Starting phenix.real_space_refine on Fri Nov 15 05:13:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hik_34819/11_2024/8hik_34819.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hik_34819/11_2024/8hik_34819.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hik_34819/11_2024/8hik_34819.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hik_34819/11_2024/8hik_34819.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hik_34819/11_2024/8hik_34819.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hik_34819/11_2024/8hik_34819.cif" } resolution = 3.72 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= 0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 27 5.16 5 C 5296 2.51 5 N 1376 2.21 5 O 1537 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8238 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3969 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 17, 'TRANS': 480} Chain breaks: 1 Chain: "H" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1686 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211} Chain: "N" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "L" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1632 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 201} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'TPP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.23, per 1000 atoms: 0.63 Number of scatterers: 8238 At special positions: 0 Unit cell: (66.34, 99.51, 148.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 2 15.00 O 1537 8.00 N 1376 7.00 C 5296 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 154 " - pdb=" SG CYS H 210 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " 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: 2.14 Conformation dependent library (CDL) restraints added in 1.1 seconds 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1972 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 14 sheets defined 39.7% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid -80 through -64 removed outlier: 3.672A pdb=" N LYS A -64 " --> pdb=" O LYS A -68 " (cutoff:3.500A) Processing helix chain 'A' and resid -57 through -43 removed outlier: 3.598A pdb=" N ALA A -43 " --> pdb=" O ALA A -47 " (cutoff:3.500A) Processing helix chain 'A' and resid -38 through -33 removed outlier: 4.020A pdb=" N ASP A -33 " --> pdb=" O PRO A -37 " (cutoff:3.500A) Processing helix chain 'A' and resid -25 through -3 removed outlier: 3.702A pdb=" N LEU A -5 " --> pdb=" O ASP A -9 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 18 removed outlier: 3.694A pdb=" N ALA A 6 " --> pdb=" O LYS A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 23 Processing helix chain 'A' and resid 27 through 39 Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 60 through 66 Processing helix chain 'A' and resid 68 through 81 Processing helix chain 'A' and resid 82 through 90 removed outlier: 4.114A pdb=" N LEU A 86 " --> pdb=" O PRO A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 112 Processing helix chain 'A' and resid 115 through 132 removed outlier: 3.884A pdb=" N MET A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR A 129 " --> pdb=" O PHE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 144 removed outlier: 4.115A pdb=" N SER A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 176 Processing helix chain 'A' and resid 181 through 202 Processing helix chain 'A' and resid 251 through 259 Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'A' and resid 264 through 296 removed outlier: 3.936A pdb=" N TYR A 287 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N HIS A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ILE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP A 296 " --> pdb=" O TRP A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 323 Processing helix chain 'A' and resid 335 through 355 Processing helix chain 'A' and resid 361 through 375 Processing helix chain 'A' and resid 379 through 389 removed outlier: 3.718A pdb=" N ILE A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER A 389 " --> pdb=" O PHE A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 418 Processing helix chain 'A' and resid 427 through 451 Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.532A pdb=" N ASP H 93 " --> pdb=" O ARG H 90 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 90 through 94' Processing helix chain 'H' and resid 107 through 112 removed outlier: 3.631A pdb=" N LYS H 112 " --> pdb=" O GLU H 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 4.097A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 188 Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA2, first strand: chain 'H' and resid 14 through 15 removed outlier: 3.588A pdb=" N VAL H 15 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU H 37 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N TYR H 53 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 134 through 138 removed outlier: 6.145A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 134 through 138 removed outlier: 6.145A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 164 through 167 removed outlier: 4.332A pdb=" N TYR H 208 " --> pdb=" O VAL H 225 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.735A pdb=" N SER N 7 " --> pdb=" O SER N 21 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.833A pdb=" N THR N 118 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR N 115 " --> pdb=" O TYR N 94 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR N 94 " --> pdb=" O THR N 115 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N MET N 34 " --> pdb=" O VAL N 50 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N VAL N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.833A pdb=" N THR N 118 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR N 115 " --> pdb=" O TYR N 94 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR N 94 " --> pdb=" O THR N 115 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N TYR N 110 " --> pdb=" O ILE N 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AB1, first strand: chain 'L' and resid 13 through 14 Processing sheet with id=AB2, first strand: chain 'L' and resid 54 through 55 removed outlier: 3.941A pdb=" N TYR L 50 " --> pdb=" O SER L 54 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN L 91 " --> pdb=" O THR L 99 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR L 99 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 54 through 55 removed outlier: 3.941A pdb=" N TYR L 50 " --> pdb=" O SER L 54 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 116 through 120 removed outlier: 5.961A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 147 through 148 446 hydrogen bonds defined for protein. 1248 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: 2.73 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2562 1.34 - 1.46: 2030 1.46 - 1.58: 3807 1.58 - 1.70: 3 1.70 - 1.81: 38 Bond restraints: 8440 Sorted by residual: bond pdb=" C5 TPP A 601 " pdb=" S1 TPP A 601 " ideal model delta sigma weight residual 1.727 1.510 0.217 1.00e-02 1.00e+04 4.69e+02 bond pdb=" C2 TPP A 601 " pdb=" S1 TPP A 601 " ideal model delta sigma weight residual 1.675 1.544 0.131 1.00e-02 1.00e+04 1.71e+02 bond pdb=" C4' TPP A 601 " pdb=" N4' TPP A 601 " ideal model delta sigma weight residual 1.337 1.454 -0.117 1.10e-02 8.26e+03 1.13e+02 bond pdb=" C2 TPP A 601 " pdb=" N3 TPP A 601 " ideal model delta sigma weight residual 1.318 1.424 -0.106 1.30e-02 5.92e+03 6.66e+01 bond pdb=" O3A TPP A 601 " pdb=" PB TPP A 601 " ideal model delta sigma weight residual 1.587 1.662 -0.075 1.10e-02 8.26e+03 4.66e+01 ... (remaining 8435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 11372 3.25 - 6.49: 91 6.49 - 9.74: 18 9.74 - 12.98: 2 12.98 - 16.23: 1 Bond angle restraints: 11484 Sorted by residual: angle pdb=" PA TPP A 601 " pdb=" O3A TPP A 601 " pdb=" PB TPP A 601 " ideal model delta sigma weight residual 139.87 123.64 16.23 1.00e+00 1.00e+00 2.63e+02 angle pdb=" C2 TPP A 601 " pdb=" S1 TPP A 601 " pdb=" C5 TPP A 601 " ideal model delta sigma weight residual 91.33 104.13 -12.80 1.00e+00 1.00e+00 1.64e+02 angle pdb=" C7 TPP A 601 " pdb=" O7 TPP A 601 " pdb=" PA TPP A 601 " ideal model delta sigma weight residual 124.29 118.57 5.72 1.00e+00 1.00e+00 3.27e+01 angle pdb=" N1' TPP A 601 " pdb=" C2' TPP A 601 " pdb=" N3' TPP A 601 " ideal model delta sigma weight residual 125.71 119.88 5.83 1.07e+00 8.80e-01 2.99e+01 angle pdb=" N3 TPP A 601 " pdb=" C2 TPP A 601 " pdb=" S1 TPP A 601 " ideal model delta sigma weight residual 112.34 107.32 5.02 1.00e+00 1.00e+00 2.52e+01 ... (remaining 11479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 4807 16.52 - 33.03: 110 33.03 - 49.54: 38 49.54 - 66.06: 1 66.06 - 82.57: 11 Dihedral angle restraints: 4967 sinusoidal: 1890 harmonic: 3077 Sorted by residual: dihedral pdb=" CB CYS H 154 " pdb=" SG CYS H 154 " pdb=" SG CYS H 210 " pdb=" CB CYS H 210 " ideal model delta sinusoidal sigma weight residual 93.00 175.57 -82.57 1 1.00e+01 1.00e-02 8.36e+01 dihedral pdb=" CB CYS L 136 " pdb=" SG CYS L 136 " pdb=" SG CYS L 196 " pdb=" CB CYS L 196 " ideal model delta sinusoidal sigma weight residual -86.00 -120.31 34.31 1 1.00e+01 1.00e-02 1.67e+01 dihedral pdb=" CA ARG A 91 " pdb=" C ARG A 91 " pdb=" N TYR A 92 " pdb=" CA TYR A 92 " ideal model delta harmonic sigma weight residual 180.00 159.67 20.33 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 4964 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 957 0.049 - 0.097: 267 0.097 - 0.146: 64 0.146 - 0.195: 7 0.195 - 0.243: 1 Chirality restraints: 1296 Sorted by residual: chirality pdb=" CA THR A 69 " pdb=" N THR A 69 " pdb=" C THR A 69 " pdb=" CB THR A 69 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB THR A 69 " pdb=" CA THR A 69 " pdb=" OG1 THR A 69 " pdb=" CG2 THR A 69 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.13e-01 chirality pdb=" CA TYR N 104 " pdb=" N TYR N 104 " pdb=" C TYR N 104 " pdb=" CB TYR N 104 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.80e-01 ... (remaining 1293 not shown) Planarity restraints: 1437 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 102 " -0.016 2.00e-02 2.50e+03 1.51e-02 5.66e+00 pdb=" CG TRP H 102 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP H 102 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP H 102 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP H 102 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP H 102 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP H 102 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 102 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 102 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP H 102 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP H 105 " 0.038 5.00e-02 4.00e+02 5.76e-02 5.31e+00 pdb=" N PRO H 106 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO H 106 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO H 106 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU H 108 " -0.035 5.00e-02 4.00e+02 5.18e-02 4.29e+00 pdb=" N PRO H 109 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO H 109 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 109 " -0.030 5.00e-02 4.00e+02 ... (remaining 1434 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2236 2.81 - 3.33: 7133 3.33 - 3.85: 13492 3.85 - 4.38: 15090 4.38 - 4.90: 26545 Nonbonded interactions: 64496 Sorted by model distance: nonbonded pdb=" OG SER A 168 " pdb=" O GLY A 307 " model vdw 2.282 3.040 nonbonded pdb=" OG SER L 64 " pdb=" OG1 THR L 75 " model vdw 2.326 3.040 nonbonded pdb=" O GLU A -26 " pdb=" OH TYR A 22 " model vdw 2.336 3.040 nonbonded pdb=" NE ARG A -49 " pdb=" O LEU L 93 " model vdw 2.340 3.120 nonbonded pdb=" O TRP H 111 " pdb=" OH TYR L 92 " model vdw 2.345 3.040 ... (remaining 64491 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.140 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6165 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.217 8440 Z= 0.324 Angle : 0.820 16.228 11484 Z= 0.473 Chirality : 0.047 0.243 1296 Planarity : 0.006 0.058 1437 Dihedral : 9.567 75.327 2980 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % 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: -3.54 (0.21), residues: 1045 helix: -1.96 (0.20), residues: 380 sheet: -1.92 (0.29), residues: 241 loop : -2.84 (0.25), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP H 102 HIS 0.006 0.002 HIS H 38 PHE 0.029 0.002 PHE A 103 TYR 0.023 0.002 TYR H 53 ARG 0.006 0.000 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A -51 LYS cc_start: 0.7460 (tttt) cc_final: 0.7258 (mtmm) REVERT: A -50 MET cc_start: 0.6245 (mmm) cc_final: 0.5921 (mmm) REVERT: A -22 PHE cc_start: 0.7319 (t80) cc_final: 0.6815 (t80) REVERT: A 27 HIS cc_start: 0.5170 (m90) cc_final: 0.4851 (m-70) REVERT: A 73 SER cc_start: 0.6585 (m) cc_final: 0.6352 (t) REVERT: A 140 ILE cc_start: 0.7951 (mt) cc_final: 0.7742 (tp) REVERT: A 281 TYR cc_start: 0.6510 (t80) cc_final: 0.6203 (t80) REVERT: A 304 VAL cc_start: 0.7185 (t) cc_final: 0.5916 (m) REVERT: A 386 GLN cc_start: 0.7578 (mm-40) cc_final: 0.7062 (tm-30) REVERT: A 387 ILE cc_start: 0.7155 (mt) cc_final: 0.6955 (mt) REVERT: H 86 MET cc_start: 0.6378 (mtm) cc_final: 0.6146 (mtm) REVERT: H 99 CYS cc_start: 0.5632 (t) cc_final: 0.5367 (t) REVERT: H 112 LYS cc_start: 0.7716 (mttt) cc_final: 0.7507 (ttmm) REVERT: H 119 GLN cc_start: 0.6958 (mt0) cc_final: 0.6698 (mt0) REVERT: H 135 VAL cc_start: 0.7872 (t) cc_final: 0.7591 (m) REVERT: H 136 PHE cc_start: 0.7525 (m-80) cc_final: 0.7085 (m-80) REVERT: N 34 MET cc_start: 0.6441 (mtp) cc_final: 0.6215 (mtp) REVERT: L 32 SER cc_start: 0.7747 (t) cc_final: 0.7452 (p) REVERT: L 37 TYR cc_start: 0.8263 (m-10) cc_final: 0.7688 (m-80) REVERT: L 43 LYS cc_start: 0.8431 (mttt) cc_final: 0.8094 (ttmm) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.2015 time to fit residues: 60.1045 Evaluate side-chains 184 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 94 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A -77 ASN A -42 GLN A 27 HIS A 120 GLN A 289 HIS A 293 ASN A 358 HIS H 178 HIS H 214 HIS ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN L 39 GLN L 90 GLN L 162 GLN ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 191 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6468 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 8440 Z= 0.270 Angle : 0.632 7.615 11484 Z= 0.330 Chirality : 0.042 0.178 1296 Planarity : 0.005 0.050 1437 Dihedral : 5.393 52.787 1163 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.35 % Allowed : 9.74 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % 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: -2.08 (0.25), residues: 1045 helix: -0.28 (0.25), residues: 389 sheet: -1.46 (0.31), residues: 240 loop : -2.31 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP H 102 HIS 0.005 0.001 HIS H 38 PHE 0.017 0.002 PHE L 211 TYR 0.033 0.002 TYR A 126 ARG 0.011 0.001 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 226 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A -51 LYS cc_start: 0.7743 (tttt) cc_final: 0.7366 (mtmm) REVERT: A -50 MET cc_start: 0.6564 (mmm) cc_final: 0.6280 (mmm) REVERT: A 27 HIS cc_start: 0.5900 (m-70) cc_final: 0.5658 (m-70) REVERT: A 73 SER cc_start: 0.7503 (m) cc_final: 0.7123 (t) REVERT: A 99 GLN cc_start: 0.7874 (tt0) cc_final: 0.7467 (tt0) REVERT: A 138 SER cc_start: 0.7446 (m) cc_final: 0.7237 (t) REVERT: A 294 GLU cc_start: 0.6920 (tt0) cc_final: 0.6673 (tt0) REVERT: A 386 GLN cc_start: 0.7489 (mm-40) cc_final: 0.7035 (tm-30) REVERT: A 387 ILE cc_start: 0.7111 (mt) cc_final: 0.6797 (mt) REVERT: H 7 LEU cc_start: 0.7565 (mm) cc_final: 0.7324 (mt) REVERT: H 46 LYS cc_start: 0.8393 (mmtt) cc_final: 0.8151 (mmmm) REVERT: H 63 TYR cc_start: 0.7705 (m-10) cc_final: 0.7315 (m-10) REVERT: H 86 MET cc_start: 0.6848 (mtm) cc_final: 0.6571 (mtm) REVERT: H 135 VAL cc_start: 0.7863 (t) cc_final: 0.7541 (m) REVERT: H 136 PHE cc_start: 0.7618 (m-80) cc_final: 0.7322 (m-80) REVERT: H 168 TRP cc_start: 0.7231 (m100) cc_final: 0.6600 (m100) REVERT: H 197 THR cc_start: 0.7186 (p) cc_final: 0.6953 (p) REVERT: N 59 PHE cc_start: 0.7108 (m-80) cc_final: 0.6785 (m-80) REVERT: L 36 TRP cc_start: 0.8120 (m100) cc_final: 0.7819 (m100) REVERT: L 43 LYS cc_start: 0.8646 (mttt) cc_final: 0.8377 (mmmm) REVERT: L 47 LEU cc_start: 0.8572 (tp) cc_final: 0.8292 (tt) REVERT: L 87 TYR cc_start: 0.8425 (m-80) cc_final: 0.8051 (m-10) REVERT: L 104 THR cc_start: 0.7823 (p) cc_final: 0.7521 (p) REVERT: L 117 VAL cc_start: 0.8234 (t) cc_final: 0.7931 (p) REVERT: L 166 THR cc_start: 0.8471 (t) cc_final: 0.7988 (m) outliers start: 21 outliers final: 10 residues processed: 233 average time/residue: 0.1882 time to fit residues: 61.3200 Evaluate side-chains 214 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 204 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -11 ILE Chi-restraints excluded: chain A residue -7 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 94 optimal weight: 0.2980 chunk 102 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 75 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A -20 HIS A 277 ASN A 377 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 160 ASN L 168 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 8440 Z= 0.270 Angle : 0.632 8.367 11484 Z= 0.323 Chirality : 0.043 0.165 1296 Planarity : 0.005 0.083 1437 Dihedral : 5.307 48.174 1163 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.69 % Allowed : 11.53 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % 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: -1.65 (0.25), residues: 1045 helix: 0.13 (0.26), residues: 386 sheet: -1.17 (0.32), residues: 243 loop : -2.18 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 102 HIS 0.004 0.001 HIS A 27 PHE 0.019 0.001 PHE A 212 TYR 0.025 0.002 TYR A 126 ARG 0.007 0.001 ARG A -49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 215 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A -56 LYS cc_start: 0.8231 (tttt) cc_final: 0.7963 (ttpt) REVERT: A -51 LYS cc_start: 0.7557 (tttt) cc_final: 0.7213 (mtmm) REVERT: A -49 ARG cc_start: 0.7874 (tpt-90) cc_final: 0.7489 (tpp80) REVERT: A 73 SER cc_start: 0.7824 (m) cc_final: 0.7368 (t) REVERT: A 99 GLN cc_start: 0.7657 (tt0) cc_final: 0.7184 (tt0) REVERT: A 138 SER cc_start: 0.7467 (m) cc_final: 0.7266 (t) REVERT: A 294 GLU cc_start: 0.6904 (tt0) cc_final: 0.6609 (tt0) REVERT: A 386 GLN cc_start: 0.7375 (mm-40) cc_final: 0.6897 (tm-30) REVERT: A 387 ILE cc_start: 0.7089 (mt) cc_final: 0.6870 (mt) REVERT: H 110 TRP cc_start: 0.8092 (t60) cc_final: 0.6744 (t60) REVERT: H 111 TRP cc_start: 0.8038 (m100) cc_final: 0.7117 (m100) REVERT: H 116 TYR cc_start: 0.7522 (m-10) cc_final: 0.7305 (m-80) REVERT: H 135 VAL cc_start: 0.7905 (t) cc_final: 0.7556 (m) REVERT: H 136 PHE cc_start: 0.7751 (m-80) cc_final: 0.7533 (m-80) REVERT: H 197 THR cc_start: 0.7159 (p) cc_final: 0.6927 (p) REVERT: N 39 GLN cc_start: 0.5851 (mp10) cc_final: 0.3832 (mp10) REVERT: L 32 SER cc_start: 0.8168 (t) cc_final: 0.7384 (p) REVERT: L 36 TRP cc_start: 0.8109 (m100) cc_final: 0.7728 (m100) REVERT: L 43 LYS cc_start: 0.8685 (mttt) cc_final: 0.8430 (mtpp) REVERT: L 48 LEU cc_start: 0.7869 (tp) cc_final: 0.7429 (tp) REVERT: L 87 TYR cc_start: 0.8521 (m-80) cc_final: 0.7999 (m-10) REVERT: L 166 THR cc_start: 0.8535 (t) cc_final: 0.8072 (m) REVERT: L 168 GLN cc_start: 0.7253 (tt0) cc_final: 0.6984 (tt0) outliers start: 24 outliers final: 15 residues processed: 225 average time/residue: 0.1919 time to fit residues: 60.5582 Evaluate side-chains 215 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 200 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -69 LEU Chi-restraints excluded: chain A residue -18 PHE Chi-restraints excluded: chain A residue -11 ILE Chi-restraints excluded: chain A residue -7 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 89 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 49 optimal weight: 0.0470 chunk 10 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 94 optimal weight: 0.0470 chunk 100 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 83 optimal weight: 0.3980 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 ASN H 169 ASN L 90 GLN L 160 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6530 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 8440 Z= 0.200 Angle : 0.597 7.968 11484 Z= 0.298 Chirality : 0.041 0.132 1296 Planarity : 0.004 0.070 1437 Dihedral : 5.021 53.143 1163 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.79 % Allowed : 15.45 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % 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: -1.28 (0.26), residues: 1045 helix: 0.53 (0.26), residues: 385 sheet: -1.05 (0.32), residues: 245 loop : -2.02 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 102 HIS 0.004 0.001 HIS A 355 PHE 0.012 0.001 PHE H 180 TYR 0.021 0.002 TYR A 126 ARG 0.007 0.000 ARG A -49 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 199 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A -56 LYS cc_start: 0.8219 (tttt) cc_final: 0.7982 (ttpt) REVERT: A -51 LYS cc_start: 0.7456 (tttt) cc_final: 0.7178 (mtmm) REVERT: A 71 VAL cc_start: 0.7357 (m) cc_final: 0.7099 (p) REVERT: A 73 SER cc_start: 0.7929 (m) cc_final: 0.7454 (t) REVERT: A 99 GLN cc_start: 0.7595 (tt0) cc_final: 0.7122 (tt0) REVERT: A 138 SER cc_start: 0.7538 (m) cc_final: 0.7291 (t) REVERT: A 294 GLU cc_start: 0.6868 (tt0) cc_final: 0.6584 (tt0) REVERT: A 386 GLN cc_start: 0.7437 (mm-40) cc_final: 0.6946 (tm-30) REVERT: A 387 ILE cc_start: 0.7065 (mt) cc_final: 0.6860 (mt) REVERT: H 20 SER cc_start: 0.8073 (m) cc_final: 0.7710 (p) REVERT: H 116 TYR cc_start: 0.7388 (m-10) cc_final: 0.7185 (m-80) REVERT: H 135 VAL cc_start: 0.7879 (t) cc_final: 0.7601 (m) REVERT: N 95 TYR cc_start: 0.5975 (m-10) cc_final: 0.5773 (m-10) REVERT: L 32 SER cc_start: 0.8168 (t) cc_final: 0.7740 (p) REVERT: L 36 TRP cc_start: 0.8137 (m100) cc_final: 0.7774 (m100) REVERT: L 43 LYS cc_start: 0.8679 (mttt) cc_final: 0.8425 (mtpp) REVERT: L 48 LEU cc_start: 0.7908 (tp) cc_final: 0.7606 (tp) REVERT: L 72 PHE cc_start: 0.8344 (m-80) cc_final: 0.8132 (m-80) REVERT: L 92 TYR cc_start: 0.8273 (p90) cc_final: 0.7305 (p90) outliers start: 16 outliers final: 12 residues processed: 205 average time/residue: 0.2057 time to fit residues: 58.2109 Evaluate side-chains 209 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 197 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -69 LEU Chi-restraints excluded: chain A residue -18 PHE Chi-restraints excluded: chain A residue -11 ILE Chi-restraints excluded: chain A residue -7 LEU Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 160 PHE Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 89 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 0.2980 chunk 85 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 51 optimal weight: 0.0870 chunk 90 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 33 optimal weight: 0.3980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6545 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8440 Z= 0.197 Angle : 0.598 8.963 11484 Z= 0.300 Chirality : 0.041 0.131 1296 Planarity : 0.005 0.083 1437 Dihedral : 4.909 46.841 1163 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.02 % Allowed : 16.80 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.26), residues: 1045 helix: 0.61 (0.27), residues: 387 sheet: -0.94 (0.32), residues: 243 loop : -1.88 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 107 HIS 0.004 0.001 HIS A 355 PHE 0.022 0.001 PHE H 136 TYR 0.021 0.002 TYR A 126 ARG 0.003 0.000 ARG N 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 202 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A -56 LYS cc_start: 0.8252 (tttt) cc_final: 0.8020 (ttpt) REVERT: A -51 LYS cc_start: 0.7493 (tttt) cc_final: 0.7275 (mtmm) REVERT: A -49 ARG cc_start: 0.8070 (tpp80) cc_final: 0.7357 (tpt-90) REVERT: A 71 VAL cc_start: 0.7423 (m) cc_final: 0.7143 (p) REVERT: A 73 SER cc_start: 0.7915 (m) cc_final: 0.7435 (t) REVERT: A 99 GLN cc_start: 0.7627 (tt0) cc_final: 0.6996 (tt0) REVERT: A 122 MET cc_start: 0.7233 (tmm) cc_final: 0.6063 (tmm) REVERT: A 138 SER cc_start: 0.7617 (m) cc_final: 0.7334 (t) REVERT: A 264 ARG cc_start: 0.4542 (mtp85) cc_final: 0.4261 (mtm110) REVERT: A 294 GLU cc_start: 0.6877 (tt0) cc_final: 0.6593 (tt0) REVERT: A 386 GLN cc_start: 0.7370 (mm-40) cc_final: 0.6931 (tt0) REVERT: A 387 ILE cc_start: 0.7089 (mt) cc_final: 0.6861 (mt) REVERT: H 7 LEU cc_start: 0.7401 (mm) cc_final: 0.7180 (mt) REVERT: H 20 SER cc_start: 0.8099 (m) cc_final: 0.7724 (p) REVERT: H 37 LEU cc_start: 0.8026 (mm) cc_final: 0.7672 (mt) REVERT: H 110 TRP cc_start: 0.8242 (t60) cc_final: 0.7034 (t60) REVERT: N 95 TYR cc_start: 0.5996 (m-10) cc_final: 0.5695 (m-10) REVERT: L 32 SER cc_start: 0.8219 (t) cc_final: 0.7810 (p) REVERT: L 36 TRP cc_start: 0.8247 (m100) cc_final: 0.7908 (m100) REVERT: L 43 LYS cc_start: 0.8694 (mttt) cc_final: 0.8416 (mtpp) REVERT: L 48 LEU cc_start: 0.7878 (tp) cc_final: 0.7576 (tp) REVERT: L 87 TYR cc_start: 0.8505 (m-80) cc_final: 0.8112 (m-80) REVERT: L 92 TYR cc_start: 0.8333 (p90) cc_final: 0.7160 (p90) outliers start: 18 outliers final: 14 residues processed: 209 average time/residue: 0.2075 time to fit residues: 60.3954 Evaluate side-chains 218 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 204 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -69 LEU Chi-restraints excluded: chain A residue -18 PHE Chi-restraints excluded: chain A residue -7 LEU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 160 PHE Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 89 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 0.3980 chunk 19 optimal weight: 0.7980 chunk 59 optimal weight: 0.2980 chunk 24 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 46 optimal weight: 0.4980 chunk 8 optimal weight: 0.0980 chunk 33 optimal weight: 0.1980 chunk 52 optimal weight: 0.5980 chunk 97 optimal weight: 0.6980 overall best weight: 0.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 27 HIS ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8440 Z= 0.176 Angle : 0.608 10.685 11484 Z= 0.298 Chirality : 0.041 0.134 1296 Planarity : 0.005 0.081 1437 Dihedral : 4.766 45.467 1163 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.13 % Allowed : 18.03 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % 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: -0.93 (0.26), residues: 1045 helix: 0.74 (0.27), residues: 386 sheet: -0.76 (0.33), residues: 243 loop : -1.81 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 168 HIS 0.004 0.001 HIS A 355 PHE 0.020 0.001 PHE H 136 TYR 0.024 0.002 TYR A 126 ARG 0.016 0.001 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 199 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A -56 LYS cc_start: 0.8249 (tttt) cc_final: 0.8002 (ttpt) REVERT: A -51 LYS cc_start: 0.7610 (tttt) cc_final: 0.7313 (mtmm) REVERT: A -50 MET cc_start: 0.6514 (mmm) cc_final: 0.6273 (tmm) REVERT: A 42 ARG cc_start: 0.7783 (mtm-85) cc_final: 0.7545 (mtm-85) REVERT: A 71 VAL cc_start: 0.7489 (m) cc_final: 0.7194 (p) REVERT: A 73 SER cc_start: 0.7923 (m) cc_final: 0.7438 (t) REVERT: A 122 MET cc_start: 0.7121 (tmm) cc_final: 0.6025 (tmm) REVERT: A 138 SER cc_start: 0.7632 (m) cc_final: 0.7309 (t) REVERT: A 264 ARG cc_start: 0.4416 (mtp85) cc_final: 0.4183 (mtm110) REVERT: A 366 TYR cc_start: 0.6563 (m-80) cc_final: 0.6072 (m-80) REVERT: A 386 GLN cc_start: 0.7369 (mm-40) cc_final: 0.6928 (tt0) REVERT: A 387 ILE cc_start: 0.7163 (mt) cc_final: 0.6943 (mt) REVERT: H 20 SER cc_start: 0.8013 (m) cc_final: 0.7640 (p) REVERT: H 37 LEU cc_start: 0.7967 (mm) cc_final: 0.7654 (mt) REVERT: N 95 TYR cc_start: 0.6026 (m-10) cc_final: 0.5722 (m-10) REVERT: L 32 SER cc_start: 0.8161 (t) cc_final: 0.7796 (p) REVERT: L 37 TYR cc_start: 0.8353 (m-80) cc_final: 0.8124 (m-80) REVERT: L 43 LYS cc_start: 0.8688 (mttt) cc_final: 0.8401 (mtpp) REVERT: L 48 LEU cc_start: 0.7888 (tp) cc_final: 0.7594 (tp) REVERT: L 87 TYR cc_start: 0.8442 (m-80) cc_final: 0.7772 (m-80) REVERT: L 92 TYR cc_start: 0.8354 (p90) cc_final: 0.7937 (p90) REVERT: L 142 TYR cc_start: 0.7443 (t80) cc_final: 0.6977 (t80) outliers start: 19 outliers final: 17 residues processed: 205 average time/residue: 0.1936 time to fit residues: 54.9500 Evaluate side-chains 212 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 195 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -69 LEU Chi-restraints excluded: chain A residue -26 GLU Chi-restraints excluded: chain A residue -18 PHE Chi-restraints excluded: chain A residue -11 ILE Chi-restraints excluded: chain A residue -7 LEU Chi-restraints excluded: chain A residue 26 ARG Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 160 PHE Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 64 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.3980 chunk 57 optimal weight: 0.9980 chunk 73 optimal weight: 0.0770 chunk 56 optimal weight: 2.9990 chunk 84 optimal weight: 0.4980 chunk 100 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 46 optimal weight: 0.3980 chunk 40 optimal weight: 0.3980 chunk 59 optimal weight: 0.3980 overall best weight: 0.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A -70 ASN ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6545 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8440 Z= 0.188 Angle : 0.607 10.591 11484 Z= 0.299 Chirality : 0.041 0.141 1296 Planarity : 0.004 0.065 1437 Dihedral : 4.667 41.297 1163 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.91 % Allowed : 18.03 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.26), residues: 1045 helix: 0.78 (0.27), residues: 387 sheet: -0.66 (0.34), residues: 243 loop : -1.70 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 168 HIS 0.004 0.001 HIS A 355 PHE 0.019 0.001 PHE H 136 TYR 0.023 0.002 TYR H 53 ARG 0.012 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 194 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A -56 LYS cc_start: 0.8264 (tttt) cc_final: 0.8021 (ttpt) REVERT: A -51 LYS cc_start: 0.7617 (tttt) cc_final: 0.7276 (mtmm) REVERT: A 71 VAL cc_start: 0.7463 (m) cc_final: 0.7162 (p) REVERT: A 73 SER cc_start: 0.7972 (m) cc_final: 0.7526 (t) REVERT: A 138 SER cc_start: 0.7621 (m) cc_final: 0.7340 (t) REVERT: A 264 ARG cc_start: 0.4414 (mtp85) cc_final: 0.4157 (mtm110) REVERT: A 386 GLN cc_start: 0.7360 (mm-40) cc_final: 0.6904 (tt0) REVERT: A 387 ILE cc_start: 0.7159 (mt) cc_final: 0.6933 (mt) REVERT: H 20 SER cc_start: 0.8013 (m) cc_final: 0.7617 (p) REVERT: H 37 LEU cc_start: 0.7970 (mm) cc_final: 0.7657 (mt) REVERT: L 32 SER cc_start: 0.8156 (t) cc_final: 0.7727 (p) REVERT: L 36 TRP cc_start: 0.8208 (m100) cc_final: 0.7799 (m100) REVERT: L 43 LYS cc_start: 0.8695 (mttt) cc_final: 0.8406 (mtpp) REVERT: L 48 LEU cc_start: 0.7961 (tp) cc_final: 0.7611 (tp) REVERT: L 74 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7958 (tt) REVERT: L 92 TYR cc_start: 0.8349 (p90) cc_final: 0.7829 (p90) REVERT: L 142 TYR cc_start: 0.7459 (t80) cc_final: 0.6950 (t80) outliers start: 26 outliers final: 22 residues processed: 204 average time/residue: 0.1878 time to fit residues: 53.2563 Evaluate side-chains 216 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 193 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -70 ASN Chi-restraints excluded: chain A residue -69 LEU Chi-restraints excluded: chain A residue -26 GLU Chi-restraints excluded: chain A residue -18 PHE Chi-restraints excluded: chain A residue -11 ILE Chi-restraints excluded: chain A residue -7 LEU Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 160 PHE Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 74 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 91 optimal weight: 0.2980 chunk 96 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A -70 ASN ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 185 GLN ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 8440 Z= 0.281 Angle : 0.668 11.561 11484 Z= 0.337 Chirality : 0.043 0.161 1296 Planarity : 0.005 0.063 1437 Dihedral : 4.986 34.055 1163 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 2.80 % Allowed : 18.25 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.26), residues: 1045 helix: 0.56 (0.26), residues: 387 sheet: -0.69 (0.33), residues: 239 loop : -1.73 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 168 HIS 0.004 0.001 HIS A 355 PHE 0.021 0.002 PHE H 136 TYR 0.032 0.002 TYR H 53 ARG 0.010 0.001 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 203 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A -56 LYS cc_start: 0.8396 (tttt) cc_final: 0.8191 (ttpt) REVERT: A -51 LYS cc_start: 0.7720 (tttt) cc_final: 0.7342 (mtmm) REVERT: A 71 VAL cc_start: 0.7424 (m) cc_final: 0.7082 (p) REVERT: A 73 SER cc_start: 0.8068 (m) cc_final: 0.7626 (t) REVERT: A 99 GLN cc_start: 0.7693 (tt0) cc_final: 0.7193 (tt0) REVERT: A 122 MET cc_start: 0.7217 (tmm) cc_final: 0.6574 (tmm) REVERT: A 138 SER cc_start: 0.7575 (m) cc_final: 0.7298 (t) REVERT: A 294 GLU cc_start: 0.6735 (tt0) cc_final: 0.6503 (tt0) REVERT: A 366 TYR cc_start: 0.6946 (m-80) cc_final: 0.6663 (m-80) REVERT: A 386 GLN cc_start: 0.7365 (mm-40) cc_final: 0.6864 (tt0) REVERT: A 387 ILE cc_start: 0.7170 (mt) cc_final: 0.6919 (mt) REVERT: H 20 SER cc_start: 0.8214 (m) cc_final: 0.7789 (p) REVERT: H 37 LEU cc_start: 0.7953 (mm) cc_final: 0.7657 (mt) REVERT: H 63 TYR cc_start: 0.7779 (m-10) cc_final: 0.7547 (m-10) REVERT: H 155 LEU cc_start: 0.7526 (tp) cc_final: 0.7252 (tt) REVERT: H 168 TRP cc_start: 0.7312 (m100) cc_final: 0.7003 (m100) REVERT: H 206 GLN cc_start: 0.7064 (tt0) cc_final: 0.6769 (tt0) REVERT: L 32 SER cc_start: 0.8225 (t) cc_final: 0.7865 (p) REVERT: L 36 TRP cc_start: 0.8276 (m100) cc_final: 0.7897 (m100) REVERT: L 48 LEU cc_start: 0.7934 (tp) cc_final: 0.7605 (tp) REVERT: L 74 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7869 (tt) REVERT: L 90 GLN cc_start: 0.8039 (pt0) cc_final: 0.7795 (pt0) REVERT: L 92 TYR cc_start: 0.8356 (p90) cc_final: 0.7879 (p90) REVERT: L 142 TYR cc_start: 0.7535 (t80) cc_final: 0.7064 (t80) REVERT: L 166 THR cc_start: 0.8570 (t) cc_final: 0.8159 (m) outliers start: 25 outliers final: 18 residues processed: 215 average time/residue: 0.2004 time to fit residues: 58.6961 Evaluate side-chains 218 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 199 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -69 LEU Chi-restraints excluded: chain A residue -18 PHE Chi-restraints excluded: chain A residue -11 ILE Chi-restraints excluded: chain A residue -7 LEU Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 74 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 40 optimal weight: 0.0980 chunk 73 optimal weight: 0.7980 chunk 28 optimal weight: 0.0980 chunk 84 optimal weight: 1.9990 chunk 88 optimal weight: 0.0570 chunk 93 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 overall best weight: 0.2898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 160 ASN ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6569 moved from start: 0.5132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8440 Z= 0.187 Angle : 0.644 9.333 11484 Z= 0.316 Chirality : 0.041 0.174 1296 Planarity : 0.005 0.065 1437 Dihedral : 4.776 36.408 1163 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.24 % Allowed : 19.71 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % 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: -0.79 (0.27), residues: 1045 helix: 0.75 (0.26), residues: 389 sheet: -0.62 (0.33), residues: 246 loop : -1.65 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.004 0.001 HIS A 355 PHE 0.020 0.001 PHE H 136 TYR 0.034 0.002 TYR A 149 ARG 0.009 0.001 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 203 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A -56 LYS cc_start: 0.8320 (tttt) cc_final: 0.8107 (ttpt) REVERT: A -51 LYS cc_start: 0.7625 (tttt) cc_final: 0.7274 (mtmm) REVERT: A 71 VAL cc_start: 0.7356 (m) cc_final: 0.7026 (p) REVERT: A 73 SER cc_start: 0.8045 (m) cc_final: 0.7563 (t) REVERT: A 99 GLN cc_start: 0.7732 (tt0) cc_final: 0.7151 (tt0) REVERT: A 122 MET cc_start: 0.7303 (tmm) cc_final: 0.6570 (tmm) REVERT: A 138 SER cc_start: 0.7629 (m) cc_final: 0.7308 (t) REVERT: A 264 ARG cc_start: 0.4136 (mtm110) cc_final: 0.3840 (mtp85) REVERT: A 366 TYR cc_start: 0.6781 (m-80) cc_final: 0.6383 (m-80) REVERT: A 386 GLN cc_start: 0.7347 (mm-40) cc_final: 0.6920 (tt0) REVERT: A 387 ILE cc_start: 0.7171 (mt) cc_final: 0.6934 (mt) REVERT: H 20 SER cc_start: 0.8081 (m) cc_final: 0.7659 (p) REVERT: H 37 LEU cc_start: 0.7920 (mm) cc_final: 0.7657 (mt) REVERT: H 155 LEU cc_start: 0.7525 (tp) cc_final: 0.7308 (tt) REVERT: L 32 SER cc_start: 0.8137 (t) cc_final: 0.7744 (p) REVERT: L 36 TRP cc_start: 0.8224 (m100) cc_final: 0.7841 (m100) REVERT: L 48 LEU cc_start: 0.7977 (tp) cc_final: 0.7686 (tp) REVERT: L 74 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7878 (tt) REVERT: L 90 GLN cc_start: 0.7979 (pt0) cc_final: 0.7639 (pt0) REVERT: L 92 TYR cc_start: 0.8353 (p90) cc_final: 0.7835 (p90) REVERT: L 142 TYR cc_start: 0.7470 (t80) cc_final: 0.6955 (t80) outliers start: 20 outliers final: 17 residues processed: 212 average time/residue: 0.1998 time to fit residues: 58.1609 Evaluate side-chains 219 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 201 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -69 LEU Chi-restraints excluded: chain A residue -18 PHE Chi-restraints excluded: chain A residue -11 ILE Chi-restraints excluded: chain A residue -7 LEU Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 74 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 103 optimal weight: 0.0980 chunk 95 optimal weight: 0.0010 chunk 82 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 63 optimal weight: 0.0670 chunk 50 optimal weight: 0.8980 chunk 65 optimal weight: 0.0970 chunk 87 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A -70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 160 ASN ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6533 moved from start: 0.5106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8440 Z= 0.169 Angle : 0.648 12.204 11484 Z= 0.315 Chirality : 0.041 0.172 1296 Planarity : 0.004 0.061 1437 Dihedral : 4.666 33.238 1163 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.24 % Allowed : 19.93 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % 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: -0.60 (0.27), residues: 1045 helix: 0.91 (0.26), residues: 390 sheet: -0.43 (0.34), residues: 243 loop : -1.63 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 168 HIS 0.004 0.001 HIS A 355 PHE 0.020 0.001 PHE H 136 TYR 0.039 0.002 TYR A 149 ARG 0.008 0.000 ARG A 373 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 199 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A -56 LYS cc_start: 0.8268 (tttt) cc_final: 0.8051 (ttpt) REVERT: A -51 LYS cc_start: 0.7534 (tttt) cc_final: 0.7197 (mtmm) REVERT: A 71 VAL cc_start: 0.7344 (m) cc_final: 0.7049 (p) REVERT: A 73 SER cc_start: 0.7870 (m) cc_final: 0.7418 (t) REVERT: A 99 GLN cc_start: 0.7732 (tt0) cc_final: 0.7176 (tt0) REVERT: A 122 MET cc_start: 0.7292 (tmm) cc_final: 0.6587 (tmm) REVERT: A 264 ARG cc_start: 0.4017 (mtm110) cc_final: 0.3656 (mtm110) REVERT: A 366 TYR cc_start: 0.6646 (m-80) cc_final: 0.6283 (m-80) REVERT: A 386 GLN cc_start: 0.7335 (mm-40) cc_final: 0.6930 (tt0) REVERT: A 387 ILE cc_start: 0.7135 (mt) cc_final: 0.6935 (mt) REVERT: H 20 SER cc_start: 0.7772 (m) cc_final: 0.7318 (p) REVERT: H 37 LEU cc_start: 0.7960 (mm) cc_final: 0.7646 (mt) REVERT: H 198 VAL cc_start: 0.8637 (p) cc_final: 0.8422 (m) REVERT: L 32 SER cc_start: 0.8143 (t) cc_final: 0.7700 (p) REVERT: L 36 TRP cc_start: 0.8213 (m100) cc_final: 0.7803 (m100) REVERT: L 48 LEU cc_start: 0.8110 (tp) cc_final: 0.7776 (tp) REVERT: L 74 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7853 (tt) REVERT: L 92 TYR cc_start: 0.8344 (p90) cc_final: 0.7609 (p90) REVERT: L 142 TYR cc_start: 0.7460 (t80) cc_final: 0.6922 (t80) outliers start: 20 outliers final: 17 residues processed: 207 average time/residue: 0.2115 time to fit residues: 59.4997 Evaluate side-chains 214 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 196 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -69 LEU Chi-restraints excluded: chain A residue -18 PHE Chi-restraints excluded: chain A residue -11 ILE Chi-restraints excluded: chain A residue -7 LEU Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 74 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 4 optimal weight: 0.0370 chunk 59 optimal weight: 0.2980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A -70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 160 ASN ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.164797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.147156 restraints weight = 13067.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.150818 restraints weight = 7110.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.153191 restraints weight = 4396.991| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6569 moved from start: 0.5360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8440 Z= 0.231 Angle : 0.661 9.064 11484 Z= 0.329 Chirality : 0.043 0.161 1296 Planarity : 0.005 0.073 1437 Dihedral : 4.812 34.093 1163 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.24 % Allowed : 20.83 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % 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: -0.59 (0.27), residues: 1045 helix: 0.89 (0.26), residues: 389 sheet: -0.41 (0.34), residues: 237 loop : -1.57 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 168 HIS 0.004 0.001 HIS A 355 PHE 0.020 0.002 PHE H 136 TYR 0.037 0.002 TYR A 149 ARG 0.007 0.000 ARG A 373 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2181.08 seconds wall clock time: 41 minutes 3.17 seconds (2463.17 seconds total)