Starting phenix.real_space_refine on Mon May 12 04:49:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9faa_50270/05_2025/9faa_50270_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9faa_50270/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9faa_50270/05_2025/9faa_50270.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9faa_50270/05_2025/9faa_50270.map" model { file = "/net/cci-nas-00/data/ceres_data/9faa_50270/05_2025/9faa_50270_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9faa_50270/05_2025/9faa_50270_trim.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: C, B, E, D Time building chain proxies: 3.97, per 1000 atoms: 0.46 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 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 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 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: 1.96 Conformation dependent library (CDL) restraints added in 722.6 milliseconds 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: 0.79 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: 2.68 Time building geometry restraints manager: 2.34 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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: 2.020 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: 0.160 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 20.620 Find NCS groups from input model: 0.140 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.040 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.034 0.008 TRP E 90 PHE 0.021 0.005 PHE C 61 TYR 0.038 0.007 TYR B 85 ARG 0.009 0.003 ARG E 53 Details of bonding type rmsd link_NAG-ASN : bond 0.01768 ( 5) link_NAG-ASN : angle 2.51192 ( 15) hydrogen bonds : bond 0.17350 ( 93) hydrogen bonds : angle 7.78236 ( 270) SS BOND : bond 0.01025 ( 5) SS BOND : angle 0.99173 ( 10) covalent geometry : bond 0.01004 ( 4575) covalent geometry : angle 1.09932 ( 6240) *********************** 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 : 0.659 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: 0.7998 (m) REVERT: A 91 ASP cc_start: 0.7857 (t0) cc_final: 0.7645 (t0) REVERT: A 108 GLN cc_start: 0.7845 (pt0) cc_final: 0.7535 (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: 0.7383 (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: 0.2669 time to fit residues: 26.8536 Evaluate side-chains 48 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 16 optimal weight: 0.0070 chunk 26 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 overall best weight: 0.7402 ------------------------------------------------------------------------------- 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 = 0.4390 r_free = 0.4390 target = 0.121838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.103217 restraints weight = 26397.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.106793 restraints weight = 10132.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.108978 restraints weight = 5350.345| |-----------------------------------------------------------------------------| r_work (final): 0.4272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 4585 Z= 0.122 Angle : 0.615 4.289 6265 Z= 0.319 Chirality : 0.051 0.254 705 Planarity : 0.005 0.046 805 Dihedral : 6.098 23.217 730 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.02 % Allowed : 4.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.84 (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 TRP 0.008 0.001 TRP E 34 PHE 0.014 0.001 PHE D 2 TYR 0.012 0.002 TYR C 85 ARG 0.003 0.000 ARG E 60 Details of bonding type rmsd link_NAG-ASN : bond 0.00299 ( 5) link_NAG-ASN : angle 2.80425 ( 15) hydrogen bonds : bond 0.03828 ( 93) hydrogen bonds : angle 6.02570 ( 270) SS BOND : bond 0.00464 ( 5) SS BOND : angle 0.31413 ( 10) covalent geometry : bond 0.00295 ( 4575) covalent geometry : angle 0.60081 ( 6240) *********************** 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 63 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.707 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: A 8 SER cc_start: 0.8274 (t) cc_final: 0.7923 (m) REVERT: A 108 GLN cc_start: 0.7841 (pt0) cc_final: 0.7524 (pp30) REVERT: A 117 LEU cc_start: 0.6463 (mt) cc_final: 0.6259 (mt) REVERT: D 108 GLN cc_start: 0.7779 (pt0) cc_final: 0.7343 (pp30) REVERT: C 91 ASP cc_start: 0.7800 (t0) cc_final: 0.7353 (m-30) REVERT: C 108 GLN cc_start: 0.7944 (pt0) cc_final: 0.7351 (pp30) REVERT: E 91 ASP cc_start: 0.8044 (t0) cc_final: 0.7440 (m-30) outliers start: 5 outliers final: 4 residues processed: 63 average time/residue: 0.2728 time to fit residues: 23.0882 Evaluate side-chains 53 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 44 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.4333 r_free = 0.4333 target = 0.118512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.100458 restraints weight = 27706.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.103823 restraints weight = 10722.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.106046 restraints weight = 5689.727| |-----------------------------------------------------------------------------| r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4585 Z= 0.192 Angle : 0.626 4.179 6265 Z= 0.323 Chirality : 0.048 0.212 705 Planarity : 0.005 0.045 805 Dihedral : 6.372 30.350 730 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.24 % Allowed : 5.31 % Favored : 92.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 34 PHE 0.012 0.002 PHE B 61 TYR 0.015 0.002 TYR A 85 ARG 0.001 0.000 ARG A 32 Details of bonding type rmsd link_NAG-ASN : bond 0.00628 ( 5) link_NAG-ASN : angle 2.65675 ( 15) hydrogen bonds : bond 0.03373 ( 93) hydrogen bonds : angle 5.32016 ( 270) SS BOND : bond 0.00856 ( 5) SS BOND : angle 0.83498 ( 10) covalent geometry : bond 0.00429 ( 4575) covalent geometry : angle 0.61240 ( 6240) *********************** 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 61 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.748 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: 0.8293 (t) cc_final: 0.7891 (m) REVERT: A 91 ASP cc_start: 0.7687 (t0) cc_final: 0.7462 (t0) REVERT: A 108 GLN cc_start: 0.7894 (pt0) cc_final: 0.7457 (pp30) REVERT: D 108 GLN cc_start: 0.7885 (pt0) cc_final: 0.7458 (pp30) REVERT: C 108 GLN cc_start: 0.7931 (pt0) cc_final: 0.7180 (pp30) REVERT: E 91 ASP cc_start: 0.8041 (t0) cc_final: 0.7336 (m-30) outliers start: 11 outliers final: 9 residues processed: 60 average time/residue: 0.2831 time to fit residues: 22.8987 Evaluate side-chains 58 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.766 ------------------------------------------------------------------------------- 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 17 THR Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain E residue 22 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 22 optimal weight: 0.2980 chunk 41 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4363 r_free = 0.4363 target = 0.121040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.102793 restraints weight = 27010.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.106326 restraints weight = 10478.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.108626 restraints weight = 5519.307| |-----------------------------------------------------------------------------| r_work (final): 0.4277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 4585 Z= 0.096 Angle : 0.542 4.399 6265 Z= 0.276 Chirality : 0.049 0.235 705 Planarity : 0.005 0.045 805 Dihedral : 5.745 25.325 730 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.84 % Allowed : 5.71 % Favored : 92.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.91 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 34 PHE 0.008 0.001 PHE A 2 TYR 0.009 0.001 TYR A 85 ARG 0.002 0.000 ARG E 60 Details of bonding type rmsd link_NAG-ASN : bond 0.00178 ( 5) link_NAG-ASN : angle 2.41604 ( 15) hydrogen bonds : bond 0.02347 ( 93) hydrogen bonds : angle 4.82426 ( 270) SS BOND : bond 0.00252 ( 5) SS BOND : angle 0.66852 ( 10) covalent geometry : bond 0.00233 ( 4575) covalent geometry : angle 0.52930 ( 6240) *********************** 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 65 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.768 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: A 8 SER cc_start: 0.8322 (t) cc_final: 0.7897 (m) REVERT: A 91 ASP cc_start: 0.7595 (t0) cc_final: 0.7371 (t0) REVERT: A 108 GLN cc_start: 0.7861 (pt0) cc_final: 0.6941 (pp30) REVERT: D 108 GLN cc_start: 0.7919 (pt0) cc_final: 0.7454 (pp30) REVERT: C 108 GLN cc_start: 0.7943 (pt0) cc_final: 0.7187 (pp30) REVERT: E 91 ASP cc_start: 0.8064 (t0) cc_final: 0.7326 (m-30) outliers start: 9 outliers final: 8 residues processed: 63 average time/residue: 0.2831 time to fit residues: 23.7840 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 : 0.677 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 = 0.4315 r_free = 0.4315 target = 0.117878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.100230 restraints weight = 27663.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.103661 restraints weight = 10625.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.105797 restraints weight = 5541.661| |-----------------------------------------------------------------------------| r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 4585 Z= 0.213 Angle : 0.640 4.766 6265 Z= 0.331 Chirality : 0.048 0.188 705 Planarity : 0.005 0.045 805 Dihedral : 6.791 37.392 730 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.38 % Favored : 93.45 % Rotamer: Outliers : 2.24 % Allowed : 6.53 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 34 PHE 0.014 0.002 PHE A 61 TYR 0.016 0.002 TYR A 85 ARG 0.003 0.000 ARG E 60 Details of bonding type rmsd link_NAG-ASN : bond 0.00887 ( 5) link_NAG-ASN : angle 2.36871 ( 15) hydrogen bonds : bond 0.03020 ( 93) hydrogen bonds : angle 4.66052 ( 270) SS BOND : bond 0.00958 ( 5) SS BOND : angle 0.68009 ( 10) covalent geometry : bond 0.00466 ( 4575) covalent geometry : angle 0.62983 ( 6240) *********************** 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 : 0.668 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: A 8 SER cc_start: 0.8347 (t) cc_final: 0.7919 (m) REVERT: A 108 GLN cc_start: 0.7835 (pt0) cc_final: 0.6881 (pp30) REVERT: D 108 GLN cc_start: 0.8122 (pt0) cc_final: 0.7538 (pp30) REVERT: C 108 GLN cc_start: 0.7992 (pt0) cc_final: 0.7170 (pp30) REVERT: E 91 ASP cc_start: 0.7971 (t0) cc_final: 0.7237 (m-30) outliers start: 11 outliers final: 9 residues processed: 64 average time/residue: 0.2745 time to fit residues: 23.4630 Evaluate side-chains 57 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 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 33 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 = 0.4307 r_free = 0.4307 target = 0.117304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.099815 restraints weight = 27846.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.103094 restraints weight = 10861.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.105229 restraints weight = 5729.579| |-----------------------------------------------------------------------------| r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4585 Z= 0.191 Angle : 0.614 5.393 6265 Z= 0.317 Chirality : 0.048 0.223 705 Planarity : 0.005 0.045 805 Dihedral : 6.539 33.457 730 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.24 % Allowed : 7.96 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.01 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 34 PHE 0.012 0.001 PHE B 61 TYR 0.014 0.002 TYR A 85 ARG 0.001 0.000 ARG A 60 Details of bonding type rmsd link_NAG-ASN : bond 0.00509 ( 5) link_NAG-ASN : angle 2.58254 ( 15) hydrogen bonds : bond 0.02832 ( 93) hydrogen bonds : angle 4.61104 ( 270) SS BOND : bond 0.00616 ( 5) SS BOND : angle 0.76062 ( 10) covalent geometry : bond 0.00418 ( 4575) covalent geometry : angle 0.60154 ( 6240) *********************** 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 61 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.658 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: 0.8366 (t) cc_final: 0.7950 (m) REVERT: D 8 SER cc_start: 0.8284 (OUTLIER) cc_final: 0.7928 (p) REVERT: D 108 GLN cc_start: 0.8137 (pt0) cc_final: 0.7536 (pp30) REVERT: B 8 SER cc_start: 0.7932 (t) cc_final: 0.7594 (m) outliers start: 11 outliers final: 9 residues processed: 61 average time/residue: 0.2702 time to fit residues: 22.1068 Evaluate side-chains 59 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 1.096 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 17 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 6 optimal weight: 8.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.4331 r_free = 0.4331 target = 0.118816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.101049 restraints weight = 27740.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.104493 restraints weight = 10568.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.106698 restraints weight = 5486.485| |-----------------------------------------------------------------------------| r_work (final): 0.4238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3068 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= 0.109 Angle : 0.557 4.190 6265 Z= 0.286 Chirality : 0.048 0.221 705 Planarity : 0.005 0.048 805 Dihedral : 6.053 30.301 730 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.43 % Allowed : 9.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.00 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 34 PHE 0.010 0.001 PHE D 61 TYR 0.008 0.001 TYR A 85 ARG 0.002 0.000 ARG E 60 Details of bonding type rmsd link_NAG-ASN : bond 0.00065 ( 5) link_NAG-ASN : angle 2.29569 ( 15) hydrogen bonds : bond 0.02152 ( 93) hydrogen bonds : angle 4.43637 ( 270) SS BOND : bond 0.00436 ( 5) SS BOND : angle 0.49062 ( 10) covalent geometry : bond 0.00257 ( 4575) covalent geometry : angle 0.54632 ( 6240) *********************** 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 59 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.644 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: 0.8386 (t) cc_final: 0.7955 (m) REVERT: D 108 GLN cc_start: 0.8125 (pt0) cc_final: 0.7551 (pp30) REVERT: B 8 SER cc_start: 0.7906 (t) cc_final: 0.7648 (m) REVERT: E 91 ASP cc_start: 0.7878 (t0) cc_final: 0.7268 (m-30) outliers start: 7 outliers final: 7 residues processed: 59 average time/residue: 0.2729 time to fit residues: 21.4690 Evaluate side-chains 57 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 0.0060 chunk 51 optimal weight: 0.9980 overall best weight: 0.9598 ------------------------------------------------------------------------------- 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 = 0.4343 r_free = 0.4343 target = 0.119857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.102058 restraints weight = 27737.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.105470 restraints weight = 10811.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.107618 restraints weight = 5686.678| |-----------------------------------------------------------------------------| r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3184 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= 0.108 Angle : 0.541 4.182 6265 Z= 0.276 Chirality : 0.047 0.204 705 Planarity : 0.005 0.046 805 Dihedral : 5.914 29.312 730 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.84 % Allowed : 9.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.96 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 34 PHE 0.009 0.001 PHE A 61 TYR 0.007 0.001 TYR A 85 ARG 0.002 0.000 ARG A 60 Details of bonding type rmsd link_NAG-ASN : bond 0.00113 ( 5) link_NAG-ASN : angle 2.09092 ( 15) hydrogen bonds : bond 0.02070 ( 93) hydrogen bonds : angle 4.25080 ( 270) SS BOND : bond 0.00302 ( 5) SS BOND : angle 0.56809 ( 10) covalent geometry : bond 0.00257 ( 4575) covalent geometry : angle 0.53175 ( 6240) *********************** 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 58 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.799 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: D 108 GLN cc_start: 0.8127 (pt0) cc_final: 0.7546 (pp30) REVERT: B 8 SER cc_start: 0.7916 (t) cc_final: 0.7639 (m) outliers start: 9 outliers final: 8 residues processed: 58 average time/residue: 0.2862 time to fit residues: 22.3557 Evaluate side-chains 56 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 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 17 optimal weight: 7.9990 chunk 16 optimal weight: 0.0000 chunk 24 optimal weight: 0.8980 chunk 44 optimal weight: 8.9990 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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** ** 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 = 0.4338 r_free = 0.4338 target = 0.119782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.101825 restraints weight = 27784.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.105245 restraints weight = 10652.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.107426 restraints weight = 5568.844| |-----------------------------------------------------------------------------| r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3260 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= 0.098 Angle : 0.527 3.781 6265 Z= 0.269 Chirality : 0.047 0.202 705 Planarity : 0.005 0.047 805 Dihedral : 5.748 28.802 730 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.84 % Allowed : 9.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 34 PHE 0.009 0.001 PHE D 61 TYR 0.007 0.001 TYR A 85 ARG 0.001 0.000 ARG A 60 Details of bonding type rmsd link_NAG-ASN : bond 0.00060 ( 5) link_NAG-ASN : angle 2.03015 ( 15) hydrogen bonds : bond 0.01931 ( 93) hydrogen bonds : angle 4.17552 ( 270) SS BOND : bond 0.00264 ( 5) SS BOND : angle 0.57350 ( 10) covalent geometry : bond 0.00237 ( 4575) covalent geometry : angle 0.51821 ( 6240) *********************** 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 58 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.650 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: D 108 GLN cc_start: 0.8142 (pt0) cc_final: 0.7552 (pp30) REVERT: B 8 SER cc_start: 0.7922 (t) cc_final: 0.7633 (m) outliers start: 9 outliers final: 8 residues processed: 58 average time/residue: 0.2753 time to fit residues: 21.4406 Evaluate side-chains 55 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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 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 46 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 16 optimal weight: 0.0060 chunk 12 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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** ** 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 = 0.4365 r_free = 0.4365 target = 0.121180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.103136 restraints weight = 27619.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.106560 restraints weight = 10661.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.108786 restraints weight = 5591.109| |-----------------------------------------------------------------------------| r_work (final): 0.4268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 4585 Z= 0.088 Angle : 0.519 4.676 6265 Z= 0.262 Chirality : 0.047 0.196 705 Planarity : 0.005 0.046 805 Dihedral : 5.546 26.706 730 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.43 % Allowed : 9.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 34 PHE 0.008 0.001 PHE D 61 TYR 0.005 0.001 TYR A 85 ARG 0.000 0.000 ARG A 60 Details of bonding type rmsd link_NAG-ASN : bond 0.00087 ( 5) link_NAG-ASN : angle 1.95139 ( 15) hydrogen bonds : bond 0.01775 ( 93) hydrogen bonds : angle 4.08301 ( 270) SS BOND : bond 0.00206 ( 5) SS BOND : angle 0.66392 ( 10) covalent geometry : bond 0.00222 ( 4575) covalent geometry : angle 0.51086 ( 6240) ********************** 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 57 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.761 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: D 108 GLN cc_start: 0.8147 (pt0) cc_final: 0.7544 (pp30) REVERT: B 8 SER cc_start: 0.7923 (t) cc_final: 0.7595 (m) outliers start: 7 outliers final: 7 residues processed: 57 average time/residue: 0.2774 time to fit residues: 21.3774 Evaluate side-chains 53 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 45 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.4337 r_free = 0.4337 target = 0.119144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.101595 restraints weight = 27760.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.105014 restraints weight = 10876.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.107053 restraints weight = 5753.550| |-----------------------------------------------------------------------------| r_work (final): 0.4238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3430 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= 0.148 Angle : 0.567 5.234 6265 Z= 0.290 Chirality : 0.047 0.191 705 Planarity : 0.005 0.047 805 Dihedral : 6.084 33.783 730 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 1.63 % Allowed : 9.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 34 PHE 0.010 0.001 PHE A 61 TYR 0.010 0.001 TYR D 85 ARG 0.001 0.000 ARG A 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00379 ( 5) link_NAG-ASN : angle 1.92799 ( 15) hydrogen bonds : bond 0.02280 ( 93) hydrogen bonds : angle 4.15261 ( 270) SS BOND : bond 0.00497 ( 5) SS BOND : angle 0.70251 ( 10) covalent geometry : bond 0.00335 ( 4575) covalent geometry : angle 0.55979 ( 6240) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3206.74 seconds wall clock time: 56 minutes 11.43 seconds (3371.43 seconds total)