Starting phenix.real_space_refine on Sat Aug 23 00:17:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9faa_50270/08_2025/9faa_50270_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9faa_50270/08_2025/9faa_50270.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9faa_50270/08_2025/9faa_50270_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9faa_50270/08_2025/9faa_50270_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9faa_50270/08_2025/9faa_50270.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9faa_50270/08_2025/9faa_50270.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 10 5.16 5 C 2815 2.51 5 N 730 2.21 5 O 905 1.98 5 H 4235 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8695 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1725 Classifications: {'peptide': 118} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 108} Chain: "A" 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: D, C, B, E Time building chain proxies: 1.54, per 1000 atoms: 0.18 Number of scatterers: 8695 At special positions: 0 Unit cell: (88.011, 124.46, 42.672, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 O 905 8.00 N 730 7.00 C 2815 6.00 H 4235 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 87 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 87 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 87 " distance=2.02 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 87 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 87 " distance=2.02 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 NAG-ASN " NAG A 201 " - " ASN A 19 " " NAG B 201 " - " ASN B 19 " " NAG C 201 " - " ASN C 19 " " NAG D 201 " - " ASN D 19 " " NAG E 201 " - " ASN E 19 " Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 339.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1040 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 37.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 2 through 5 removed outlier: 6.194A pdb=" N GLU A 3 " --> pdb=" O LEU B 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 9 through 12 removed outlier: 6.360A pdb=" N VAL D 10 " --> pdb=" O SER B 11 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N SER A 9 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N VAL B 12 " --> pdb=" O SER A 9 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N SER A 11 " --> pdb=" O VAL B 12 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 17 through 23 removed outlier: 6.672A pdb=" N THR A 17 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ILE B 20 " --> pdb=" O THR A 17 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ASN A 19 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N CYS B 22 " --> pdb=" O ASN A 19 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR A 21 " --> pdb=" O CYS B 22 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 26 through 30 removed outlier: 6.588A pdb=" N TYR A 26 " --> pdb=" O LEU B 27 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N GLU B 29 " --> pdb=" O TYR A 26 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLY A 28 " --> pdb=" O GLU B 29 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 36 through 37 removed outlier: 6.779A pdb=" N GLN D 36 " --> pdb=" O GLN B 37 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLN A 36 " --> pdb=" O GLN C 37 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN C 36 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 44 through 52 removed outlier: 6.662A pdb=" N VAL A 44 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N ILE B 47 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL A 46 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N GLN B 49 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TYR A 48 " --> pdb=" O GLN B 49 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N SER B 51 " --> pdb=" O TYR A 48 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N SER A 50 " --> pdb=" O SER B 51 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 64 through 65 removed outlier: 6.621A pdb=" N SER A 62 " --> pdb=" O GLY B 63 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ASN B 65 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER A 64 " --> pdb=" O ASN B 65 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 72 through 75 removed outlier: 6.788A pdb=" N LEU D 72 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N SER B 75 " --> pdb=" O LEU D 72 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE D 74 " --> pdb=" O SER B 75 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR A 73 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU A 72 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N SER C 75 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE A 74 " --> pdb=" O SER C 75 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU C 72 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N SER E 75 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE C 74 " --> pdb=" O SER E 75 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 84 through 86 removed outlier: 6.542A pdb=" N ALA A 83 " --> pdb=" O ASP B 84 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N PHE B 86 " --> pdb=" O ALA A 83 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TYR A 85 " --> pdb=" O PHE B 86 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 89 through 97 removed outlier: 6.457A pdb=" N TRP D 90 " --> pdb=" O ASP B 91 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N THR B 93 " --> pdb=" O TRP D 90 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N PHE D 92 " --> pdb=" O THR B 93 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N VAL B 95 " --> pdb=" O PHE D 92 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N SER D 94 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N PHE B 97 " --> pdb=" O SER D 94 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N VAL D 96 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N PHE A 97 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N TRP A 90 " --> pdb=" O ASP C 91 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N THR C 93 " --> pdb=" O TRP A 90 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N PHE A 92 " --> pdb=" O THR C 93 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL C 95 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N SER A 94 " --> pdb=" O VAL C 95 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N PHE C 97 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL A 96 " --> pdb=" O PHE C 97 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N TRP C 90 " --> pdb=" O ASP E 91 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N THR E 93 " --> pdb=" O TRP C 90 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N PHE C 92 " --> pdb=" O THR E 93 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N VAL E 95 " --> pdb=" O PHE C 92 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N SER C 94 " --> pdb=" O VAL E 95 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N PHE E 97 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL C 96 " --> pdb=" O PHE E 97 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 102 through 106 removed outlier: 6.707A pdb=" N LEU D 103 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N LEU B 106 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL D 105 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU A 103 " --> pdb=" O THR C 104 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N LEU C 106 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL A 105 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU C 103 " --> pdb=" O THR E 104 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N LEU E 106 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL C 105 " --> pdb=" O LEU E 106 " (cutoff:3.500A) 93 hydrogen bonds defined for protein. 270 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.64 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4235 1.03 - 1.22: 5 1.22 - 1.42: 1960 1.42 - 1.61: 2600 1.61 - 1.81: 10 Bond restraints: 8810 Sorted by residual: bond pdb=" CB ILE E 20 " pdb=" CG2 ILE E 20 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.41e+00 bond pdb=" CB ILE B 20 " pdb=" CG2 ILE B 20 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.34e+00 bond pdb=" CA GLY C 67 " pdb=" C GLY C 67 " ideal model delta sigma weight residual 1.516 1.498 0.018 1.18e-02 7.18e+03 2.34e+00 bond pdb=" CB ILE C 20 " pdb=" CG2 ILE C 20 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.33e+00 bond pdb=" CB ILE A 20 " pdb=" CG2 ILE A 20 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.29e+00 ... (remaining 8805 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 14447 1.41 - 2.82: 1160 2.82 - 4.23: 173 4.23 - 5.64: 40 5.64 - 7.05: 10 Bond angle restraints: 15830 Sorted by residual: angle pdb=" N THR A 69 " pdb=" CA THR A 69 " pdb=" C THR A 69 " ideal model delta sigma weight residual 109.94 102.89 7.05 1.57e+00 4.06e-01 2.02e+01 angle pdb=" N THR D 69 " pdb=" CA THR D 69 " pdb=" C THR D 69 " ideal model delta sigma weight residual 109.94 102.91 7.03 1.57e+00 4.06e-01 2.00e+01 angle pdb=" N THR E 69 " pdb=" CA THR E 69 " pdb=" C THR E 69 " ideal model delta sigma weight residual 109.94 102.93 7.01 1.57e+00 4.06e-01 1.99e+01 angle pdb=" N THR B 69 " pdb=" CA THR B 69 " pdb=" C THR B 69 " ideal model delta sigma weight residual 109.94 102.93 7.01 1.57e+00 4.06e-01 1.99e+01 angle pdb=" N THR C 69 " pdb=" CA THR C 69 " pdb=" C THR C 69 " ideal model delta sigma weight residual 109.94 102.95 6.99 1.57e+00 4.06e-01 1.98e+01 ... (remaining 15825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.86: 3772 14.86 - 29.73: 338 29.73 - 44.59: 115 44.59 - 59.45: 95 59.45 - 74.31: 30 Dihedral angle restraints: 4350 sinusoidal: 2390 harmonic: 1960 Sorted by residual: dihedral pdb=" CA PHE B 61 " pdb=" C PHE B 61 " pdb=" N SER B 62 " pdb=" CA SER B 62 " ideal model delta harmonic sigma weight residual 180.00 164.55 15.45 0 5.00e+00 4.00e-02 9.55e+00 dihedral pdb=" CA PHE D 61 " pdb=" C PHE D 61 " pdb=" N SER D 62 " pdb=" CA SER D 62 " ideal model delta harmonic sigma weight residual 180.00 164.55 15.45 0 5.00e+00 4.00e-02 9.54e+00 dihedral pdb=" CA PHE E 61 " pdb=" C PHE E 61 " pdb=" N SER E 62 " pdb=" CA SER E 62 " ideal model delta harmonic sigma weight residual 180.00 164.56 15.44 0 5.00e+00 4.00e-02 9.54e+00 ... (remaining 4347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 476 0.048 - 0.096: 181 0.096 - 0.144: 43 0.144 - 0.192: 0 0.192 - 0.241: 5 Chirality restraints: 705 Sorted by residual: chirality pdb=" C1 NAG A 201 " pdb=" ND2 ASN A 19 " pdb=" C2 NAG A 201 " pdb=" O5 NAG A 201 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C1 NAG E 201 " pdb=" ND2 ASN E 19 " pdb=" C2 NAG E 201 " pdb=" O5 NAG E 201 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" C1 NAG D 201 " pdb=" ND2 ASN D 19 " pdb=" C2 NAG D 201 " pdb=" O5 NAG D 201 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 702 not shown) Planarity restraints: 1350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN E 49 " 0.029 2.00e-02 2.50e+03 3.69e-02 2.04e+01 pdb=" CD GLN E 49 " -0.022 2.00e-02 2.50e+03 pdb=" OE1 GLN E 49 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 GLN E 49 " -0.060 2.00e-02 2.50e+03 pdb="HE21 GLN E 49 " -0.001 2.00e-02 2.50e+03 pdb="HE22 GLN E 49 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 49 " 0.029 2.00e-02 2.50e+03 3.68e-02 2.03e+01 pdb=" CD GLN D 49 " -0.022 2.00e-02 2.50e+03 pdb=" OE1 GLN D 49 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 GLN D 49 " -0.060 2.00e-02 2.50e+03 pdb="HE21 GLN D 49 " -0.001 2.00e-02 2.50e+03 pdb="HE22 GLN D 49 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 49 " 0.029 2.00e-02 2.50e+03 3.68e-02 2.03e+01 pdb=" CD GLN A 49 " -0.022 2.00e-02 2.50e+03 pdb=" OE1 GLN A 49 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 GLN A 49 " -0.060 2.00e-02 2.50e+03 pdb="HE21 GLN A 49 " -0.001 2.00e-02 2.50e+03 pdb="HE22 GLN A 49 " 0.056 2.00e-02 2.50e+03 ... (remaining 1347 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 183 2.09 - 2.72: 14912 2.72 - 3.34: 22417 3.34 - 3.97: 31298 3.97 - 4.60: 46361 Nonbonded interactions: 115171 Sorted by model distance: nonbonded pdb=" H ASN A 68 " pdb=" OD1 ASN B 68 " model vdw 1.461 2.450 nonbonded pdb=" OD1 ASN A 68 " pdb=" H ASN C 68 " model vdw 1.553 2.450 nonbonded pdb=" OD1 ASN C 68 " pdb=" H ASN E 68 " model vdw 1.598 2.450 nonbonded pdb=" OD1 ASN D 68 " pdb=" H ASN B 68 " model vdw 1.649 2.450 nonbonded pdb="HG21 THR E 69 " pdb=" H ALA E 70 " model vdw 1.788 2.270 ... (remaining 115166 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'C' selection = chain 'B' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.620 Find NCS groups from input model: 0.060 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 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 : 0.010 0.053 4585 Z= 0.429 Angle : 1.105 7.048 6265 Z= 0.623 Chirality : 0.053 0.241 705 Planarity : 0.006 0.042 805 Dihedral : 11.734 74.313 1690 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.21 (0.24), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.19), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.003 ARG E 53 TYR 0.038 0.007 TYR B 85 PHE 0.021 0.005 PHE C 61 TRP 0.034 0.008 TRP E 90 Details of bonding type rmsd covalent geometry : bond 0.01004 ( 4575) covalent geometry : angle 1.09932 ( 6240) SS BOND : bond 0.01025 ( 5) SS BOND : angle 0.99173 ( 10) hydrogen bonds : bond 0.17350 ( 93) hydrogen bonds : angle 7.78236 ( 270) link_NAG-ASN : bond 0.01768 ( 5) link_NAG-ASN : angle 2.51192 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 SER cc_start: 0.8275 (t) cc_final: 0.7997 (m) REVERT: A 91 ASP cc_start: 0.7857 (t0) cc_final: 0.7644 (t0) REVERT: A 108 GLN cc_start: 0.7845 (pt0) cc_final: 0.7534 (pp30) REVERT: A 117 LEU cc_start: 0.5983 (mt) cc_final: 0.5694 (mt) REVERT: D 49 GLN cc_start: 0.7584 (tt0) cc_final: 0.7382 (tt0) REVERT: D 108 GLN cc_start: 0.7793 (pt0) cc_final: 0.7496 (pp30) REVERT: C 108 GLN cc_start: 0.7868 (pt0) cc_final: 0.7408 (pp30) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1273 time to fit residues: 12.8469 Evaluate side-chains 49 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.121956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.103243 restraints weight = 26568.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.106796 restraints weight = 10162.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.109122 restraints weight = 5334.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.110484 restraints weight = 3428.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.111356 restraints weight = 2572.264| |-----------------------------------------------------------------------------| r_work (final): 0.4294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 4585 Z= 0.122 Angle : 0.607 4.115 6265 Z= 0.314 Chirality : 0.051 0.256 705 Planarity : 0.005 0.045 805 Dihedral : 6.151 23.222 730 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.22 % Allowed : 4.69 % Favored : 94.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.85 (0.25), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.19), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 60 TYR 0.013 0.002 TYR C 85 PHE 0.013 0.001 PHE D 2 TRP 0.008 0.001 TRP E 34 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 4575) covalent geometry : angle 0.59337 ( 6240) SS BOND : bond 0.00512 ( 5) SS BOND : angle 0.30793 ( 10) hydrogen bonds : bond 0.03382 ( 93) hydrogen bonds : angle 6.00061 ( 270) link_NAG-ASN : bond 0.00279 ( 5) link_NAG-ASN : angle 2.74950 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.249 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: symmetry clash revert: symmetry clash REVERT: A 8 SER cc_start: 0.8251 (t) cc_final: 0.7911 (m) REVERT: A 108 GLN cc_start: 0.7820 (pt0) cc_final: 0.7510 (pp30) REVERT: A 117 LEU cc_start: 0.6380 (mt) cc_final: 0.6171 (mt) REVERT: D 108 GLN cc_start: 0.7765 (pt0) cc_final: 0.7340 (pp30) REVERT: C 91 ASP cc_start: 0.7787 (t0) cc_final: 0.7325 (m-30) REVERT: C 108 GLN cc_start: 0.7916 (pt0) cc_final: 0.7276 (pp30) REVERT: E 91 ASP cc_start: 0.8007 (t0) cc_final: 0.7388 (m-30) outliers start: 6 outliers final: 4 residues processed: 65 average time/residue: 0.1330 time to fit residues: 11.6165 Evaluate side-chains 56 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain E residue 22 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 32 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 16 optimal weight: 0.0060 chunk 18 optimal weight: 0.0770 chunk 38 optimal weight: 3.9990 overall best weight: 1.1558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** 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 = 0.4358 r_free = 0.4358 target = 0.120271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.101925 restraints weight = 27204.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.105425 restraints weight = 10522.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.107732 restraints weight = 5578.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.109131 restraints weight = 3547.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.109798 restraints weight = 2633.710| |-----------------------------------------------------------------------------| r_work (final): 0.4289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4585 Z= 0.131 Angle : 0.574 5.317 6265 Z= 0.293 Chirality : 0.048 0.220 705 Planarity : 0.005 0.046 805 Dihedral : 5.911 25.977 730 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.84 % Allowed : 5.31 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.79 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 60 TYR 0.012 0.001 TYR A 85 PHE 0.009 0.001 PHE D 2 TRP 0.005 0.001 TRP E 34 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 4575) covalent geometry : angle 0.56210 ( 6240) SS BOND : bond 0.00340 ( 5) SS BOND : angle 0.92715 ( 10) hydrogen bonds : bond 0.02890 ( 93) hydrogen bonds : angle 5.16181 ( 270) link_NAG-ASN : bond 0.00282 ( 5) link_NAG-ASN : angle 2.41597 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.235 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: A 8 SER cc_start: 0.8268 (t) cc_final: 0.7870 (m) REVERT: A 91 ASP cc_start: 0.7648 (t0) cc_final: 0.7277 (m-30) REVERT: A 108 GLN cc_start: 0.7857 (pt0) cc_final: 0.7488 (pp30) REVERT: D 108 GLN cc_start: 0.7857 (pt0) cc_final: 0.7437 (pp30) REVERT: C 108 GLN cc_start: 0.7938 (pt0) cc_final: 0.7213 (pp30) REVERT: E 91 ASP cc_start: 0.8050 (t0) cc_final: 0.7368 (m-30) outliers start: 9 outliers final: 9 residues processed: 59 average time/residue: 0.1356 time to fit residues: 10.7325 Evaluate side-chains 59 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 68 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 30 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** 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 = 0.4297 r_free = 0.4297 target = 0.116287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.098775 restraints weight = 28610.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.102104 restraints weight = 10883.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.104267 restraints weight = 5681.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.105549 restraints weight = 3631.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.106010 restraints weight = 2698.149| |-----------------------------------------------------------------------------| r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 4585 Z= 0.266 Angle : 0.697 5.125 6265 Z= 0.362 Chirality : 0.048 0.195 705 Planarity : 0.006 0.045 805 Dihedral : 7.183 39.322 730 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.45 % Allowed : 6.53 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.98 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.03 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 53 TYR 0.020 0.003 TYR A 85 PHE 0.016 0.002 PHE A 61 TRP 0.007 0.002 TRP D 34 Details of bonding type rmsd covalent geometry : bond 0.00581 ( 4575) covalent geometry : angle 0.68304 ( 6240) SS BOND : bond 0.01233 ( 5) SS BOND : angle 0.89618 ( 10) hydrogen bonds : bond 0.03386 ( 93) hydrogen bonds : angle 4.87168 ( 270) link_NAG-ASN : bond 0.01171 ( 5) link_NAG-ASN : angle 2.91307 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.142 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: A 8 SER cc_start: 0.8372 (t) cc_final: 0.7967 (m) REVERT: A 108 GLN cc_start: 0.7865 (pt0) cc_final: 0.6927 (pp30) REVERT: D 108 GLN cc_start: 0.8112 (pt0) cc_final: 0.7529 (pp30) REVERT: C 108 GLN cc_start: 0.8015 (pt0) cc_final: 0.7180 (pp30) REVERT: E 97 PHE cc_start: 0.8088 (m-80) cc_final: 0.5741 (p90) outliers start: 12 outliers final: 10 residues processed: 67 average time/residue: 0.0860 time to fit residues: 7.7844 Evaluate side-chains 61 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 68 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 23 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** 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 = 0.4294 r_free = 0.4294 target = 0.116323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.098976 restraints weight = 28560.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.102222 restraints weight = 11096.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.104330 restraints weight = 5881.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.105587 restraints weight = 3782.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.106113 restraints weight = 2837.344| |-----------------------------------------------------------------------------| r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 4585 Z= 0.227 Angle : 0.655 4.633 6265 Z= 0.342 Chirality : 0.048 0.217 705 Planarity : 0.006 0.047 805 Dihedral : 6.834 35.170 730 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.24 % Allowed : 8.98 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.10 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 60 TYR 0.016 0.002 TYR A 85 PHE 0.013 0.002 PHE A 61 TRP 0.006 0.001 TRP D 34 Details of bonding type rmsd covalent geometry : bond 0.00495 ( 4575) covalent geometry : angle 0.64034 ( 6240) SS BOND : bond 0.01014 ( 5) SS BOND : angle 0.88181 ( 10) hydrogen bonds : bond 0.03146 ( 93) hydrogen bonds : angle 4.82850 ( 270) link_NAG-ASN : bond 0.00654 ( 5) link_NAG-ASN : angle 2.79996 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.165 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: symmetry clash revert: symmetry clash REVERT: A 8 SER cc_start: 0.8381 (t) cc_final: 0.7976 (m) REVERT: D 108 GLN cc_start: 0.8081 (pt0) cc_final: 0.7506 (pp30) outliers start: 11 outliers final: 10 residues processed: 64 average time/residue: 0.1059 time to fit residues: 9.0615 Evaluate side-chains 60 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 68 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 39 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.117550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.100280 restraints weight = 27952.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.103606 restraints weight = 10798.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.105737 restraints weight = 5665.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.106994 restraints weight = 3641.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.107728 restraints weight = 2715.350| |-----------------------------------------------------------------------------| r_work (final): 0.4221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4585 Z= 0.128 Angle : 0.567 3.896 6265 Z= 0.292 Chirality : 0.048 0.224 705 Planarity : 0.005 0.046 805 Dihedral : 6.377 32.411 730 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 2.04 % Allowed : 9.59 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.13 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.14 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 60 TYR 0.009 0.001 TYR A 85 PHE 0.010 0.001 PHE D 61 TRP 0.004 0.001 TRP B 34 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 4575) covalent geometry : angle 0.55432 ( 6240) SS BOND : bond 0.00552 ( 5) SS BOND : angle 0.58408 ( 10) hydrogen bonds : bond 0.02407 ( 93) hydrogen bonds : angle 4.58346 ( 270) link_NAG-ASN : bond 0.00137 ( 5) link_NAG-ASN : angle 2.48605 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.241 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: A 8 SER cc_start: 0.8398 (t) cc_final: 0.7980 (m) REVERT: D 108 GLN cc_start: 0.8073 (pt0) cc_final: 0.7532 (pp30) outliers start: 10 outliers final: 8 residues processed: 62 average time/residue: 0.1154 time to fit residues: 9.4345 Evaluate side-chains 58 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 68 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 29 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 33 optimal weight: 0.2980 chunk 1 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 52 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 50 optimal weight: 5.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** 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 = 0.4347 r_free = 0.4347 target = 0.119688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.102087 restraints weight = 27776.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.105552 restraints weight = 10711.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.107588 restraints weight = 5603.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.108923 restraints weight = 3641.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.109741 restraints weight = 2715.426| |-----------------------------------------------------------------------------| r_work (final): 0.4272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 4585 Z= 0.093 Angle : 0.547 4.473 6265 Z= 0.281 Chirality : 0.048 0.216 705 Planarity : 0.005 0.047 805 Dihedral : 5.913 27.876 730 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.63 % Allowed : 9.39 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.06 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 60 TYR 0.006 0.001 TYR C 85 PHE 0.010 0.001 PHE D 61 TRP 0.003 0.001 TRP C 34 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 4575) covalent geometry : angle 0.53597 ( 6240) SS BOND : bond 0.00206 ( 5) SS BOND : angle 0.74970 ( 10) hydrogen bonds : bond 0.02016 ( 93) hydrogen bonds : angle 4.39281 ( 270) link_NAG-ASN : bond 0.00125 ( 5) link_NAG-ASN : angle 2.26879 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.237 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: A 8 SER cc_start: 0.8369 (t) cc_final: 0.7939 (m) REVERT: D 8 SER cc_start: 0.8245 (OUTLIER) cc_final: 0.7904 (p) REVERT: D 108 GLN cc_start: 0.8055 (pt0) cc_final: 0.7502 (pp30) outliers start: 8 outliers final: 6 residues processed: 61 average time/residue: 0.1080 time to fit residues: 8.6535 Evaluate side-chains 58 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain E residue 22 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 51 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.117051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.099735 restraints weight = 28149.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.103020 restraints weight = 11023.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.104989 restraints weight = 5849.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.106293 restraints weight = 3827.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.107001 restraints weight = 2863.582| |-----------------------------------------------------------------------------| r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4585 Z= 0.178 Angle : 0.605 4.279 6265 Z= 0.312 Chirality : 0.048 0.197 705 Planarity : 0.005 0.045 805 Dihedral : 6.688 37.555 730 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 1.84 % Allowed : 9.59 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.12 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 60 TYR 0.013 0.002 TYR D 85 PHE 0.013 0.002 PHE A 61 TRP 0.005 0.001 TRP D 34 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 4575) covalent geometry : angle 0.59525 ( 6240) SS BOND : bond 0.00721 ( 5) SS BOND : angle 0.76023 ( 10) hydrogen bonds : bond 0.02629 ( 93) hydrogen bonds : angle 4.34636 ( 270) link_NAG-ASN : bond 0.00589 ( 5) link_NAG-ASN : angle 2.22920 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.202 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: A 8 SER cc_start: 0.8394 (t) cc_final: 0.7965 (m) REVERT: D 8 SER cc_start: 0.8276 (OUTLIER) cc_final: 0.7911 (p) REVERT: D 108 GLN cc_start: 0.8141 (pt0) cc_final: 0.7557 (pp30) outliers start: 9 outliers final: 8 residues processed: 61 average time/residue: 0.1056 time to fit residues: 8.7598 Evaluate side-chains 60 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain E residue 22 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 0.0170 chunk 1 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 overall best weight: 1.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** 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 = 0.4316 r_free = 0.4316 target = 0.117713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.100428 restraints weight = 28014.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.103725 restraints weight = 10882.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.105811 restraints weight = 5758.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.107075 restraints weight = 3693.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.107847 restraints weight = 2762.764| |-----------------------------------------------------------------------------| r_work (final): 0.4243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4585 Z= 0.126 Angle : 0.568 4.365 6265 Z= 0.293 Chirality : 0.048 0.214 705 Planarity : 0.005 0.048 805 Dihedral : 6.295 32.970 730 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.84 % Allowed : 10.00 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.11 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 60 TYR 0.009 0.001 TYR A 85 PHE 0.011 0.001 PHE A 61 TRP 0.003 0.001 TRP D 34 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 4575) covalent geometry : angle 0.55781 ( 6240) SS BOND : bond 0.00459 ( 5) SS BOND : angle 0.59226 ( 10) hydrogen bonds : bond 0.02254 ( 93) hydrogen bonds : angle 4.30743 ( 270) link_NAG-ASN : bond 0.00155 ( 5) link_NAG-ASN : angle 2.28942 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.228 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: A 8 SER cc_start: 0.8358 (t) cc_final: 0.7937 (m) REVERT: D 8 SER cc_start: 0.8260 (OUTLIER) cc_final: 0.7883 (p) REVERT: D 108 GLN cc_start: 0.8088 (pt0) cc_final: 0.7508 (pp30) outliers start: 9 outliers final: 8 residues processed: 63 average time/residue: 0.1107 time to fit residues: 9.5917 Evaluate side-chains 61 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain E residue 22 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 16 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.118119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.100929 restraints weight = 27993.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.104292 restraints weight = 10604.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.106319 restraints weight = 5535.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.107645 restraints weight = 3589.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.108470 restraints weight = 2660.444| |-----------------------------------------------------------------------------| r_work (final): 0.4250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4585 Z= 0.130 Angle : 0.566 4.288 6265 Z= 0.290 Chirality : 0.047 0.206 705 Planarity : 0.005 0.047 805 Dihedral : 6.259 32.942 730 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 1.84 % Allowed : 10.61 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.11 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 60 TYR 0.009 0.001 TYR C 85 PHE 0.010 0.001 PHE D 61 TRP 0.003 0.001 TRP D 34 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 4575) covalent geometry : angle 0.55684 ( 6240) SS BOND : bond 0.00466 ( 5) SS BOND : angle 0.60026 ( 10) hydrogen bonds : bond 0.02235 ( 93) hydrogen bonds : angle 4.26938 ( 270) link_NAG-ASN : bond 0.00204 ( 5) link_NAG-ASN : angle 2.18242 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.249 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: A 8 SER cc_start: 0.8320 (t) cc_final: 0.7892 (m) REVERT: D 8 SER cc_start: 0.8263 (OUTLIER) cc_final: 0.7893 (p) REVERT: D 108 GLN cc_start: 0.8072 (pt0) cc_final: 0.7510 (pp30) outliers start: 9 outliers final: 8 residues processed: 64 average time/residue: 0.1060 time to fit residues: 9.1408 Evaluate side-chains 62 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain E residue 22 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 31 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.118167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.101013 restraints weight = 27924.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.104341 restraints weight = 10571.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.106450 restraints weight = 5512.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.107738 restraints weight = 3517.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.108552 restraints weight = 2614.998| |-----------------------------------------------------------------------------| r_work (final): 0.4256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4585 Z= 0.124 Angle : 0.561 4.578 6265 Z= 0.286 Chirality : 0.047 0.206 705 Planarity : 0.005 0.047 805 Dihedral : 6.196 32.515 730 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.84 % Allowed : 10.82 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.08 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 60 TYR 0.008 0.001 TYR C 85 PHE 0.010 0.001 PHE D 61 TRP 0.003 0.001 TRP D 34 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 4575) covalent geometry : angle 0.55138 ( 6240) SS BOND : bond 0.00413 ( 5) SS BOND : angle 0.62914 ( 10) hydrogen bonds : bond 0.02135 ( 93) hydrogen bonds : angle 4.19358 ( 270) link_NAG-ASN : bond 0.00173 ( 5) link_NAG-ASN : angle 2.15126 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1690.13 seconds wall clock time: 29 minutes 28.18 seconds (1768.18 seconds total)