (mttp) outliers start: 17 outliers final: 10 residues processed: 270 average time/residue: 0.2787 time to fit residues: 99.2903 Evaluate side-chains 242 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 231 time to evaluate : 1.108 ------------------------------------------------------------------------------- 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 210 THR Chi-restraints excluded: chain C residue 27 VAL 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 26 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 0.0970 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 123 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 195 ASN B 179 GLN B 183 ASN ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN F 21 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.175503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.136238 restraints weight = 36593.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.138901 restraints weight = 15940.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.139870 restraints weight = 11782.347| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3626 r_free = 0.3626 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3626 r_free = 0.3626 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2327 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= 0.124 Angle : 0.554 7.299 14374 Z= 0.286 Chirality : 0.042 0.275 1606 Planarity : 0.005 0.053 1880 Dihedral : 3.787 18.522 1410 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.78 % Allowed : 16.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.24), residues: 1312 helix: 0.95 (0.18), residues: 868 sheet: -2.67 (0.57), residues: 54 loop : 0.31 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 117 HIS 0.006 0.001 HIS C 12 PHE 0.015 0.001 PHE B 161 TYR 0.012 0.001 TYR F 130 ARG 0.004 0.000 ARG E 97 Details of bonding type rmsd hydrogen bonds : bond 0.03991 ( 595) hydrogen bonds : angle 4.14767 ( 1776) SS BOND : bond 0.00207 ( 6) SS BOND : angle 0.90397 ( 12) covalent geometry : bond 0.00282 (10560) covalent geometry : angle 0.55398 (14362) *********************** 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 268 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 250 time to evaluate : 1.169 Fit side-chains REVERT: A 100 ARG cc_start: 0.7402 (tpt-90) cc_final: 0.7186 (tpt-90) REVERT: A 118 MET cc_start: 0.8491 (mtm) cc_final: 0.7999 (mtp) REVERT: A 172 LEU cc_start: 0.8911 (tp) cc_final: 0.8479 (tt) REVERT: B 55 MET cc_start: 0.8060 (mtp) cc_final: 0.7782 (mtp) REVERT: B 97 ARG cc_start: 0.8357 (ptt-90) cc_final: 0.8090 (ptt-90) REVERT: C 25 LYS cc_start: 0.8238 (mttt) cc_final: 0.7912 (mttp) REVERT: C 117 TRP cc_start: 0.7900 (m-90) cc_final: 0.7625 (m-90) REVERT: C 182 LYS cc_start: 0.8668 (ttmm) cc_final: 0.8281 (mtpt) REVERT: C 185 MET cc_start: 0.7118 (mtm) cc_final: 0.6816 (mtp) REVERT: C 214 MET cc_start: 0.8667 (tpp) cc_final: 0.8439 (tpt) REVERT: D 100 ARG cc_start: 0.7206 (tpt-90) cc_final: 0.6383 (tpt90) REVERT: D 118 MET cc_start: 0.8389 (mtm) cc_final: 0.7956 (mtp) REVERT: D 144 MET cc_start: 0.7836 (ttp) cc_final: 0.7618 (ttp) REVERT: D 149 SER cc_start: 0.8483 (OUTLIER) cc_final: 0.8268 (t) REVERT: D 203 LYS cc_start: 0.7462 (mmmt) cc_final: 0.7065 (tttm) REVERT: E 144 MET cc_start: 0.7844 (ttt) cc_final: 0.7599 (ttt) REVERT: E 151 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7574 (mm) REVERT: F 44 SER cc_start: 0.8912 (p) cc_final: 0.8706 (t) REVERT: F 71 GLU cc_start: 0.7436 (mm-30) cc_final: 0.7227 (mm-30) outliers start: 18 outliers final: 10 residues processed: 257 average time/residue: 0.2562 time to fit residues: 88.1478 Evaluate side-chains 240 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 228 time to evaluate : 1.219 ------------------------------------------------------------------------------- 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 210 THR Chi-restraints excluded: chain C residue 110 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 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 16 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 69 optimal weight: 0.1980 chunk 81 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 130 optimal weight: 0.0070 chunk 14 optimal weight: 1.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN F 21 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.176473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.138073 restraints weight = 41740.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.140907 restraints weight = 17739.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.142448 restraints weight = 12676.393| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3646 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3646 r_free = 0.3646 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3646 r_free = 0.3646 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3646 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2556 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= 0.119 Angle : 0.566 9.494 14374 Z= 0.291 Chirality : 0.042 0.272 1606 Planarity : 0.005 0.050 1880 Dihedral : 3.822 18.613 1410 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.78 % Allowed : 16.96 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.24), residues: 1312 helix: 1.09 (0.18), residues: 882 sheet: -2.39 (0.62), residues: 54 loop : 0.32 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 117 HIS 0.007 0.001 HIS C 12 PHE 0.011 0.001 PHE F 168 TYR 0.010 0.001 TYR F 164 ARG 0.004 0.000 ARG E 97 Details of bonding type rmsd hydrogen bonds : bond 0.03774 ( 595) hydrogen bonds : angle 4.07477 ( 1776) SS BOND : bond 0.00180 ( 6) SS BOND : angle 0.98790 ( 12) covalent geometry : bond 0.00268 (10560) covalent geometry : angle 0.56560 (14362) *********************** 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 270 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 252 time to evaluate : 1.382 Fit side-chains revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7417 (tpt-90) cc_final: 0.7175 (tpt-90) REVERT: A 118 MET cc_start: 0.8427 (mtm) cc_final: 0.7886 (mtp) REVERT: A 140 LYS cc_start: 0.8095 (tptp) cc_final: 0.7881 (tttt) REVERT: B 55 MET cc_start: 0.7981 (mtp) cc_final: 0.7754 (mtp) REVERT: B 102 SER cc_start: 0.8439 (OUTLIER) cc_final: 0.7870 (m) REVERT: C 25 LYS cc_start: 0.8237 (mttt) cc_final: 0.7876 (mttm) REVERT: C 100 ARG cc_start: 0.7842 (ptm160) cc_final: 0.7403 (ttp-110) REVERT: C 182 LYS cc_start: 0.8706 (ttmm) cc_final: 0.8132 (mtpp) REVERT: C 185 MET cc_start: 0.7062 (mtm) cc_final: 0.6752 (mtp) REVERT: C 214 MET cc_start: 0.8727 (tpp) cc_final: 0.8422 (tpt) REVERT: D 118 MET cc_start: 0.8435 (mtm) cc_final: 0.7973 (mtp) REVERT: D 145 TYR cc_start: 0.7536 (OUTLIER) cc_final: 0.7227 (m-80) REVERT: D 149 SER cc_start: 0.8455 (OUTLIER) cc_final: 0.8251 (t) REVERT: D 203 LYS cc_start: 0.7424 (mmmt) cc_final: 0.7024 (tttm) REVERT: E 114 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7993 (mp10) REVERT: E 151 LEU cc_start: 0.7956 (mm) cc_final: 0.7588 (mm) REVERT: F 28 GLU cc_start: 0.6496 (mm-30) cc_final: 0.6038 (mm-30) REVERT: F 213 GLU cc_start: 0.8457 (pt0) cc_final: 0.8184 (pm20) outliers start: 18 outliers final: 9 residues processed: 262 average time/residue: 0.2842 time to fit residues: 99.5151 Evaluate side-chains 237 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 224 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 39 MET Chi-restraints excluded: chain D residue 145 TYR 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 94 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 104 optimal weight: 8.9990 chunk 109 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 80 optimal weight: 0.0370 chunk 17 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 overall best weight: 1.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.174169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.135605 restraints weight = 38473.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.138280 restraints weight = 16700.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.139222 restraints weight = 11944.863| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3609 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3609 r_free = 0.3609 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3609 r_free = 0.3609 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10566 Z= 0.142 Angle : 0.583 8.008 14374 Z= 0.299 Chirality : 0.043 0.227 1606 Planarity : 0.005 0.049 1880 Dihedral : 3.895 18.848 1410 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.78 % Allowed : 18.38 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.24), residues: 1312 helix: 1.16 (0.18), residues: 872 sheet: -2.28 (0.64), residues: 54 loop : 0.35 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP C 117 HIS 0.006 0.001 HIS C 12 PHE 0.015 0.001 PHE E 161 TYR 0.009 0.001 TYR E 130 ARG 0.004 0.001 ARG F 143 Details of bonding type rmsd hydrogen bonds : bond 0.04018 ( 595) hydrogen bonds : angle 4.15467 ( 1776) SS BOND : bond 0.00240 ( 6) SS BOND : angle 1.13678 ( 12) covalent geometry : bond 0.00342 (10560) covalent geometry : angle 0.58269 (14362) *********************** 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 248 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 230 time to evaluate : 1.072 Fit side-chains REVERT: A 100 ARG cc_start: 0.7391 (tpt-90) cc_final: 0.7102 (tpt-90) REVERT: A 118 MET cc_start: 0.8487 (mtm) cc_final: 0.7922 (mtp) REVERT: B 98 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6708 (tm-30) REVERT: B 102 SER cc_start: 0.8411 (OUTLIER) cc_final: 0.7858 (m) REVERT: C 25 LYS cc_start: 0.8302 (mttt) cc_final: 0.7929 (mttm) REVERT: C 71 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7251 (mp0) REVERT: C 100 ARG cc_start: 0.7828 (ptm160) cc_final: 0.7464 (ttp-110) REVERT: C 117 TRP cc_start: 0.8031 (m-90) cc_final: 0.7828 (m-90) REVERT: C 182 LYS cc_start: 0.8736 (ttmm) cc_final: 0.8145 (mtpp) REVERT: C 185 MET cc_start: 0.6972 (mtm) cc_final: 0.6720 (mtp) REVERT: C 214 MET cc_start: 0.8614 (tpp) cc_final: 0.8341 (tpt) REVERT: D 100 ARG cc_start: 0.7359 (tpt-90) cc_final: 0.6910 (tpt-90) REVERT: D 118 MET cc_start: 0.8481 (mtm) cc_final: 0.8008 (mtp) REVERT: D 149 SER cc_start: 0.8439 (OUTLIER) cc_final: 0.8231 (t) REVERT: D 203 LYS cc_start: 0.7416 (mmmt) cc_final: 0.7017 (tttm) REVERT: E 114 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7943 (mp10) REVERT: E 151 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7706 (mm) REVERT: F 28 GLU cc_start: 0.6590 (mm-30) cc_final: 0.6015 (mm-30) REVERT: F 143 ARG cc_start: 0.8212 (mmm-85) cc_final: 0.7308 (mmm160) REVERT: F 213 GLU cc_start: 0.8461 (pt0) cc_final: 0.8247 (pm20) outliers start: 18 outliers final: 9 residues processed: 241 average time/residue: 0.2643 time to fit residues: 84.8293 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 : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 SER 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 136 LEU 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 39 MET 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 151 LEU 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 29 optimal weight: 1.9990 chunk 98 optimal weight: 20.0000 chunk 43 optimal weight: 0.0370 chunk 81 optimal weight: 0.3980 chunk 42 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 30 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 overall best weight: 1.0862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN C 114 GLN ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.175544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.136472 restraints weight = 38881.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.139239 restraints weight = 16796.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.140182 restraints weight = 12336.159| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3626 r_free = 0.3626 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3626 r_free = 0.3626 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2883 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= 0.123 Angle : 0.584 9.471 14374 Z= 0.297 Chirality : 0.042 0.215 1606 Planarity : 0.005 0.047 1880 Dihedral : 3.886 19.163 1410 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.78 % Allowed : 18.47 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.24), residues: 1312 helix: 1.28 (0.18), residues: 872 sheet: -2.05 (0.66), residues: 54 loop : 0.43 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 117 HIS 0.004 0.001 HIS C 12 PHE 0.010 0.001 PHE E 161 TYR 0.008 0.001 TYR F 164 ARG 0.005 0.000 ARG E 97 Details of bonding type rmsd hydrogen bonds : bond 0.03840 ( 595) hydrogen bonds : angle 4.04236 ( 1776) SS BOND : bond 0.00183 ( 6) SS BOND : angle 1.11801 ( 12) covalent geometry : bond 0.00288 (10560) covalent geometry : angle 0.58359 (14362) *********************** 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 259 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 241 time to evaluate : 1.087 Fit side-chains revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7272 (tpt-90) cc_final: 0.7011 (tpt-90) REVERT: A 118 MET cc_start: 0.8461 (mtm) cc_final: 0.7978 (mtp) REVERT: A 144 MET cc_start: 0.6529 (ttt) cc_final: 0.6243 (ttt) REVERT: B 98 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6551 (tm-30) REVERT: B 102 SER cc_start: 0.8455 (OUTLIER) cc_final: 0.7933 (m) REVERT: C 100 ARG cc_start: 0.7806 (ptm160) cc_final: 0.7339 (ttp-110) REVERT: C 114 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.6366 (mp-120) REVERT: C 117 TRP cc_start: 0.7992 (m-90) cc_final: 0.7731 (m-90) REVERT: C 133 TRP cc_start: 0.7952 (m-10) cc_final: 0.7010 (m-10) REVERT: C 185 MET cc_start: 0.7047 (mtm) cc_final: 0.6735 (mtp) REVERT: C 214 MET cc_start: 0.8628 (tpp) cc_final: 0.8334 (tpt) REVERT: D 100 ARG cc_start: 0.7450 (tpt-90) cc_final: 0.7173 (tpt-90) REVERT: D 118 MET cc_start: 0.8496 (mtm) cc_final: 0.7966 (mtp) REVERT: D 143 ARG cc_start: 0.7830 (ttm170) cc_final: 0.6852 (mtm110) REVERT: D 149 SER cc_start: 0.8332 (OUTLIER) cc_final: 0.8100 (t) REVERT: D 203 LYS cc_start: 0.7419 (mmmt) cc_final: 0.7016 (tttm) REVERT: E 114 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7878 (mp10) REVERT: E 151 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7705 (mm) REVERT: F 28 GLU cc_start: 0.6494 (mm-30) cc_final: 0.5939 (mm-30) REVERT: F 143 ARG cc_start: 0.8159 (mmm-85) cc_final: 0.7528 (mmm160) outliers start: 18 outliers final: 7 residues processed: 250 average time/residue: 0.2681 time to fit residues: 88.5442 Evaluate side-chains 240 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 227 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 SER 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 216 THR Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain D residue 39 MET 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 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 45 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 41 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.169104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.128843 restraints weight = 43134.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.131558 restraints weight = 17948.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.133154 restraints weight = 12886.570| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3534 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 10566 Z= 0.256 Angle : 0.712 9.465 14374 Z= 0.366 Chirality : 0.048 0.179 1606 Planarity : 0.005 0.051 1880 Dihedral : 4.256 18.124 1410 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.87 % Allowed : 18.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.23), residues: 1312 helix: 0.91 (0.18), residues: 868 sheet: -2.12 (0.64), residues: 54 loop : 0.25 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 117 HIS 0.006 0.002 HIS C 12 PHE 0.012 0.002 PHE D 32 TYR 0.033 0.003 TYR D 169 ARG 0.006 0.001 ARG E 97 Details of bonding type rmsd hydrogen bonds : bond 0.04904 ( 595) hydrogen bonds : angle 4.62533 ( 1776) SS BOND : bond 0.00549 ( 6) SS BOND : angle 1.19381 ( 12) covalent geometry : bond 0.00627 (10560) covalent geometry : angle 0.71141 (14362) *********************** 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 250 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 231 time to evaluate : 1.141 Fit side-chains REVERT: A 100 ARG cc_start: 0.7425 (tpt-90) cc_final: 0.7070 (tpt-90) REVERT: A 118 MET cc_start: 0.8410 (mtm) cc_final: 0.7911 (mtp) REVERT: B 98 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6598 (tm-30) REVERT: C 25 LYS cc_start: 0.8465 (ttmt) cc_final: 0.7722 (tttp) REVERT: C 71 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7453 (mm-30) REVERT: C 100 ARG cc_start: 0.7848 (ptm160) cc_final: 0.7380 (ttp-110) REVERT: C 133 TRP cc_start: 0.8034 (m-10) cc_final: 0.7202 (m-10) REVERT: C 182 LYS cc_start: 0.8824 (ttmm) cc_final: 0.8441 (mttt) REVERT: C 185 MET cc_start: 0.7077 (mtm) cc_final: 0.6758 (mtp) REVERT: C 214 MET cc_start: 0.8721 (tpp) cc_final: 0.8420 (tpt) REVERT: D 99 PRO cc_start: 0.6664 (Cg_exo) cc_final: 0.6238 (Cg_endo) REVERT: D 100 ARG cc_start: 0.7449 (tpt-90) cc_final: 0.6745 (tpt90) REVERT: D 118 MET cc_start: 0.8700 (mtm) cc_final: 0.8289 (mtp) REVERT: D 143 ARG cc_start: 0.8196 (ttm170) cc_final: 0.7648 (mtm180) REVERT: D 203 LYS cc_start: 0.7498 (mmmt) cc_final: 0.7103 (tttm) REVERT: E 114 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7947 (mp10) REVERT: E 151 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7748 (mm) REVERT: F 143 ARG cc_start: 0.8196 (mmm-85) cc_final: 0.7424 (mmm160) REVERT: F 182 LYS cc_start: 0.8471 (mmmt) cc_final: 0.8240 (mmmt) outliers start: 19 outliers final: 12 residues processed: 238 average time/residue: 0.2729 time to fit residues: 85.6175 Evaluate side-chains 234 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 219 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 MET Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 136 LEU 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 B residue 216 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain D residue 140 LYS Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 210 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 123 optimal weight: 0.0970 chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 127 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 74 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 9 GLN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN F 21 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.173807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.134161 restraints weight = 39507.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.137086 restraints weight = 16666.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.137925 restraints weight = 12239.301| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3596 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3596 r_free = 0.3596 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3596 r_free = 0.3596 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3596 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10566 Z= 0.131 Angle : 0.626 10.491 14374 Z= 0.319 Chirality : 0.043 0.182 1606 Planarity : 0.005 0.048 1880 Dihedral : 4.097 19.172 1410 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.51 % Allowed : 19.72 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.24), residues: 1312 helix: 1.21 (0.18), residues: 868 sheet: -2.07 (0.63), residues: 54 loop : 0.35 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.001 TRP C 117 HIS 0.004 0.001 HIS C 12 PHE 0.011 0.001 PHE E 161 TYR 0.024 0.002 TYR D 169 ARG 0.006 0.000 ARG E 97 Details of bonding type rmsd hydrogen bonds : bond 0.04070 ( 595) hydrogen bonds : angle 4.19349 ( 1776) SS BOND : bond 0.00259 ( 6) SS BOND : angle 1.08780 ( 12) covalent geometry : bond 0.00307 (10560) covalent geometry : angle 0.62506 (14362) *********************** 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 251 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 236 time to evaluate : 1.150 Fit side-chains REVERT: A 100 ARG cc_start: 0.7321 (tpt-90) cc_final: 0.7062 (tpt-90) REVERT: A 118 MET cc_start: 0.8279 (mtm) cc_final: 0.7759 (mtp) REVERT: B 98 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6480 (tm-30) REVERT: B 151 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7489 (mm) REVERT: B 180 GLU cc_start: 0.8144 (mp0) cc_final: 0.7461 (tm-30) REVERT: C 100 ARG cc_start: 0.7803 (ptm160) cc_final: 0.7354 (ttp-110) REVERT: C 117 TRP cc_start: 0.8039 (m-90) cc_final: 0.7759 (m-90) REVERT: C 133 TRP cc_start: 0.7932 (m-10) cc_final: 0.7054 (m-10) REVERT: C 182 LYS cc_start: 0.8806 (ttmm) cc_final: 0.8374 (ttmm) REVERT: C 185 MET cc_start: 0.7058 (mtm) cc_final: 0.6685 (mtp) REVERT: C 214 MET cc_start: 0.8711 (tpp) cc_final: 0.8399 (tpt) REVERT: D 99 PRO cc_start: 0.6525 (Cg_exo) cc_final: 0.6093 (Cg_endo) REVERT: D 100 ARG cc_start: 0.7319 (tpt-90) cc_final: 0.6743 (tpt90) REVERT: D 118 MET cc_start: 0.8559 (mtm) cc_final: 0.8093 (mtp) REVERT: D 143 ARG cc_start: 0.8059 (ttm170) cc_final: 0.7533 (mtm180) REVERT: D 179 GLN cc_start: 0.6644 (OUTLIER) cc_final: 0.5787 (mm110) REVERT: D 203 LYS cc_start: 0.7480 (mmmt) cc_final: 0.7089 (tttm) REVERT: E 114 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7889 (mp10) REVERT: E 151 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7727 (mm) REVERT: F 143 ARG cc_start: 0.8176 (mmm-85) cc_final: 0.7389 (mmm160) REVERT: F 213 GLU cc_start: 0.8472 (pm20) cc_final: 0.8234 (pm20) outliers start: 15 outliers final: 6 residues processed: 245 average time/residue: 0.2942 time to fit residues: 97.9030 Evaluate side-chains 229 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 218 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 146 SER 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 210 THR Chi-restraints excluded: chain D residue 179 GLN Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 151 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 5 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 9 GLN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 HIS D 179 GLN F 21 ASN ** F 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.169923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.126495 restraints weight = 32770.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.130628 restraints weight = 14568.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.133037 restraints weight = 8725.980| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3525 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3525 r_free = 0.3525 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3524 r_free = 0.3524 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3524 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10566 Z= 0.213 Angle : 0.694 12.682 14374 Z= 0.357 Chirality : 0.046 0.179 1606 Planarity : 0.005 0.052 1880 Dihedral : 4.219 18.353 1410 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.51 % Allowed : 19.98 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.24), residues: 1312 helix: 1.01 (0.18), residues: 859 sheet: -2.03 (0.63), residues: 54 loop : 0.14 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP C 117 HIS 0.005 0.001 HIS C 12 PHE 0.009 0.002 PHE D 32 TYR 0.025 0.002 TYR A 169 ARG 0.007 0.001 ARG E 97 Details of bonding type rmsd hydrogen bonds : bond 0.04548 ( 595) hydrogen bonds : angle 4.52858 ( 1776) SS BOND : bond 0.00438 ( 6) SS BOND : angle 1.18554 ( 12) covalent geometry : bond 0.00525 (10560) covalent geometry : angle 0.69386 (14362) *********************** 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 239 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 224 time to evaluate : 1.074 Fit side-chains revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7322 (tpt-90) cc_final: 0.7023 (tpt-90) REVERT: A 118 MET cc_start: 0.8329 (mtm) cc_final: 0.7822 (mtp) REVERT: B 98 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6450 (tm-30) REVERT: B 128 GLU cc_start: 0.7441 (tp30) cc_final: 0.7233 (tp30) REVERT: B 151 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7649 (mm) REVERT: B 180 GLU cc_start: 0.8138 (mp0) cc_final: 0.7388 (tm-30) REVERT: C 28 GLU cc_start: 0.6542 (mm-30) cc_final: 0.6187 (mm-30) REVERT: C 100 ARG cc_start: 0.7763 (ptm160) cc_final: 0.7309 (ttp-110) REVERT: C 117 TRP cc_start: 0.8186 (m-90) cc_final: 0.7739 (m-90) REVERT: C 133 TRP cc_start: 0.8091 (m-10) cc_final: 0.7176 (m-10) REVERT: C 182 LYS cc_start: 0.8810 (ttmm) cc_final: 0.8541 (mttt) REVERT: C 214 MET cc_start: 0.8742 (tpp) cc_final: 0.8421 (tpt) REVERT: D 99 PRO cc_start: 0.6528 (Cg_exo) cc_final: 0.6100 (Cg_endo) REVERT: D 100 ARG cc_start: 0.7359 (tpt-90) cc_final: 0.6723 (tpt90) REVERT: D 118 MET cc_start: 0.8671 (mtm) cc_final: 0.8258 (mtp) REVERT: D 179 GLN cc_start: 0.6616 (OUTLIER) cc_final: 0.5797 (mm110) REVERT: D 203 LYS cc_start: 0.7550 (mmmt) cc_final: 0.7145 (tttm) REVERT: D 215 MET cc_start: 0.7067 (ptp) cc_final: 0.6858 (pmm) REVERT: E 112 GLN cc_start: 0.8493 (tp40) cc_final: 0.8241 (tp40) REVERT: E 114 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7907 (mp10) REVERT: E 132 ARG cc_start: 0.7659 (mtm-85) cc_final: 0.7450 (mtt90) REVERT: E 151 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7706 (mm) REVERT: F 25 LYS cc_start: 0.8231 (ttmt) cc_final: 0.7522 (tttt) REVERT: F 28 GLU cc_start: 0.6908 (mm-30) cc_final: 0.6702 (mm-30) REVERT: F 143 ARG cc_start: 0.8217 (mmm-85) cc_final: 0.7660 (mmm160) REVERT: F 212 GLU cc_start: 0.7344 (tt0) cc_final: 0.7058 (tt0) REVERT: F 215 MET cc_start: 0.7859 (ptp) cc_final: 0.7432 (mpp) outliers start: 15 outliers final: 9 residues processed: 230 average time/residue: 0.2686 time to fit residues: 81.6097 Evaluate side-chains 233 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 219 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain B residue 98 GLU 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 27 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain D residue 179 GLN 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 Chi-restraints excluded: chain E residue 210 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 83 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 12 optimal weight: 0.1980 chunk 130 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 9 GLN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN F 21 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.173144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.129087 restraints weight = 34073.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.134163 restraints weight = 14479.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.137281 restraints weight = 8473.182| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3578 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3578 r_free = 0.3578 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3578 r_free = 0.3578 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3578 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3237 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= 0.139 Angle : 0.649 13.027 14374 Z= 0.333 Chirality : 0.043 0.167 1606 Planarity : 0.005 0.051 1880 Dihedral : 4.138 19.040 1410 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.33 % Allowed : 20.60 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.24), residues: 1312 helix: 1.16 (0.18), residues: 859 sheet: -1.87 (0.65), residues: 54 loop : 0.21 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP C 117 HIS 0.005 0.001 HIS C 12 PHE 0.009 0.001 PHE E 161 TYR 0.022 0.002 TYR A 169 ARG 0.006 0.000 ARG E 97 Details of bonding type rmsd hydrogen bonds : bond 0.04098 ( 595) hydrogen bonds : angle 4.30645 ( 1776) SS BOND : bond 0.00273 ( 6) SS BOND : angle 1.10595 ( 12) covalent geometry : bond 0.00329 (10560) covalent geometry : angle 0.64849 (14362) ********************** 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 246 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 233 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7272 (tpt-90) cc_final: 0.6981 (tpt-90) REVERT: A 118 MET cc_start: 0.8268 (mtm) cc_final: 0.7759 (mtp) REVERT: B 98 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6369 (tm-30) REVERT: B 128 GLU cc_start: 0.7382 (tp30) cc_final: 0.7176 (tp30) REVERT: B 151 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7588 (mm) REVERT: B 180 GLU cc_start: 0.8128 (mp0) cc_final: 0.7417 (tm-30) REVERT: C 28 GLU cc_start: 0.6619 (mm-30) cc_final: 0.6276 (mm-30) REVERT: C 100 ARG cc_start: 0.7765 (ptm160) cc_final: 0.7348 (ttp-110) REVERT: C 117 TRP cc_start: 0.8110 (m-90) cc_final: 0.7715 (m-90) REVERT: C 176 GLN cc_start: 0.7804 (tm-30) cc_final: 0.7064 (mp10) REVERT: C 214 MET cc_start: 0.8710 (tpp) cc_final: 0.8329 (tpt) REVERT: C 215 MET cc_start: 0.7592 (ptp) cc_final: 0.7163 (mpp) REVERT: D 99 PRO cc_start: 0.6245 (Cg_exo) cc_final: 0.5785 (Cg_endo) REVERT: D 100 ARG cc_start: 0.7287 (tpt-90) cc_final: 0.6668 (tpt90) REVERT: D 118 MET cc_start: 0.8568 (mtm) cc_final: 0.8065 (mtp) REVERT: D 179 GLN cc_start: 0.6397 (OUTLIER) cc_final: 0.5589 (mm110) REVERT: D 203 LYS cc_start: 0.7596 (mmmt) cc_final: 0.7169 (tttm) REVERT: E 114 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7820 (mp10) REVERT: E 151 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7732 (mm) REVERT: F 25 LYS cc_start: 0.8152 (ttmt) cc_final: 0.7465 (tttt) REVERT: F 28 GLU cc_start: 0.6746 (mm-30) cc_final: 0.6539 (mm-30) REVERT: F 71 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7205 (mm-30) REVERT: F 143 ARG cc_start: 0.8203 (mmm-85) cc_final: 0.7629 (mmm160) REVERT: F 182 LYS cc_start: 0.8367 (mmmt) cc_final: 0.7832 (mtpp) REVERT: F 212 GLU cc_start: 0.7329 (tt0) cc_final: 0.7072 (tt0) REVERT: F 215 MET cc_start: 0.7796 (ptp) cc_final: 0.7389 (mpp) outliers start: 13 outliers final: 8 residues processed: 239 average time/residue: 0.3575 time to fit residues: 117.1209 Evaluate side-chains 235 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 222 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain B residue 98 GLU 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 27 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain D residue 179 GLN 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 210 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 16 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 114 optimal weight: 8.9990 chunk 81 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 25 optimal weight: 0.2980 chunk 130 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 9 GLN ** C 114 GLN ** 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 = 0.4037 r_free = 0.4037 target = 0.173136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.128898 restraints weight = 34079.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.134118 restraints weight = 14564.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.137044 restraints weight = 8471.977| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3568 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3568 r_free = 0.3568 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3568 r_free = 0.3568 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3568 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 10566 Z= 0.185 Angle : 0.915 59.192 14374 Z= 0.513 Chirality : 0.044 0.163 1606 Planarity : 0.005 0.051 1880 Dihedral : 4.122 19.069 1410 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.51 % Allowed : 20.78 % Favored : 77.71 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.24), residues: 1312 helix: 1.13 (0.18), residues: 859 sheet: -1.85 (0.65), residues: 54 loop : 0.21 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP C 117 HIS 0.004 0.001 HIS C 12 PHE 0.008 0.001 PHE E 161 TYR 0.013 0.002 TYR A 169 ARG 0.006 0.000 ARG E 97 Details of bonding type rmsd hydrogen bonds : bond 0.04126 ( 595) hydrogen bonds : angle 4.31596 ( 1776) SS BOND : bond 0.00292 ( 6) SS BOND : angle 1.11097 ( 12) covalent geometry : bond 0.00422 (10560) covalent geometry : angle 0.91442 (14362) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3947.07 seconds wall clock time: 71 minutes 14.02 seconds (4274.02 seconds total)