Starting phenix.real_space_refine on Fri Feb 14 07:42:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6skk_10226/02_2025/6skk_10226.cif Found real_map, /net/cci-nas-00/data/ceres_data/6skk_10226/02_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_10226/02_2025/6skk_10226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6skk_10226/02_2025/6skk_10226.map" model { file = "/net/cci-nas-00/data/ceres_data/6skk_10226/02_2025/6skk_10226.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6skk_10226/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 8.70, per 1000 atoms: 0.84 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: 2.34 Conformation dependent library (CDL) restraints added in 1.9 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: 1.01 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: 2.60 Time building geometry restraints manager: 2.72 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: 0.160 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.460 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.660 ------------------------------------------------------------------------------- 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 10560 Z= 0.227 Angle : 0.605 5.622 14362 Z= 0.392 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 *********************** 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 : 1.274 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: 0.2932 time to fit residues: 132.5015 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 : 1.154 ------------------------------------------------------------------------------- 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 = 15693.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.143982 restraints weight = 11851.937| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3659 r_free = 0.3659 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3658 r_free = 0.3658 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3658 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 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 10560 Z= 0.207 Angle : 0.592 9.911 14362 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 *********************** 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 : 1.107 Fit side-chains revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7291 (tpt-90) cc_final: 0.6805 (tpt90) REVERT: A 118 MET cc_start: 0.8509 (mtm) cc_final: 0.8013 (mtp) REVERT: A 140 LYS cc_start: 0.8125 (tptt) cc_final: 0.7919 (tptp) REVERT: A 182 LYS cc_start: 0.8981 (mtpp) cc_final: 0.8717 (mtpt) REVERT: A 214 MET cc_start: 0.8206 (mtp) cc_final: 0.7925 (mtt) REVERT: B 55 MET cc_start: 0.8206 (mtp) cc_final: 0.7882 (mtp) REVERT: B 144 MET cc_start: 0.7792 (ttt) cc_final: 0.7509 (ttm) REVERT: C 25 LYS cc_start: 0.8255 (mttt) cc_final: 0.7887 (mttm) REVERT: C 28 GLU cc_start: 0.6509 (mm-30) cc_final: 0.6209 (mm-30) REVERT: C 66 MET cc_start: 0.8656 (mmm) cc_final: 0.8293 (mmt) REVERT: C 182 LYS cc_start: 0.8674 (ttmm) cc_final: 0.8168 (mtpt) REVERT: C 185 MET cc_start: 0.7194 (mtm) cc_final: 0.6917 (mtp) REVERT: C 214 MET cc_start: 0.8570 (tpp) cc_final: 0.8292 (tpt) REVERT: D 100 ARG cc_start: 0.7277 (tpt-90) cc_final: 0.7075 (tpt-90) REVERT: D 118 MET cc_start: 0.8436 (mtm) cc_final: 0.7989 (mtp) REVERT: D 144 MET cc_start: 0.7683 (ttp) cc_final: 0.7396 (ttp) REVERT: D 203 LYS cc_start: 0.7426 (mmmt) cc_final: 0.7057 (tttm) REVERT: E 114 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7919 (mp10) REVERT: E 117 TRP cc_start: 0.8047 (m-10) cc_final: 0.7807 (m-10) REVERT: F 25 LYS cc_start: 0.8354 (mttt) cc_final: 0.7986 (mttp) outliers start: 17 outliers final: 10 residues processed: 270 average time/residue: 0.2778 time to fit residues: 98.3648 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 : 1.172 ------------------------------------------------------------------------------- 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: 3.9990 chunk 128 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 66 optimal weight: 0.0470 chunk 123 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 overall best weight: 0.7282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.175667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.136732 restraints weight = 36436.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.139252 restraints weight = 15619.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.140198 restraints weight = 11662.244| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3628 r_free = 0.3628 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3628 r_free = 0.3628 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10560 Z= 0.172 Angle : 0.555 8.173 14362 Z= 0.285 Chirality : 0.042 0.283 1606 Planarity : 0.005 0.053 1880 Dihedral : 3.786 18.617 1410 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.51 % Allowed : 16.43 % 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: 0.80 (0.24), residues: 1312 helix: 0.96 (0.18), residues: 868 sheet: -2.65 (0.57), residues: 54 loop : 0.30 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 117 HIS 0.006 0.001 HIS C 12 PHE 0.016 0.001 PHE B 161 TYR 0.012 0.001 TYR F 130 ARG 0.004 0.000 ARG D 162 *********************** 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 266 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 251 time to evaluate : 1.180 Fit side-chains revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7404 (tpt-90) cc_final: 0.7185 (tpt-90) REVERT: A 118 MET cc_start: 0.8494 (mtm) cc_final: 0.7994 (mtp) REVERT: A 140 LYS cc_start: 0.8116 (tptt) cc_final: 0.7908 (tptp) REVERT: A 172 LEU cc_start: 0.8902 (tp) cc_final: 0.8463 (tt) REVERT: B 55 MET cc_start: 0.8044 (mtp) cc_final: 0.7755 (mtp) REVERT: B 97 ARG cc_start: 0.8359 (ptt-90) cc_final: 0.8100 (ptt-90) REVERT: B 144 MET cc_start: 0.7610 (ttt) cc_final: 0.7352 (ttt) REVERT: C 25 LYS cc_start: 0.8252 (mttt) cc_final: 0.7918 (mttm) REVERT: C 117 TRP cc_start: 0.7883 (m-90) cc_final: 0.7669 (m-90) REVERT: C 182 LYS cc_start: 0.8666 (ttmm) cc_final: 0.8280 (mtpt) REVERT: C 185 MET cc_start: 0.7087 (mtm) cc_final: 0.6792 (mtp) REVERT: C 214 MET cc_start: 0.8674 (tpp) cc_final: 0.8441 (tpt) REVERT: D 100 ARG cc_start: 0.7272 (tpt-90) cc_final: 0.7043 (tpt-90) REVERT: D 118 MET cc_start: 0.8384 (mtm) cc_final: 0.7960 (mtp) REVERT: D 133 TRP cc_start: 0.8290 (m-10) cc_final: 0.7898 (m-10) REVERT: D 149 SER cc_start: 0.8484 (OUTLIER) cc_final: 0.8267 (t) REVERT: D 203 LYS cc_start: 0.7490 (mmmt) cc_final: 0.7089 (tttm) REVERT: E 66 MET cc_start: 0.8887 (mmt) cc_final: 0.8639 (mmt) REVERT: E 151 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7580 (mm) REVERT: F 44 SER cc_start: 0.8907 (p) cc_final: 0.8701 (t) REVERT: F 71 GLU cc_start: 0.7417 (mm-30) cc_final: 0.7202 (mm-30) outliers start: 15 outliers final: 10 residues processed: 257 average time/residue: 0.2702 time to fit residues: 92.6486 Evaluate side-chains 243 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 231 time to evaluate : 1.508 ------------------------------------------------------------------------------- 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: 10.0000 chunk 36 optimal weight: 8.9990 chunk 76 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 69 optimal weight: 0.0010 chunk 81 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 overall best weight: 3.3994 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN B 183 ASN D 12 HIS ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 21 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.171205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.131911 restraints weight = 41877.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.135089 restraints weight = 17584.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.136106 restraints weight = 13275.728| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- 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 = 0.34 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 = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3568 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10560 Z= 0.311 Angle : 0.623 8.410 14362 Z= 0.327 Chirality : 0.045 0.256 1606 Planarity : 0.005 0.052 1880 Dihedral : 4.045 17.671 1410 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.31 % Allowed : 16.61 % Favored : 81.08 % 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: 0.71 (0.24), residues: 1312 helix: 0.88 (0.18), residues: 872 sheet: -2.58 (0.60), residues: 54 loop : 0.29 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 117 HIS 0.007 0.001 HIS C 12 PHE 0.009 0.002 PHE D 40 TYR 0.013 0.002 TYR E 130 ARG 0.004 0.000 ARG E 97 *********************** 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 256 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 232 time to evaluate : 1.363 Fit side-chains REVERT: A 100 ARG cc_start: 0.7394 (tpt-90) cc_final: 0.7152 (tpt-90) REVERT: A 118 MET cc_start: 0.8427 (mtm) cc_final: 0.7879 (mtp) REVERT: B 55 MET cc_start: 0.8281 (mtp) cc_final: 0.8055 (mtp) REVERT: B 98 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6724 (tm-30) REVERT: C 25 LYS cc_start: 0.8334 (mttt) cc_final: 0.7899 (mttm) REVERT: C 71 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7257 (mm-30) REVERT: C 182 LYS cc_start: 0.8715 (ttmm) cc_final: 0.8134 (mtpp) REVERT: C 185 MET cc_start: 0.7299 (mtm) cc_final: 0.6865 (mtp) REVERT: D 100 ARG cc_start: 0.7366 (tpt-90) cc_final: 0.7140 (tpt-90) REVERT: D 118 MET cc_start: 0.8554 (mtm) cc_final: 0.8037 (mtp) REVERT: D 145 TYR cc_start: 0.7571 (OUTLIER) cc_final: 0.7134 (m-80) REVERT: D 203 LYS cc_start: 0.7491 (mmmt) cc_final: 0.7065 (tttm) REVERT: E 66 MET cc_start: 0.9042 (mmt) cc_final: 0.8807 (mmt) REVERT: E 98 GLU cc_start: 0.6779 (tm-30) cc_final: 0.6562 (tm-30) REVERT: E 114 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7964 (mp10) REVERT: E 151 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7729 (mm) REVERT: F 71 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7357 (mm-30) outliers start: 24 outliers final: 12 residues processed: 246 average time/residue: 0.2716 time to fit residues: 89.3261 Evaluate side-chains 238 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 222 time to evaluate : 1.206 ------------------------------------------------------------------------------- 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 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 D residue 16 SER Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 145 TYR Chi-restraints excluded: chain E residue 114 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 94 optimal weight: 0.6980 chunk 106 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 31 optimal weight: 20.0000 chunk 73 optimal weight: 3.9990 chunk 80 optimal weight: 0.2980 chunk 17 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN B 183 ASN D 195 ASN F 21 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.172803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.133846 restraints weight = 38458.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.136552 restraints weight = 16289.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.138319 restraints weight = 11867.543| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3605 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3605 r_free = 0.3605 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3605 r_free = 0.3605 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3605 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10560 Z= 0.197 Angle : 0.587 8.616 14362 Z= 0.300 Chirality : 0.043 0.236 1606 Planarity : 0.005 0.051 1880 Dihedral : 4.009 18.707 1410 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.87 % Allowed : 18.29 % 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: 0.97 (0.24), residues: 1312 helix: 1.08 (0.18), residues: 872 sheet: -2.35 (0.62), residues: 54 loop : 0.35 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP C 117 HIS 0.006 0.001 HIS C 12 PHE 0.017 0.001 PHE E 161 TYR 0.009 0.002 TYR F 130 ARG 0.006 0.000 ARG B 154 *********************** 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 260 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 241 time to evaluate : 1.196 Fit side-chains REVERT: A 100 ARG cc_start: 0.7409 (tpt-90) cc_final: 0.7110 (tpt-90) REVERT: A 118 MET cc_start: 0.8368 (mtm) cc_final: 0.7767 (mtp) REVERT: B 55 MET cc_start: 0.8180 (mtp) cc_final: 0.7872 (mtp) REVERT: B 98 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6630 (tm-30) REVERT: C 25 LYS cc_start: 0.8256 (mttt) cc_final: 0.7887 (mttm) REVERT: C 100 ARG cc_start: 0.7872 (ptm160) cc_final: 0.7360 (ttp-110) REVERT: C 114 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7946 (mp10) REVERT: C 133 TRP cc_start: 0.7895 (m-10) cc_final: 0.7011 (m-10) REVERT: C 182 LYS cc_start: 0.8721 (ttmm) cc_final: 0.8172 (mtpp) REVERT: C 185 MET cc_start: 0.7086 (mtm) cc_final: 0.6748 (mtp) REVERT: C 214 MET cc_start: 0.8457 (tpp) cc_final: 0.8189 (tpt) REVERT: D 100 ARG cc_start: 0.7336 (tpt-90) cc_final: 0.7116 (tpt-90) REVERT: D 118 MET cc_start: 0.8462 (mtm) cc_final: 0.7996 (mtp) REVERT: D 203 LYS cc_start: 0.7473 (mmmt) cc_final: 0.7050 (tttm) REVERT: E 66 MET cc_start: 0.8934 (mmt) cc_final: 0.8691 (mmt) REVERT: E 114 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7970 (mp10) REVERT: E 151 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7677 (mm) REVERT: F 28 GLU cc_start: 0.6725 (mm-30) cc_final: 0.6516 (mm-30) outliers start: 19 outliers final: 14 residues processed: 251 average time/residue: 0.2732 time to fit residues: 90.6108 Evaluate side-chains 236 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 218 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain F residue 110 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 29 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 43 optimal weight: 0.8980 chunk 81 optimal weight: 0.3980 chunk 42 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 54 optimal weight: 0.0050 chunk 30 optimal weight: 0.0970 chunk 79 optimal weight: 0.7980 chunk 131 optimal weight: 4.9990 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN 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 = 0.4063 r_free = 0.4063 target = 0.175726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.136048 restraints weight = 38766.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.138891 restraints weight = 16688.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.139756 restraints weight = 12209.916| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- 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 = 0.33 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 = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10560 Z= 0.169 Angle : 0.589 10.571 14362 Z= 0.300 Chirality : 0.042 0.218 1606 Planarity : 0.005 0.050 1880 Dihedral : 3.933 19.177 1410 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % 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: 1.19 (0.24), residues: 1312 helix: 1.26 (0.18), residues: 868 sheet: -2.04 (0.65), residues: 54 loop : 0.37 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.001 TRP C 117 HIS 0.006 0.000 HIS C 12 PHE 0.013 0.001 PHE E 161 TYR 0.009 0.001 TYR F 164 ARG 0.008 0.001 ARG F 162 *********************** 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 256 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 241 time to evaluate : 1.261 Fit side-chains revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7309 (tpt-90) cc_final: 0.7013 (tpt-90) REVERT: A 118 MET cc_start: 0.8432 (mtm) cc_final: 0.7846 (mtp) REVERT: B 55 MET cc_start: 0.8037 (mtp) cc_final: 0.7775 (mtp) REVERT: C 100 ARG cc_start: 0.7808 (ptm160) cc_final: 0.7479 (ttp-110) REVERT: C 114 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7730 (mp10) REVERT: C 133 TRP cc_start: 0.7877 (m-10) cc_final: 0.7001 (m-10) REVERT: C 144 MET cc_start: 0.7297 (tmm) cc_final: 0.6946 (tmm) REVERT: C 185 MET cc_start: 0.7107 (mtm) cc_final: 0.6782 (mtp) REVERT: C 214 MET cc_start: 0.8492 (tpp) cc_final: 0.8174 (tpt) REVERT: D 100 ARG cc_start: 0.7412 (tpt-90) cc_final: 0.7120 (tpt-90) REVERT: D 118 MET cc_start: 0.8450 (mtm) cc_final: 0.8100 (mtp) REVERT: D 143 ARG cc_start: 0.7873 (ttm170) cc_final: 0.6998 (mtm110) REVERT: D 203 LYS cc_start: 0.7442 (mmmt) cc_final: 0.7026 (tttm) REVERT: E 39 MET cc_start: 0.7965 (tpp) cc_final: 0.7658 (tpp) REVERT: E 114 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7814 (mp10) REVERT: E 151 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7728 (mm) REVERT: F 143 ARG cc_start: 0.8190 (mmm-85) cc_final: 0.7534 (mmm160) REVERT: F 182 LYS cc_start: 0.8174 (mmmt) cc_final: 0.7948 (mtpt) REVERT: F 214 MET cc_start: 0.8470 (tpp) cc_final: 0.8109 (tpp) outliers start: 15 outliers final: 7 residues processed: 249 average time/residue: 0.2629 time to fit residues: 87.6576 Evaluate side-chains 232 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 222 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain 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: 4.9990 chunk 73 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 119 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 0.3980 chunk 41 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN D 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.172986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.133250 restraints weight = 42562.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.136525 restraints weight = 17086.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.137905 restraints weight = 12530.736| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3544 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3544 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10560 Z= 0.241 Angle : 0.621 10.926 14362 Z= 0.317 Chirality : 0.043 0.166 1606 Planarity : 0.005 0.050 1880 Dihedral : 3.987 18.725 1410 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.69 % Allowed : 19.89 % Favored : 78.42 % 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: 1.10 (0.24), residues: 1312 helix: 1.18 (0.18), residues: 872 sheet: -1.99 (0.64), residues: 54 loop : 0.35 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.002 TRP C 117 HIS 0.005 0.001 HIS C 12 PHE 0.010 0.001 PHE E 161 TYR 0.023 0.002 TYR D 169 ARG 0.006 0.001 ARG E 97 *********************** 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 249 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 232 time to evaluate : 1.461 Fit side-chains REVERT: A 29 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7318 (mm-30) REVERT: A 100 ARG cc_start: 0.7394 (tpt-90) cc_final: 0.7045 (tpt-90) REVERT: A 118 MET cc_start: 0.8476 (mtm) cc_final: 0.7809 (mtp) REVERT: B 98 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6583 (tm-30) REVERT: B 102 SER cc_start: 0.8423 (OUTLIER) cc_final: 0.7894 (m) REVERT: B 151 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7504 (mm) REVERT: C 25 LYS cc_start: 0.8428 (ttmt) cc_final: 0.7616 (tttp) REVERT: C 100 ARG cc_start: 0.7816 (ptm160) cc_final: 0.7365 (ttp-110) REVERT: C 114 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.6519 (mp-120) REVERT: C 117 TRP cc_start: 0.7941 (m-90) cc_final: 0.7691 (m-90) REVERT: C 133 TRP cc_start: 0.7947 (m-10) cc_final: 0.7036 (m-10) REVERT: C 182 LYS cc_start: 0.8772 (ttmm) cc_final: 0.8295 (ttmm) REVERT: C 185 MET cc_start: 0.7063 (mtm) cc_final: 0.6764 (mtp) REVERT: C 214 MET cc_start: 0.8537 (tpp) cc_final: 0.8241 (tpt) REVERT: D 100 ARG cc_start: 0.7255 (tpt-90) cc_final: 0.7007 (tpt-90) REVERT: D 118 MET cc_start: 0.8588 (mtm) cc_final: 0.8107 (mtp) REVERT: D 143 ARG cc_start: 0.8029 (ttm170) cc_final: 0.6722 (tpt170) REVERT: D 203 LYS cc_start: 0.7455 (mmmt) cc_final: 0.7053 (tttm) REVERT: E 39 MET cc_start: 0.8049 (tpp) cc_final: 0.7847 (tpp) REVERT: E 114 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7909 (mp10) REVERT: E 151 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7685 (mm) REVERT: F 28 GLU cc_start: 0.6538 (mm-30) cc_final: 0.6016 (mm-30) REVERT: F 143 ARG cc_start: 0.8176 (mmm-85) cc_final: 0.7691 (mmm160) outliers start: 17 outliers final: 7 residues processed: 244 average time/residue: 0.2712 time to fit residues: 88.0113 Evaluate side-chains 234 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 221 time to evaluate : 1.147 ------------------------------------------------------------------------------- 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 C residue 114 GLN Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 189 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 123 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 3 optimal weight: 0.0980 chunk 127 optimal weight: 0.8980 chunk 65 optimal weight: 9.9990 chunk 122 optimal weight: 0.5980 chunk 56 optimal weight: 8.9990 chunk 74 optimal weight: 0.8980 chunk 94 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 9 GLN D 179 GLN D 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.175587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.135673 restraints weight = 39291.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.139033 restraints weight = 16183.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.139981 restraints weight = 11433.133| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3629 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3629 r_free = 0.3629 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3629 r_free = 0.3629 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3629 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10560 Z= 0.183 Angle : 0.620 11.898 14362 Z= 0.315 Chirality : 0.042 0.168 1606 Planarity : 0.005 0.049 1880 Dihedral : 3.966 19.353 1410 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.33 % Allowed : 20.52 % Favored : 78.15 % 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: 1.18 (0.24), residues: 1312 helix: 1.22 (0.18), residues: 874 sheet: -1.86 (0.64), residues: 54 loop : 0.43 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.001 TRP C 117 HIS 0.005 0.000 HIS C 12 PHE 0.014 0.001 PHE F 168 TYR 0.019 0.001 TYR D 169 ARG 0.006 0.000 ARG E 97 *********************** 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 252 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 239 time to evaluate : 1.155 Fit side-chains revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7280 (mm-30) REVERT: A 100 ARG cc_start: 0.7266 (tpt-90) cc_final: 0.7013 (tpt-90) REVERT: A 118 MET cc_start: 0.8420 (mtm) cc_final: 0.7755 (mtp) REVERT: B 102 SER cc_start: 0.8407 (OUTLIER) cc_final: 0.7915 (m) REVERT: B 132 ARG cc_start: 0.8116 (mtp-110) cc_final: 0.7745 (mtt90) REVERT: B 151 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7507 (mm) REVERT: B 213 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8689 (mm-30) REVERT: C 100 ARG cc_start: 0.7770 (ptm160) cc_final: 0.7490 (ttp-110) REVERT: C 114 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.6588 (mp-120) REVERT: C 117 TRP cc_start: 0.7778 (m-90) cc_final: 0.7563 (m-90) REVERT: C 185 MET cc_start: 0.7054 (mtm) cc_final: 0.6770 (mtp) REVERT: C 214 MET cc_start: 0.8545 (tpp) cc_final: 0.8239 (tpt) REVERT: D 100 ARG cc_start: 0.7310 (tpt-90) cc_final: 0.7035 (tpt-90) REVERT: D 118 MET cc_start: 0.8516 (mtm) cc_final: 0.8036 (mtp) REVERT: D 143 ARG cc_start: 0.7977 (ttm170) cc_final: 0.7412 (mtm-85) REVERT: D 179 GLN cc_start: 0.6027 (OUTLIER) cc_final: 0.5324 (mm110) REVERT: D 203 LYS cc_start: 0.7408 (mmmt) cc_final: 0.6995 (tttm) REVERT: E 39 MET cc_start: 0.7984 (tpp) cc_final: 0.7669 (tpp) REVERT: E 114 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7832 (mp10) REVERT: E 151 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7711 (mm) REVERT: F 28 GLU cc_start: 0.6524 (mm-30) cc_final: 0.5972 (mm-30) REVERT: F 143 ARG cc_start: 0.8207 (mmm-85) cc_final: 0.7667 (mmm160) outliers start: 13 outliers final: 5 residues processed: 246 average time/residue: 0.2664 time to fit residues: 87.9116 Evaluate side-chains 236 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 225 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 SER 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 C residue 114 GLN Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 179 GLN Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 189 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 5 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 chunk 104 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 58 optimal weight: 0.0060 chunk 8 optimal weight: 8.9990 chunk 115 optimal weight: 0.8980 overall best weight: 1.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 9 GLN D 179 GLN D 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.174161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.130759 restraints weight = 32678.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.135664 restraints weight = 14359.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.138485 restraints weight = 8696.932| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3557 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3557 r_free = 0.3557 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3557 r_free = 0.3557 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3557 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10560 Z= 0.240 Angle : 0.655 12.718 14362 Z= 0.333 Chirality : 0.043 0.166 1606 Planarity : 0.005 0.050 1880 Dihedral : 3.979 18.937 1410 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.87 % Allowed : 20.16 % Favored : 77.98 % 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 (0.24), residues: 1312 helix: 1.21 (0.18), residues: 868 sheet: -1.77 (0.65), residues: 54 loop : 0.34 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.001 TRP C 117 HIS 0.005 0.001 HIS C 12 PHE 0.014 0.002 PHE C 168 TYR 0.024 0.002 TYR D 169 ARG 0.007 0.000 ARG E 97 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 231 time to evaluate : 1.214 Fit side-chains revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7237 (tpt-90) cc_final: 0.6959 (tpt-90) REVERT: A 118 MET cc_start: 0.8398 (mtm) cc_final: 0.7778 (mtp) REVERT: B 98 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6538 (tm-30) REVERT: B 102 SER cc_start: 0.8432 (OUTLIER) cc_final: 0.7922 (m) REVERT: B 132 ARG cc_start: 0.8105 (mtp-110) cc_final: 0.7693 (mtt90) REVERT: B 151 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7596 (mm) REVERT: C 25 LYS cc_start: 0.8317 (ttmt) cc_final: 0.7283 (ttpp) REVERT: C 100 ARG cc_start: 0.7717 (ptm160) cc_final: 0.7315 (ttp-110) REVERT: C 114 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.6506 (mp-120) REVERT: C 117 TRP cc_start: 0.7936 (m-90) cc_final: 0.7652 (m-90) REVERT: C 214 MET cc_start: 0.8575 (tpp) cc_final: 0.8267 (tpt) REVERT: D 99 PRO cc_start: 0.6463 (Cg_exo) cc_final: 0.5965 (Cg_endo) REVERT: D 100 ARG cc_start: 0.7225 (tpt-90) cc_final: 0.6955 (tpt-90) REVERT: D 118 MET cc_start: 0.8596 (mtm) cc_final: 0.8114 (mtp) REVERT: D 143 ARG cc_start: 0.8076 (ttm170) cc_final: 0.7451 (mtm-85) REVERT: D 179 GLN cc_start: 0.6672 (OUTLIER) cc_final: 0.5853 (mm110) REVERT: D 203 LYS cc_start: 0.7530 (mmmt) cc_final: 0.7109 (tttm) REVERT: D 213 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7512 (mp0) REVERT: E 39 MET cc_start: 0.8026 (tpp) cc_final: 0.7717 (tpp) REVERT: E 114 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7843 (mp10) REVERT: E 151 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7728 (mm) REVERT: F 28 GLU cc_start: 0.6524 (mm-30) cc_final: 0.5978 (mm-30) REVERT: F 71 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7349 (mm-30) REVERT: F 114 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7514 (mp10) REVERT: F 143 ARG cc_start: 0.8254 (mmm-85) cc_final: 0.7670 (mmm160) REVERT: F 215 MET cc_start: 0.7499 (ptp) cc_final: 0.7163 (mpp) outliers start: 19 outliers final: 7 residues processed: 242 average time/residue: 0.2683 time to fit residues: 86.2884 Evaluate side-chains 237 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 222 time to evaluate : 1.199 ------------------------------------------------------------------------------- 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 144 MET Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 179 GLN Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain F residue 114 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 83 optimal weight: 0.0040 chunk 116 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 111 optimal weight: 0.3980 chunk 71 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 12 optimal weight: 0.0970 chunk 130 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 9 GLN D 179 GLN D 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.175309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.131803 restraints weight = 33929.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.137158 restraints weight = 15379.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.138635 restraints weight = 8477.126| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3599 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3599 r_free = 0.3599 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3599 r_free = 0.3599 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3599 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 10560 Z= 0.200 Angle : 0.653 12.857 14362 Z= 0.332 Chirality : 0.043 0.167 1606 Planarity : 0.005 0.049 1880 Dihedral : 3.974 18.987 1410 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.69 % Allowed : 20.34 % Favored : 77.98 % 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: 1.17 (0.24), residues: 1312 helix: 1.21 (0.18), residues: 872 sheet: -1.70 (0.65), residues: 54 loop : 0.41 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.001 TRP C 117 HIS 0.005 0.000 HIS C 12 PHE 0.014 0.001 PHE C 168 TYR 0.008 0.001 TYR A 169 ARG 0.007 0.000 ARG E 97 ********************** 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 244 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 227 time to evaluate : 1.121 Fit side-chains REVERT: A 100 ARG cc_start: 0.7209 (tpt-90) cc_final: 0.6920 (tpt-90) REVERT: A 118 MET cc_start: 0.8381 (mtm) cc_final: 0.7892 (mtp) REVERT: A 215 MET cc_start: 0.7271 (mtm) cc_final: 0.7066 (mpp) REVERT: B 98 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6522 (tm-30) REVERT: B 102 SER cc_start: 0.8422 (OUTLIER) cc_final: 0.7916 (m) REVERT: B 132 ARG cc_start: 0.8092 (mtp-110) cc_final: 0.7705 (mtt90) REVERT: B 151 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7580 (mm) REVERT: C 25 LYS cc_start: 0.8030 (ttmt) cc_final: 0.7364 (tttt) REVERT: C 114 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.6551 (mp-120) REVERT: C 117 TRP cc_start: 0.7906 (m-90) cc_final: 0.7578 (m-90) REVERT: C 133 TRP cc_start: 0.7937 (m-10) cc_final: 0.6853 (m100) REVERT: C 176 GLN cc_start: 0.7867 (tm-30) cc_final: 0.7622 (tm-30) REVERT: C 214 MET cc_start: 0.8566 (tpp) cc_final: 0.8042 (tpt) REVERT: C 215 MET cc_start: 0.7565 (ptp) cc_final: 0.7166 (mpp) REVERT: D 99 PRO cc_start: 0.6409 (Cg_exo) cc_final: 0.5931 (Cg_endo) REVERT: D 100 ARG cc_start: 0.7271 (tpt-90) cc_final: 0.7019 (tpt-90) REVERT: D 118 MET cc_start: 0.8562 (mtm) cc_final: 0.8073 (mtp) REVERT: D 143 ARG cc_start: 0.8090 (ttm170) cc_final: 0.7493 (mtm-85) REVERT: D 179 GLN cc_start: 0.6558 (OUTLIER) cc_final: 0.5818 (mm110) REVERT: D 203 LYS cc_start: 0.7526 (mmmt) cc_final: 0.7091 (tttm) REVERT: D 213 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7564 (mp0) REVERT: E 114 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7802 (mp10) REVERT: E 151 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7728 (mm) REVERT: F 28 GLU cc_start: 0.6583 (mm-30) cc_final: 0.5972 (mm-30) REVERT: F 71 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7300 (mm-30) REVERT: F 143 ARG cc_start: 0.8220 (mmm-85) cc_final: 0.7497 (mmm160) REVERT: F 215 MET cc_start: 0.7398 (ptp) cc_final: 0.7018 (mpp) outliers start: 17 outliers final: 6 residues processed: 239 average time/residue: 0.2620 time to fit residues: 84.3350 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 : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 144 MET Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 179 GLN Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 151 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 16 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 130 optimal weight: 0.0270 chunk 39 optimal weight: 4.9990 chunk 88 optimal weight: 0.0470 chunk 18 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 overall best weight: 1.1940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 9 GLN D 179 GLN D 195 ASN F 114 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.175391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.131251 restraints weight = 33931.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.136441 restraints weight = 15229.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.139919 restraints weight = 8585.916| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3579 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3579 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10560 Z= 0.205 Angle : 0.652 12.969 14362 Z= 0.331 Chirality : 0.043 0.163 1606 Planarity : 0.005 0.048 1880 Dihedral : 3.979 18.860 1410 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.51 % Allowed : 20.25 % Favored : 78.24 % 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: 1.16 (0.24), residues: 1312 helix: 1.20 (0.18), residues: 872 sheet: -1.61 (0.65), residues: 54 loop : 0.38 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.001 TRP C 117 HIS 0.005 0.001 HIS C 12 PHE 0.015 0.001 PHE C 168 TYR 0.009 0.001 TYR D 169 ARG 0.007 0.000 ARG E 97 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3479.32 seconds wall clock time: 63 minutes 0.22 seconds (3780.22 seconds total)