Starting phenix.real_space_refine on Thu Jul 2 05:11:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wp8_32678/07_2026/7wp8_32678.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wp8_32678/07_2026/7wp8_32678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wp8_32678/07_2026/7wp8_32678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wp8_32678/07_2026/7wp8_32678.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7wp8_32678/07_2026/7wp8_32678.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wp8_32678/07_2026/7wp8_32678.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wp8_32678/07_2026/7wp8_32678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wp8_32678/07_2026/7wp8_32678.map" } resolution = 3.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 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 31 5.16 5 C 4313 2.51 5 N 1123 2.21 5 O 1330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6797 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 805 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 98} Chain: "D" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 919 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "E" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 966 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "F" Number of atoms: 1470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1470 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 173} Chain: "G" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 874 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 107} Chain: "H" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 930 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "L" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 791 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 97} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.36, per 1000 atoms: 0.20 Number of scatterers: 6797 At special positions: 0 Unit cell: (89.47, 112.032, 112.032, 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 31 16.00 O 1330 8.00 N 1123 7.00 C 4313 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.15 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 94 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " 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 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN F 343 " " NAG L 201 " - " ASN L 26 " Time building additional restraints: 0.37 Conformation dependent library (CDL) restraints added in 331.1 milliseconds 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB VAL F 503 " Number of C-beta restraints generated: 1574 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 21 sheets defined 3.6% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.850A pdb=" N ARG D 31 " --> pdb=" O THR D 28 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.866A pdb=" N SER D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.703A pdb=" N ASP E 90 " --> pdb=" O THR E 87 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing helix chain 'F' and resid 403 through 410 removed outlier: 3.524A pdb=" N GLU F 406 " --> pdb=" O ARG F 403 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ARG F 408 " --> pdb=" O ASP F 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.893A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 5 through 6 removed outlier: 4.160A pdb=" N ASP C 70 " --> pdb=" O SER C 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.158A pdb=" N LEU C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 47 " --> pdb=" O TRP C 35 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.697A pdb=" N LEU D 4 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER D 25 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR D 78 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 18 through 19 Processing sheet with id=AA5, first strand: chain 'D' and resid 59 through 60 removed outlier: 6.289A pdb=" N TRP D 47 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LYS D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ARG D 98 " --> pdb=" O ALA D 108 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 59 through 60 removed outlier: 6.289A pdb=" N TRP D 47 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LYS D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 3 through 5 removed outlier: 3.511A pdb=" N THR E 71 " --> pdb=" O TYR E 80 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 9 through 12 Processing sheet with id=AA9, first strand: chain 'E' and resid 59 through 60 removed outlier: 3.565A pdb=" N HIS E 59 " --> pdb=" O ARG E 50 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ARG E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N MET E 34 " --> pdb=" O ARG E 50 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL E 37 " --> pdb=" O TYR E 95 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N TYR E 108 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 357 through 358 removed outlier: 3.737A pdb=" N ASP F 398 " --> pdb=" O VAL F 512 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL F 433 " --> pdb=" O LYS F 378 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS F 378 " --> pdb=" O VAL F 433 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.502A pdb=" N MET G 13 " --> pdb=" O GLU G 111 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 19 through 20 Processing sheet with id=AB5, first strand: chain 'G' and resid 50 through 52 Processing sheet with id=AB6, first strand: chain 'G' and resid 54 through 55 removed outlier: 3.783A pdb=" N THR G 59 " --> pdb=" O TYR G 55 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.590A pdb=" N GLU H 10 " --> pdb=" O THR H 115 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR H 112 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR H 94 " --> pdb=" O THR H 112 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU H 114 " --> pdb=" O ALA H 92 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.518A pdb=" N ILE H 59 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY H 98 " --> pdb=" O PHE H 107 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AC2, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.727A pdb=" N TYR L 70 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER L 69 " --> pdb=" O SER L 66 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 43 through 47 removed outlier: 6.722A pdb=" N TRP L 34 " --> pdb=" O TRP L 46 " (cutoff:3.500A) 143 hydrogen bonds defined for protein. 321 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: 0.87 Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 1092 1.25 - 1.39: 1865 1.39 - 1.54: 3785 1.54 - 1.68: 193 1.68 - 1.82: 42 Bond restraints: 6977 Sorted by residual: bond pdb=" CA VAL F 503 " pdb=" C VAL F 503 " ideal model delta sigma weight residual 1.523 1.336 0.188 1.27e-02 6.20e+03 2.18e+02 bond pdb=" C GLN F 498 " pdb=" N PRO F 499 " ideal model delta sigma weight residual 1.337 1.206 0.131 1.11e-02 8.12e+03 1.39e+02 bond pdb=" CA VAL F 503 " pdb=" CB VAL F 503 " ideal model delta sigma weight residual 1.540 1.400 0.141 1.25e-02 6.40e+03 1.26e+02 bond pdb=" CA GLN F 498 " pdb=" C GLN F 498 " ideal model delta sigma weight residual 1.524 1.390 0.134 1.28e-02 6.10e+03 1.09e+02 bond pdb=" C VAL F 503 " pdb=" O VAL F 503 " ideal model delta sigma weight residual 1.237 1.121 0.116 1.17e-02 7.31e+03 9.88e+01 ... (remaining 6972 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 9196 2.50 - 5.01: 214 5.01 - 7.51: 44 7.51 - 10.02: 14 10.02 - 12.52: 7 Bond angle restraints: 9475 Sorted by residual: angle pdb=" N VAL F 503 " pdb=" CA VAL F 503 " pdb=" CB VAL F 503 " ideal model delta sigma weight residual 110.54 123.06 -12.52 1.36e+00 5.41e-01 8.48e+01 angle pdb=" CA GLY F 504 " pdb=" C GLY F 504 " pdb=" O GLY F 504 " ideal model delta sigma weight residual 120.75 111.28 9.47 1.03e+00 9.43e-01 8.46e+01 angle pdb=" C GLN F 498 " pdb=" N PRO F 499 " pdb=" CA PRO F 499 " ideal model delta sigma weight residual 119.87 129.27 -9.40 1.04e+00 9.25e-01 8.17e+01 angle pdb=" CA PRO F 499 " pdb=" C PRO F 499 " pdb=" O PRO F 499 " ideal model delta sigma weight residual 118.86 108.34 10.52 1.38e+00 5.25e-01 5.82e+01 angle pdb=" N THR E 113 " pdb=" CA THR E 113 " pdb=" C THR E 113 " ideal model delta sigma weight residual 108.52 120.80 -12.28 1.63e+00 3.76e-01 5.68e+01 ... (remaining 9470 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 3631 17.87 - 35.74: 351 35.74 - 53.61: 53 53.61 - 71.48: 9 71.48 - 89.35: 12 Dihedral angle restraints: 4056 sinusoidal: 1570 harmonic: 2486 Sorted by residual: dihedral pdb=" CA TYR G 55 " pdb=" C TYR G 55 " pdb=" N PHE G 56 " pdb=" CA PHE G 56 " ideal model delta harmonic sigma weight residual 180.00 -132.22 -47.78 0 5.00e+00 4.00e-02 9.13e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual -86.00 0.81 -86.81 1 1.00e+01 1.00e-02 9.07e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 157.16 -64.16 1 1.00e+01 1.00e-02 5.42e+01 ... (remaining 4053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.531: 1006 0.531 - 1.062: 0 1.062 - 1.593: 0 1.593 - 2.124: 0 2.124 - 2.655: 1 Chirality restraints: 1007 Sorted by residual: chirality pdb=" CA VAL F 503 " pdb=" N VAL F 503 " pdb=" C VAL F 503 " pdb=" CB VAL F 503 " both_signs ideal model delta sigma weight residual False 2.44 -0.21 2.66 2.00e-01 2.50e+01 1.76e+02 chirality pdb=" CA PRO F 499 " pdb=" N PRO F 499 " pdb=" C PRO F 499 " pdb=" CB PRO F 499 " both_signs ideal model delta sigma weight residual False 2.72 2.31 0.40 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" CA ASN F 343 " pdb=" N ASN F 343 " pdb=" C ASN F 343 " pdb=" CB ASN F 343 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.74e+00 ... (remaining 1004 not shown) Planarity restraints: 1214 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 1 " 0.310 2.00e-02 2.50e+03 2.59e-01 8.41e+02 pdb=" C7 NAG A 1 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG A 1 " 0.191 2.00e-02 2.50e+03 pdb=" N2 NAG A 1 " -0.444 2.00e-02 2.50e+03 pdb=" O7 NAG A 1 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 201 " -0.201 2.00e-02 2.50e+03 1.65e-01 3.39e+02 pdb=" C7 NAG L 201 " 0.059 2.00e-02 2.50e+03 pdb=" C8 NAG L 201 " -0.148 2.00e-02 2.50e+03 pdb=" N2 NAG L 201 " 0.263 2.00e-02 2.50e+03 pdb=" O7 NAG L 201 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 2 " 0.151 2.00e-02 2.50e+03 1.24e-01 1.93e+02 pdb=" C7 NAG A 2 " -0.043 2.00e-02 2.50e+03 pdb=" C8 NAG A 2 " 0.113 2.00e-02 2.50e+03 pdb=" N2 NAG A 2 " -0.199 2.00e-02 2.50e+03 pdb=" O7 NAG A 2 " -0.022 2.00e-02 2.50e+03 ... (remaining 1211 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1556 2.78 - 3.31: 5631 3.31 - 3.84: 11082 3.84 - 4.37: 12156 4.37 - 4.90: 21565 Nonbonded interactions: 51990 Sorted by model distance: nonbonded pdb=" O GLY F 447 " pdb=" OH TYR H 33 " model vdw 2.250 3.040 nonbonded pdb=" CG2 VAL F 503 " pdb=" OE1 GLN F 506 " model vdw 2.269 3.460 nonbonded pdb=" OG SER D 17 " pdb=" O LEU D 83 " model vdw 2.276 3.040 nonbonded pdb=" OG SER C 43 " pdb=" O GLY D 111 " model vdw 2.283 3.040 nonbonded pdb=" O THR H 112 " pdb=" OG1 THR H 112 " model vdw 2.296 3.040 ... (remaining 51985 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: 6.030 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: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.120 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 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 : 0.008 0.188 6987 Z= 0.544 Angle : 1.072 31.715 9498 Z= 0.616 Chirality : 0.106 2.655 1007 Planarity : 0.012 0.259 1212 Dihedral : 14.628 89.355 2461 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.97 % Favored : 90.91 % Rotamer: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.12 (0.25), residues: 847 helix: -4.94 (0.50), residues: 8 sheet: -2.25 (0.29), residues: 284 loop : -3.16 (0.22), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 99 TYR 0.029 0.002 TYR D 104 PHE 0.017 0.002 PHE G 104 TRP 0.016 0.002 TRP E 33 HIS 0.008 0.002 HIS H 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00832 / 0.54 ( 6977) covalent geometry : angle 1.00631 / 0.59 ( 9475) SS BOND : bond 0.04502 / 1.67 ( 7) SS BOND : angle 9.41555 / 5.21 ( 14) hydrogen bonds : bond 0.30581 / 21.65 ( 132) hydrogen bonds : angle 12.38828 / 8.40 ( 321) link_BETA1-4 : bond 0.00742 / 0.39 ( 1) link_BETA1-4 : angle 2.55604 / 1.32 ( 3) link_NAG-ASN : bond 0.00950 / 0.50 ( 2) link_NAG-ASN : angle 3.38705 / 1.73 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 MET cc_start: 0.8524 (mmm) cc_final: 0.8310 (mmt) REVERT: D 38 LYS cc_start: 0.8200 (ptmt) cc_final: 0.7776 (ttpt) REVERT: E 13 ARG cc_start: 0.7980 (mmt180) cc_final: 0.7345 (mtp85) REVERT: E 46 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7574 (mt-10) REVERT: E 65 LYS cc_start: 0.7906 (mttt) cc_final: 0.7594 (mtmt) REVERT: G 13 MET cc_start: 0.7521 (tpt) cc_final: 0.7214 (tpt) REVERT: G 35 GLN cc_start: 0.8008 (mp10) cc_final: 0.7519 (mp10) REVERT: G 78 THR cc_start: 0.9036 (p) cc_final: 0.8799 (p) REVERT: G 85 GLN cc_start: 0.8801 (mm110) cc_final: 0.8514 (mm110) REVERT: H 29 PHE cc_start: 0.7988 (t80) cc_final: 0.7696 (t80) REVERT: H 60 TYR cc_start: 0.8299 (m-80) cc_final: 0.7759 (m-80) REVERT: L 4 LEU cc_start: 0.8584 (mt) cc_final: 0.8255 (mp) REVERT: L 37 GLN cc_start: 0.6974 (tm-30) cc_final: 0.6514 (tm-30) REVERT: L 88 GLN cc_start: 0.8262 (mp10) cc_final: 0.8020 (mp10) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.0981 time to fit residues: 27.7613 Evaluate side-chains 166 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.0870 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 GLN D 39 GLN ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 448 ASN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 ASN H 101 HIS ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.130949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.106149 restraints weight = 12502.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.108786 restraints weight = 7888.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.110560 restraints weight = 5874.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.111656 restraints weight = 4852.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.112464 restraints weight = 4298.306| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6987 Z= 0.144 Angle : 0.668 7.736 9498 Z= 0.348 Chirality : 0.046 0.175 1007 Planarity : 0.005 0.068 1212 Dihedral : 6.257 61.174 949 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 1.78 % Allowed : 14.62 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.62 (0.26), residues: 847 helix: -4.75 (0.69), residues: 8 sheet: -1.87 (0.28), residues: 323 loop : -2.84 (0.24), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 60 TYR 0.027 0.002 TYR E 32 PHE 0.015 0.001 PHE G 104 TRP 0.022 0.001 TRP D 36 HIS 0.003 0.001 HIS G 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 6977) covalent geometry : angle 0.65410 / 0.35 ( 9475) SS BOND : bond 0.00413 / 0.17 ( 7) SS BOND : angle 1.29316 / 0.65 ( 14) hydrogen bonds : bond 0.03628 / 2.48 ( 132) hydrogen bonds : angle 7.94430 / 5.33 ( 321) link_BETA1-4 : bond 0.00623 / 0.33 ( 1) link_BETA1-4 : angle 1.38369 / 0.75 ( 3) link_NAG-ASN : bond 0.00256 / 0.12 ( 2) link_NAG-ASN : angle 5.03305 / 2.79 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 184 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 ARG cc_start: 0.7891 (mmt180) cc_final: 0.7636 (mmt180) REVERT: G 4 MET cc_start: 0.7923 (tpp) cc_final: 0.7288 (mmm) REVERT: G 35 GLN cc_start: 0.7985 (mp10) cc_final: 0.7738 (mp10) REVERT: G 55 TYR cc_start: 0.7831 (p90) cc_final: 0.7630 (p90) REVERT: G 78 THR cc_start: 0.9071 (p) cc_final: 0.8871 (p) REVERT: H 29 PHE cc_start: 0.7869 (t80) cc_final: 0.7601 (t80) REVERT: H 81 MET cc_start: 0.6133 (ttt) cc_final: 0.5931 (ttt) REVERT: H 106 ASP cc_start: 0.7180 (m-30) cc_final: 0.6816 (m-30) REVERT: L 32 MET cc_start: 0.7654 (mtp) cc_final: 0.7441 (mtp) REVERT: L 37 GLN cc_start: 0.6557 (tm-30) cc_final: 0.6166 (tm-30) outliers start: 13 outliers final: 8 residues processed: 187 average time/residue: 0.1041 time to fit residues: 24.9383 Evaluate side-chains 176 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 168 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain L residue 22 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 55 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN D 43 GLN ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 HIS ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.128583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.104361 restraints weight = 12754.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.106701 restraints weight = 8130.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.108345 restraints weight = 6150.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.109425 restraints weight = 5143.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.109950 restraints weight = 4579.711| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6987 Z= 0.168 Angle : 0.645 6.461 9498 Z= 0.338 Chirality : 0.046 0.197 1007 Planarity : 0.004 0.053 1212 Dihedral : 6.005 55.701 949 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 2.60 % Allowed : 15.71 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.45 (0.26), residues: 847 helix: -4.85 (0.60), residues: 8 sheet: -1.68 (0.29), residues: 311 loop : -2.77 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 60 TYR 0.016 0.001 TYR G 55 PHE 0.016 0.002 PHE G 104 TRP 0.032 0.002 TRP D 36 HIS 0.004 0.001 HIS H 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 ( 6977) covalent geometry : angle 0.63617 / 0.34 ( 9475) SS BOND : bond 0.00277 / 0.10 ( 7) SS BOND : angle 1.17963 / 0.58 ( 14) hydrogen bonds : bond 0.03378 / 2.24 ( 132) hydrogen bonds : angle 7.23530 / 4.86 ( 321) link_BETA1-4 : bond 0.00597 / 0.31 ( 1) link_BETA1-4 : angle 1.45642 / 0.71 ( 3) link_NAG-ASN : bond 0.00274 / 0.14 ( 2) link_NAG-ASN : angle 3.95337 / 2.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 180 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 65 SER cc_start: 0.9019 (m) cc_final: 0.8778 (t) REVERT: D 29 PHE cc_start: 0.8603 (t80) cc_final: 0.8383 (t80) REVERT: E 13 ARG cc_start: 0.7911 (mmt180) cc_final: 0.7630 (mmt180) REVERT: G 4 MET cc_start: 0.7943 (tpp) cc_final: 0.7263 (mmm) REVERT: G 35 GLN cc_start: 0.8003 (mp10) cc_final: 0.7749 (mp10) REVERT: G 55 TYR cc_start: 0.7892 (p90) cc_final: 0.7622 (p90) REVERT: H 29 PHE cc_start: 0.8018 (t80) cc_final: 0.7718 (t80) REVERT: H 106 ASP cc_start: 0.7231 (m-30) cc_final: 0.6749 (m-30) REVERT: L 37 GLN cc_start: 0.6611 (tm130) cc_final: 0.6241 (tm-30) outliers start: 19 outliers final: 15 residues processed: 185 average time/residue: 0.1050 time to fit residues: 25.0460 Evaluate side-chains 177 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain F residue 418 ILE Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 22 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 25 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 22 optimal weight: 0.0070 chunk 26 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 1 GLN E 3 GLN F 439 ASN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.130187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.105392 restraints weight = 12645.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.107968 restraints weight = 7986.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.109701 restraints weight = 5974.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.110758 restraints weight = 4955.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.111613 restraints weight = 4411.841| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6987 Z= 0.129 Angle : 0.609 6.204 9498 Z= 0.318 Chirality : 0.044 0.149 1007 Planarity : 0.004 0.047 1212 Dihedral : 5.643 48.837 949 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 2.87 % Allowed : 16.80 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.23 (0.27), residues: 847 helix: -5.02 (0.43), residues: 14 sheet: -1.53 (0.29), residues: 320 loop : -2.57 (0.24), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 60 TYR 0.017 0.001 TYR G 55 PHE 0.017 0.001 PHE F 456 TRP 0.016 0.001 TRP D 36 HIS 0.002 0.001 HIS H 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 6977) covalent geometry : angle 0.60168 / 0.32 ( 9475) SS BOND : bond 0.00300 / 0.12 ( 7) SS BOND : angle 1.05260 / 0.50 ( 14) hydrogen bonds : bond 0.02924 / 1.97 ( 132) hydrogen bonds : angle 6.76752 / 4.54 ( 321) link_BETA1-4 : bond 0.00669 / 0.35 ( 1) link_BETA1-4 : angle 1.43090 / 0.71 ( 3) link_NAG-ASN : bond 0.00085 / 0.04 ( 2) link_NAG-ASN : angle 3.40638 / 1.83 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 65 SER cc_start: 0.9030 (m) cc_final: 0.8781 (t) REVERT: E 13 ARG cc_start: 0.7911 (mmt180) cc_final: 0.7624 (mmt180) REVERT: G 4 MET cc_start: 0.7973 (tpp) cc_final: 0.7714 (mmt) REVERT: G 13 MET cc_start: 0.6914 (tpt) cc_final: 0.6512 (tpt) REVERT: G 35 GLN cc_start: 0.7995 (mp10) cc_final: 0.7779 (mp10) REVERT: G 59 THR cc_start: 0.8015 (p) cc_final: 0.7639 (p) REVERT: H 29 PHE cc_start: 0.8020 (t80) cc_final: 0.7720 (t80) REVERT: H 106 ASP cc_start: 0.6832 (m-30) cc_final: 0.6450 (m-30) REVERT: L 37 GLN cc_start: 0.6594 (tm130) cc_final: 0.6193 (tm-30) outliers start: 21 outliers final: 13 residues processed: 184 average time/residue: 0.1002 time to fit residues: 23.9239 Evaluate side-chains 173 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain F residue 418 ILE Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 489 TYR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain L residue 22 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 63 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 5 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 1 GLN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.128873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.104469 restraints weight = 12893.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.106912 restraints weight = 8294.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.108506 restraints weight = 6252.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.109664 restraints weight = 5253.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.110340 restraints weight = 4650.387| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6987 Z= 0.163 Angle : 0.634 7.923 9498 Z= 0.331 Chirality : 0.045 0.185 1007 Planarity : 0.004 0.047 1212 Dihedral : 5.685 49.292 949 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 3.42 % Allowed : 17.49 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.16 (0.27), residues: 847 helix: -4.95 (0.48), residues: 14 sheet: -1.50 (0.29), residues: 330 loop : -2.52 (0.25), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 60 TYR 0.034 0.001 TYR G 55 PHE 0.018 0.002 PHE F 456 TRP 0.035 0.002 TRP D 36 HIS 0.005 0.001 HIS H 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 ( 6977) covalent geometry : angle 0.62791 / 0.33 ( 9475) SS BOND : bond 0.00258 / 0.10 ( 7) SS BOND : angle 0.96678 / 0.46 ( 14) hydrogen bonds : bond 0.02947 / 1.95 ( 132) hydrogen bonds : angle 6.64983 / 4.46 ( 321) link_BETA1-4 : bond 0.00515 / 0.27 ( 1) link_BETA1-4 : angle 1.33742 / 0.66 ( 3) link_NAG-ASN : bond 0.00233 / 0.12 ( 2) link_NAG-ASN : angle 3.25546 / 1.76 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 MET cc_start: 0.8242 (mmt) cc_final: 0.8035 (tpp) REVERT: C 45 LYS cc_start: 0.8910 (mtpt) cc_final: 0.8698 (mtmt) REVERT: E 13 ARG cc_start: 0.7903 (mmt180) cc_final: 0.7690 (mmt180) REVERT: E 37 VAL cc_start: 0.8268 (t) cc_final: 0.8062 (m) REVERT: F 501 TYR cc_start: 0.7582 (m-10) cc_final: 0.7361 (m-10) REVERT: G 4 MET cc_start: 0.7966 (tpp) cc_final: 0.7637 (mmt) REVERT: G 35 GLN cc_start: 0.7975 (mp10) cc_final: 0.7750 (mp10) REVERT: H 29 PHE cc_start: 0.8098 (t80) cc_final: 0.7813 (t80) REVERT: H 106 ASP cc_start: 0.6846 (OUTLIER) cc_final: 0.6401 (m-30) REVERT: L 37 GLN cc_start: 0.6698 (tm130) cc_final: 0.6327 (tm-30) outliers start: 25 outliers final: 19 residues processed: 166 average time/residue: 0.0931 time to fit residues: 20.3211 Evaluate side-chains 170 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain F residue 418 ILE Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 489 TYR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 22 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 80 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 26 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 42 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.128372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.103293 restraints weight = 12943.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.105793 restraints weight = 8291.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.107519 restraints weight = 6267.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.108544 restraints weight = 5224.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.109375 restraints weight = 4662.928| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6987 Z= 0.184 Angle : 0.654 7.168 9498 Z= 0.342 Chirality : 0.045 0.165 1007 Planarity : 0.004 0.049 1212 Dihedral : 5.833 50.037 949 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 3.55 % Allowed : 18.99 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.05 (0.27), residues: 847 helix: -4.97 (0.46), residues: 14 sheet: -1.42 (0.29), residues: 336 loop : -2.45 (0.25), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 60 TYR 0.031 0.002 TYR G 55 PHE 0.017 0.002 PHE F 456 TRP 0.024 0.002 TRP D 36 HIS 0.005 0.001 HIS H 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 ( 6977) covalent geometry : angle 0.64825 / 0.34 ( 9475) SS BOND : bond 0.00280 / 0.12 ( 7) SS BOND : angle 1.03658 / 0.50 ( 14) hydrogen bonds : bond 0.03012 / 1.99 ( 132) hydrogen bonds : angle 6.58390 / 4.42 ( 321) link_BETA1-4 : bond 0.00653 / 0.34 ( 1) link_BETA1-4 : angle 1.27452 / 0.63 ( 3) link_NAG-ASN : bond 0.00241 / 0.13 ( 2) link_NAG-ASN : angle 3.32397 / 1.81 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 LYS cc_start: 0.8947 (mtpt) cc_final: 0.8738 (mtmt) REVERT: E 13 ARG cc_start: 0.7909 (mmt180) cc_final: 0.7685 (mmt180) REVERT: E 37 VAL cc_start: 0.8335 (t) cc_final: 0.8134 (m) REVERT: G 4 MET cc_start: 0.8010 (tpp) cc_final: 0.7330 (mmm) REVERT: G 35 GLN cc_start: 0.7921 (mp10) cc_final: 0.7711 (mp10) REVERT: G 55 TYR cc_start: 0.8003 (p90) cc_final: 0.7760 (p90) REVERT: H 29 PHE cc_start: 0.8114 (t80) cc_final: 0.7832 (t80) REVERT: H 106 ASP cc_start: 0.6814 (OUTLIER) cc_final: 0.6492 (m-30) REVERT: L 37 GLN cc_start: 0.6666 (tm130) cc_final: 0.6299 (tm-30) outliers start: 26 outliers final: 23 residues processed: 161 average time/residue: 0.0929 time to fit residues: 19.5751 Evaluate side-chains 173 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain F residue 418 ILE Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 489 TYR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 77 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 14 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 1 optimal weight: 0.0870 chunk 32 optimal weight: 0.4980 chunk 49 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 chunk 2 optimal weight: 0.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.131318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.106702 restraints weight = 12475.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.109292 restraints weight = 7938.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.111081 restraints weight = 5936.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.112196 restraints weight = 4913.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.112828 restraints weight = 4355.347| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6987 Z= 0.126 Angle : 0.639 9.444 9498 Z= 0.329 Chirality : 0.045 0.184 1007 Planarity : 0.004 0.044 1212 Dihedral : 5.518 45.717 949 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.87 % Allowed : 20.08 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.95 (0.27), residues: 847 helix: -4.85 (0.56), residues: 14 sheet: -1.30 (0.29), residues: 332 loop : -2.42 (0.25), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 76 TYR 0.026 0.001 TYR G 55 PHE 0.018 0.001 PHE G 104 TRP 0.020 0.001 TRP D 36 HIS 0.001 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 6977) covalent geometry : angle 0.63361 / 0.33 ( 9475) SS BOND : bond 0.00243 / 0.11 ( 7) SS BOND : angle 0.87597 / 0.42 ( 14) hydrogen bonds : bond 0.02572 / 1.71 ( 132) hydrogen bonds : angle 6.29008 / 4.23 ( 321) link_BETA1-4 : bond 0.00609 / 0.32 ( 1) link_BETA1-4 : angle 1.46101 / 0.71 ( 3) link_NAG-ASN : bond 0.00146 / 0.08 ( 2) link_NAG-ASN : angle 2.95626 / 1.61 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 LYS cc_start: 0.8904 (mtpt) cc_final: 0.8693 (mtmt) REVERT: E 13 ARG cc_start: 0.7891 (mmt180) cc_final: 0.7617 (mmt180) REVERT: F 454 ARG cc_start: 0.8711 (tpp80) cc_final: 0.8428 (ttm110) REVERT: F 462 LYS cc_start: 0.9084 (mptt) cc_final: 0.8862 (mmtp) REVERT: G 55 TYR cc_start: 0.7747 (p90) cc_final: 0.7538 (p90) REVERT: G 98 TYR cc_start: 0.7681 (t80) cc_final: 0.7443 (t80) REVERT: H 29 PHE cc_start: 0.8102 (t80) cc_final: 0.7799 (t80) REVERT: L 37 GLN cc_start: 0.6587 (tm130) cc_final: 0.6227 (tm-30) outliers start: 21 outliers final: 17 residues processed: 167 average time/residue: 0.0978 time to fit residues: 21.1330 Evaluate side-chains 166 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 489 TYR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 93 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 19 optimal weight: 4.9990 chunk 37 optimal weight: 0.1980 chunk 79 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 22 optimal weight: 7.9990 chunk 80 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 89 GLN ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN G 43 GLN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.130800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.106195 restraints weight = 12685.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.108859 restraints weight = 8000.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.110645 restraints weight = 5942.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.111829 restraints weight = 4910.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.112475 restraints weight = 4322.246| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6987 Z= 0.140 Angle : 0.663 7.832 9498 Z= 0.342 Chirality : 0.046 0.265 1007 Planarity : 0.004 0.042 1212 Dihedral : 5.489 46.028 949 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 3.01 % Allowed : 19.54 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.27), residues: 847 helix: -4.79 (0.60), residues: 14 sheet: -1.30 (0.29), residues: 336 loop : -2.36 (0.25), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 76 TYR 0.024 0.001 TYR G 55 PHE 0.017 0.001 PHE F 456 TRP 0.048 0.002 TRP D 36 HIS 0.003 0.001 HIS H 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 6977) covalent geometry : angle 0.65851 / 0.34 ( 9475) SS BOND : bond 0.00236 / 0.10 ( 7) SS BOND : angle 0.94061 / 0.45 ( 14) hydrogen bonds : bond 0.02702 / 1.79 ( 132) hydrogen bonds : angle 6.21302 / 4.19 ( 321) link_BETA1-4 : bond 0.00564 / 0.30 ( 1) link_BETA1-4 : angle 1.32627 / 0.65 ( 3) link_NAG-ASN : bond 0.00151 / 0.08 ( 2) link_NAG-ASN : angle 2.96009 / 1.60 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 LYS cc_start: 0.8908 (mtpt) cc_final: 0.8696 (mtmt) REVERT: C 89 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7967 (tt0) REVERT: D 29 PHE cc_start: 0.8586 (t80) cc_final: 0.8354 (t80) REVERT: E 13 ARG cc_start: 0.7868 (mmt180) cc_final: 0.7405 (mmm160) REVERT: E 37 VAL cc_start: 0.8467 (t) cc_final: 0.8224 (m) REVERT: G 21 MET cc_start: 0.7471 (mtp) cc_final: 0.7262 (mtt) REVERT: H 29 PHE cc_start: 0.8087 (t80) cc_final: 0.7794 (t80) REVERT: H 63 LYS cc_start: 0.8230 (mttp) cc_final: 0.7907 (ttmm) REVERT: L 37 GLN cc_start: 0.6623 (tm130) cc_final: 0.6247 (tm-30) outliers start: 22 outliers final: 19 residues processed: 167 average time/residue: 0.0956 time to fit residues: 20.7773 Evaluate side-chains 172 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain F residue 418 ILE Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 489 TYR Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 22 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 40 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 34 optimal weight: 0.0970 chunk 57 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 HIS ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.131477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.106766 restraints weight = 12649.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.109409 restraints weight = 8068.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.111254 restraints weight = 5980.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.112448 restraints weight = 4921.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.113043 restraints weight = 4334.375| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6987 Z= 0.139 Angle : 0.685 10.592 9498 Z= 0.351 Chirality : 0.046 0.263 1007 Planarity : 0.004 0.045 1212 Dihedral : 5.555 47.391 949 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 2.87 % Allowed : 20.08 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.27), residues: 847 helix: -4.76 (0.63), residues: 14 sheet: -1.25 (0.29), residues: 335 loop : -2.33 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 76 TYR 0.026 0.001 TYR F 365 PHE 0.018 0.001 PHE G 104 TRP 0.037 0.001 TRP D 36 HIS 0.004 0.001 HIS H 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 6977) covalent geometry : angle 0.68016 / 0.35 ( 9475) SS BOND : bond 0.00274 / 0.12 ( 7) SS BOND : angle 0.96430 / 0.46 ( 14) hydrogen bonds : bond 0.02663 / 1.76 ( 132) hydrogen bonds : angle 6.18807 / 4.17 ( 321) link_BETA1-4 : bond 0.00599 / 0.32 ( 1) link_BETA1-4 : angle 1.39294 / 0.68 ( 3) link_NAG-ASN : bond 0.00192 / 0.10 ( 2) link_NAG-ASN : angle 2.88308 / 1.56 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 MET cc_start: 0.8076 (mmt) cc_final: 0.7829 (tpp) REVERT: C 45 LYS cc_start: 0.8902 (mtpt) cc_final: 0.8686 (mtmt) REVERT: C 89 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7860 (tt0) REVERT: D 29 PHE cc_start: 0.8545 (t80) cc_final: 0.8322 (t80) REVERT: E 13 ARG cc_start: 0.7871 (mmt180) cc_final: 0.7412 (mmm160) REVERT: E 37 VAL cc_start: 0.8421 (t) cc_final: 0.8153 (m) REVERT: E 63 LYS cc_start: 0.8614 (mtmm) cc_final: 0.8171 (ptpt) REVERT: H 29 PHE cc_start: 0.8076 (t80) cc_final: 0.7786 (t80) REVERT: H 63 LYS cc_start: 0.8232 (mttp) cc_final: 0.7900 (ttmm) REVERT: L 37 GLN cc_start: 0.6615 (tm130) cc_final: 0.6255 (tm-30) outliers start: 21 outliers final: 19 residues processed: 165 average time/residue: 0.0920 time to fit residues: 19.8765 Evaluate side-chains 176 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain F residue 418 ILE Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 489 TYR Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 101 HIS Chi-restraints excluded: chain L residue 22 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 61 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 25 optimal weight: 0.5980 chunk 17 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 56 optimal weight: 0.0770 chunk 8 optimal weight: 0.3980 chunk 23 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 89 GLN ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.132014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.107501 restraints weight = 12548.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.110189 restraints weight = 7890.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.112018 restraints weight = 5849.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.113065 restraints weight = 4808.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.113922 restraints weight = 4252.059| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6987 Z= 0.137 Angle : 0.677 8.089 9498 Z= 0.349 Chirality : 0.046 0.275 1007 Planarity : 0.004 0.041 1212 Dihedral : 5.483 47.221 949 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 2.73 % Allowed : 20.63 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.80 (0.28), residues: 847 helix: -4.74 (0.64), residues: 14 sheet: -1.25 (0.29), residues: 333 loop : -2.27 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 76 TYR 0.029 0.001 TYR C 91 PHE 0.016 0.001 PHE G 104 TRP 0.034 0.001 TRP D 36 HIS 0.005 0.001 HIS H 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 6977) covalent geometry : angle 0.67293 / 0.35 ( 9475) SS BOND : bond 0.00249 / 0.11 ( 7) SS BOND : angle 0.94866 / 0.44 ( 14) hydrogen bonds : bond 0.02666 / 1.73 ( 132) hydrogen bonds : angle 6.14154 / 4.13 ( 321) link_BETA1-4 : bond 0.00591 / 0.31 ( 1) link_BETA1-4 : angle 1.37518 / 0.67 ( 3) link_NAG-ASN : bond 0.00139 / 0.07 ( 2) link_NAG-ASN : angle 2.84876 / 1.55 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 MET cc_start: 0.8054 (mmt) cc_final: 0.7830 (tpp) REVERT: C 45 LYS cc_start: 0.8911 (mtpt) cc_final: 0.8695 (mtmt) REVERT: C 89 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7888 (tt0) REVERT: D 29 PHE cc_start: 0.8528 (t80) cc_final: 0.8299 (t80) REVERT: E 13 ARG cc_start: 0.7877 (mmt180) cc_final: 0.7467 (mmm160) REVERT: E 37 VAL cc_start: 0.8428 (t) cc_final: 0.8169 (m) REVERT: E 63 LYS cc_start: 0.8622 (mtmm) cc_final: 0.8157 (ptpt) REVERT: H 29 PHE cc_start: 0.8082 (t80) cc_final: 0.7766 (t80) REVERT: H 63 LYS cc_start: 0.8255 (mttp) cc_final: 0.7924 (ttmm) REVERT: L 37 GLN cc_start: 0.6600 (tm130) cc_final: 0.6253 (tm-30) REVERT: L 76 ARG cc_start: 0.8450 (mmp80) cc_final: 0.7820 (mmp80) outliers start: 20 outliers final: 19 residues processed: 169 average time/residue: 0.0910 time to fit residues: 20.1356 Evaluate side-chains 175 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain F residue 418 ILE Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 489 TYR Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 101 HIS Chi-restraints excluded: chain L residue 22 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 22 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 89 GLN ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 HIS ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.131522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.107053 restraints weight = 12566.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.109700 restraints weight = 7938.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.111506 restraints weight = 5910.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.112688 restraints weight = 4881.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.113270 restraints weight = 4305.191| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6987 Z= 0.148 Angle : 0.686 8.710 9498 Z= 0.353 Chirality : 0.046 0.269 1007 Planarity : 0.004 0.041 1212 Dihedral : 5.538 47.995 949 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 2.87 % Allowed : 20.49 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.27), residues: 847 helix: -4.74 (0.63), residues: 14 sheet: -1.26 (0.29), residues: 321 loop : -2.30 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 76 TYR 0.036 0.001 TYR C 91 PHE 0.018 0.002 PHE L 97 TRP 0.031 0.001 TRP D 36 HIS 0.003 0.001 HIS H 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 6977) covalent geometry : angle 0.68182 / 0.35 ( 9475) SS BOND : bond 0.00212 / 0.09 ( 7) SS BOND : angle 0.98370 / 0.47 ( 14) hydrogen bonds : bond 0.02638 / 1.71 ( 132) hydrogen bonds : angle 6.14390 / 4.12 ( 321) link_BETA1-4 : bond 0.00561 / 0.30 ( 1) link_BETA1-4 : angle 1.34781 / 0.66 ( 3) link_NAG-ASN : bond 0.00233 / 0.12 ( 2) link_NAG-ASN : angle 2.89789 / 1.57 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1438.50 seconds wall clock time: 25 minutes 40.77 seconds (1540.77 seconds total)