Starting phenix.real_space_refine on Tue Aug 4 19:07:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sj2_54935/08_2026/9sj2_54935.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sj2_54935/08_2026/9sj2_54935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sj2_54935/08_2026/9sj2_54935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sj2_54935/08_2026/9sj2_54935.map" model { file = "/net/cci-nas-00/data/ceres_data/9sj2_54935/08_2026/9sj2_54935.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sj2_54935/08_2026/9sj2_54935.cif" } resolution = 3.57 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= 0.002 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 Ca 15 9.91 5 S 10 5.16 5 C 3769 2.51 5 N 954 2.21 5 O 1334 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6082 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 1228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1228 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 155} Chain: "D" Number of atoms: 1228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1228 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 155} Chain: "E" Number of atoms: 1228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1228 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 155} Chain: "B" Number of atoms: 1228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1228 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 155} Chain: "A" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1155 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 146} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.35, per 1000 atoms: 0.22 Number of scatterers: 6082 At special positions: 0 Unit cell: (81.315, 72.975, 253.675, 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) Ca 15 19.99 S 10 16.00 O 1334 8.00 N 954 7.00 C 3769 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 99 " - pdb=" SG CYS C 138 " distance=2.03 Simple disulfide: pdb=" SG CYS D 99 " - pdb=" SG CYS D 138 " distance=2.03 Simple disulfide: pdb=" SG CYS E 99 " - pdb=" SG CYS E 138 " distance=2.03 Simple disulfide: pdb=" SG CYS B 99 " - pdb=" SG CYS B 138 " distance=2.03 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 138 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.37 Conformation dependent library (CDL) restraints added in 262.1 milliseconds 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1542 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 20 sheets defined 3.7% alpha, 58.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'C' and resid 93 through 98 Processing helix chain 'D' and resid 93 through 98 removed outlier: 3.550A pdb=" N ALA D 98 " --> pdb=" O SER D 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 98 removed outlier: 3.828A pdb=" N ALA E 98 " --> pdb=" O SER E 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 98 removed outlier: 3.528A pdb=" N ALA B 98 " --> pdb=" O SER B 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 98 removed outlier: 3.571A pdb=" N ALA A 98 " --> pdb=" O SER A 94 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 37 through 43 removed outlier: 4.195A pdb=" N VAL B 154 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU B 159 " --> pdb=" O LEU B 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 37 through 43 Processing sheet with id=AA3, first strand: chain 'C' and resid 20 through 22 Processing sheet with id=AA4, first strand: chain 'C' and resid 20 through 22 Processing sheet with id=AA5, first strand: chain 'C' and resid 37 through 43 removed outlier: 6.639A pdb=" N LEU C 54 " --> pdb=" O SER D 9 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N THR D 11 " --> pdb=" O LEU C 54 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE C 56 " --> pdb=" O THR D 11 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N SER D 13 " --> pdb=" O ILE C 56 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE C 58 " --> pdb=" O SER D 13 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL C 154 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU C 159 " --> pdb=" O LEU C 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 37 through 43 removed outlier: 6.639A pdb=" N LEU C 54 " --> pdb=" O SER D 9 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N THR D 11 " --> pdb=" O LEU C 54 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE C 56 " --> pdb=" O THR D 11 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N SER D 13 " --> pdb=" O ILE C 56 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE C 58 " --> pdb=" O SER D 13 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 20 through 22 Processing sheet with id=AA8, first strand: chain 'D' and resid 20 through 22 Processing sheet with id=AA9, first strand: chain 'D' and resid 37 through 43 removed outlier: 5.998A pdb=" N GLN D 53 " --> pdb=" O THR E 5 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N SER E 7 " --> pdb=" O GLN D 53 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N SER D 55 " --> pdb=" O SER E 7 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N SER E 9 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N THR D 57 " --> pdb=" O SER E 9 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR E 11 " --> pdb=" O THR D 57 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N GLU D 59 " --> pdb=" O THR E 11 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N SER E 13 " --> pdb=" O GLU D 59 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL D 154 " --> pdb=" O LEU E 8 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 37 through 43 removed outlier: 5.998A pdb=" N GLN D 53 " --> pdb=" O THR E 5 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N SER E 7 " --> pdb=" O GLN D 53 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N SER D 55 " --> pdb=" O SER E 7 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N SER E 9 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N THR D 57 " --> pdb=" O SER E 9 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR E 11 " --> pdb=" O THR D 57 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N GLU D 59 " --> pdb=" O THR E 11 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N SER E 13 " --> pdb=" O GLU D 59 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 20 through 22 Processing sheet with id=AB3, first strand: chain 'E' and resid 20 through 22 Processing sheet with id=AB4, first strand: chain 'E' and resid 37 through 43 Processing sheet with id=AB5, first strand: chain 'E' and resid 116 through 120 Processing sheet with id=AB6, first strand: chain 'A' and resid 37 through 43 removed outlier: 12.325A pdb=" N GLN A 53 " --> pdb=" O SER B 3 " (cutoff:3.500A) removed outlier: 11.392A pdb=" N THR B 5 " --> pdb=" O GLN A 53 " (cutoff:3.500A) removed outlier: 11.485A pdb=" N SER A 55 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 11.297A pdb=" N SER B 7 " --> pdb=" O SER A 55 " (cutoff:3.500A) removed outlier: 11.119A pdb=" N THR A 57 " --> pdb=" O SER B 7 " (cutoff:3.500A) removed outlier: 10.787A pdb=" N SER B 9 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 10.437A pdb=" N GLU A 59 " --> pdb=" O SER B 9 " (cutoff:3.500A) removed outlier: 10.250A pdb=" N THR B 11 " --> pdb=" O GLU A 59 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ALA A 61 " --> pdb=" O THR B 11 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER B 13 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL A 154 " --> pdb=" O LEU B 8 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 37 through 43 removed outlier: 12.325A pdb=" N GLN A 53 " --> pdb=" O SER B 3 " (cutoff:3.500A) removed outlier: 11.392A pdb=" N THR B 5 " --> pdb=" O GLN A 53 " (cutoff:3.500A) removed outlier: 11.485A pdb=" N SER A 55 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 11.297A pdb=" N SER B 7 " --> pdb=" O SER A 55 " (cutoff:3.500A) removed outlier: 11.119A pdb=" N THR A 57 " --> pdb=" O SER B 7 " (cutoff:3.500A) removed outlier: 10.787A pdb=" N SER B 9 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 10.437A pdb=" N GLU A 59 " --> pdb=" O SER B 9 " (cutoff:3.500A) removed outlier: 10.250A pdb=" N THR B 11 " --> pdb=" O GLU A 59 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ALA A 61 " --> pdb=" O THR B 11 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER B 13 " --> pdb=" O ALA A 61 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 20 through 22 Processing sheet with id=AB9, first strand: chain 'B' and resid 20 through 22 Processing sheet with id=AC1, first strand: chain 'A' and resid 20 through 22 Processing sheet with id=AC2, first strand: chain 'A' and resid 20 through 22 308 hydrogen bonds defined for protein. 783 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.71 Time building geometry restraints manager: 0.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2056 1.34 - 1.46: 1136 1.46 - 1.58: 2938 1.58 - 1.70: 0 1.70 - 1.81: 10 Bond restraints: 6140 Sorted by residual: bond pdb=" CB ASP D 37 " pdb=" CG ASP D 37 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.36e+00 bond pdb=" CB GLN B 34 " pdb=" CG GLN B 34 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.31e+00 bond pdb=" CG GLU C 141 " pdb=" CD GLU C 141 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.28e+00 bond pdb=" CB ASP B 37 " pdb=" CG ASP B 37 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.25e+00 bond pdb=" CB GLN E 49 " pdb=" CG GLN E 49 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.10e+00 ... (remaining 6135 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 8231 1.79 - 3.59: 129 3.59 - 5.38: 35 5.38 - 7.17: 6 7.17 - 8.97: 1 Bond angle restraints: 8402 Sorted by residual: angle pdb=" CA GLN B 34 " pdb=" CB GLN B 34 " pdb=" CG GLN B 34 " ideal model delta sigma weight residual 114.10 120.73 -6.63 2.00e+00 2.50e-01 1.10e+01 angle pdb=" CB LYS A 145 " pdb=" CG LYS A 145 " pdb=" CD LYS A 145 " ideal model delta sigma weight residual 111.30 118.38 -7.08 2.30e+00 1.89e-01 9.47e+00 angle pdb=" C GLN D 49 " pdb=" CA GLN D 49 " pdb=" CB GLN D 49 " ideal model delta sigma weight residual 109.54 114.97 -5.43 1.84e+00 2.95e-01 8.72e+00 angle pdb=" N VAL E 76 " pdb=" CA VAL E 76 " pdb=" C VAL E 76 " ideal model delta sigma weight residual 112.98 109.47 3.51 1.25e+00 6.40e-01 7.89e+00 angle pdb=" CB GLN B 34 " pdb=" CG GLN B 34 " pdb=" CD GLN B 34 " ideal model delta sigma weight residual 112.60 117.13 -4.53 1.70e+00 3.46e-01 7.11e+00 ... (remaining 8397 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 3349 17.90 - 35.80: 322 35.80 - 53.71: 95 53.71 - 71.61: 17 71.61 - 89.51: 4 Dihedral angle restraints: 3787 sinusoidal: 1424 harmonic: 2363 Sorted by residual: dihedral pdb=" CA ASN C 143 " pdb=" C ASN C 143 " pdb=" N LYS C 144 " pdb=" CA LYS C 144 " ideal model delta harmonic sigma weight residual 180.00 156.72 23.28 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CB CYS A 99 " pdb=" SG CYS A 99 " pdb=" SG CYS A 138 " pdb=" CB CYS A 138 " ideal model delta sinusoidal sigma weight residual -86.00 -49.16 -36.84 1 1.00e+01 1.00e-02 1.92e+01 dihedral pdb=" CB CYS E 99 " pdb=" SG CYS E 99 " pdb=" SG CYS E 138 " pdb=" CB CYS E 138 " ideal model delta sinusoidal sigma weight residual -86.00 -49.24 -36.76 1 1.00e+01 1.00e-02 1.91e+01 ... (remaining 3784 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 622 0.028 - 0.055: 241 0.055 - 0.083: 97 0.083 - 0.110: 79 0.110 - 0.138: 19 Chirality restraints: 1058 Sorted by residual: chirality pdb=" CA ILE A 134 " pdb=" N ILE A 134 " pdb=" C ILE A 134 " pdb=" CB ILE A 134 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" CA ILE C 134 " pdb=" N ILE C 134 " pdb=" C ILE C 134 " pdb=" CB ILE C 134 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CA ILE B 134 " pdb=" N ILE B 134 " pdb=" C ILE B 134 " pdb=" CB ILE B 134 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 1055 not shown) Planarity restraints: 1103 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU C 141 " 0.004 2.00e-02 2.50e+03 8.90e-03 7.92e-01 pdb=" CD GLU C 141 " -0.015 2.00e-02 2.50e+03 pdb=" OE1 GLU C 141 " 0.006 2.00e-02 2.50e+03 pdb=" OE2 GLU C 141 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 154 " -0.004 2.00e-02 2.50e+03 8.53e-03 7.28e-01 pdb=" C VAL D 154 " 0.015 2.00e-02 2.50e+03 pdb=" O VAL D 154 " -0.006 2.00e-02 2.50e+03 pdb=" N GLU D 155 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU E 141 " 0.004 2.00e-02 2.50e+03 8.22e-03 6.76e-01 pdb=" CD GLU E 141 " -0.014 2.00e-02 2.50e+03 pdb=" OE1 GLU E 141 " 0.005 2.00e-02 2.50e+03 pdb=" OE2 GLU E 141 " 0.005 2.00e-02 2.50e+03 ... (remaining 1100 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 52 2.50 - 3.10: 4592 3.10 - 3.70: 8909 3.70 - 4.30: 12806 4.30 - 4.90: 21434 Nonbonded interactions: 47793 Sorted by model distance: nonbonded pdb=" OE1 GLU C 52 " pdb="CA CA C 202 " model vdw 1.905 2.510 nonbonded pdb=" OD1 ASP C 46 " pdb="CA CA C 202 " model vdw 2.175 2.510 nonbonded pdb=" OE2 GLU D 4 " pdb="CA CA C 201 " model vdw 2.184 2.510 nonbonded pdb=" OD1 ASP B 18 " pdb="CA CA B 203 " model vdw 2.215 2.510 nonbonded pdb=" OE2 GLU C 4 " pdb="CA CA B 201 " model vdw 2.221 2.510 ... (remaining 47788 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 10 through 203) selection = (chain 'C' and resid 10 through 203) selection = (chain 'D' and resid 10 through 203) selection = (chain 'E' and resid 10 through 203) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.060 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6145 Z= 0.158 Angle : 0.631 8.967 8412 Z= 0.340 Chirality : 0.043 0.138 1058 Planarity : 0.003 0.020 1103 Dihedral : 15.918 89.511 2230 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.55 % Allowed : 21.52 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 are not related in a simple way. whole: 1.75 (0.31), residues: 796 helix: None (None), residues: 0 sheet: 1.40 (0.30), residues: 317 loop : 1.16 (0.30), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.001 TYR B 35 PHE 0.006 0.001 PHE E 71 TRP 0.002 0.001 TRP E 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 ( 6140) covalent geometry : angle 0.63110 / 0.34 ( 8402) SS BOND : bond 0.00178 / 0.10 ( 5) SS BOND : angle 0.66347 / 0.39 ( 10) hydrogen bonds : bond 0.17324 / 11.85 ( 248) hydrogen bonds : angle 9.83537 / 6.89 ( 783) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.240 Fit side-chains REVERT: C 139 ASP cc_start: 0.8477 (p0) cc_final: 0.8183 (p0) REVERT: D 86 LYS cc_start: 0.8405 (mtpp) cc_final: 0.8110 (mttm) REVERT: D 139 ASP cc_start: 0.8359 (p0) cc_final: 0.8045 (p0) REVERT: E 20 ASP cc_start: 0.7440 (m-30) cc_final: 0.7047 (t0) REVERT: E 22 LYS cc_start: 0.8448 (mttm) cc_final: 0.8243 (ptpp) REVERT: E 35 TYR cc_start: 0.6180 (m-80) cc_final: 0.4645 (t80) REVERT: E 127 LYS cc_start: 0.9211 (mtmm) cc_final: 0.8863 (mtpp) REVERT: B 139 ASP cc_start: 0.8186 (p0) cc_final: 0.7741 (p0) REVERT: A 145 LYS cc_start: 0.8975 (tppt) cc_final: 0.8630 (tptp) outliers start: 11 outliers final: 10 residues processed: 69 average time/residue: 0.0849 time to fit residues: 7.4628 Evaluate side-chains 63 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 99 CYS Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 138 CYS Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 162 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN A 108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.083452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.066135 restraints weight = 16607.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.068538 restraints weight = 8700.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.070160 restraints weight = 5522.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.071259 restraints weight = 3949.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.072022 restraints weight = 3048.616| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 6145 Z= 0.254 Angle : 0.604 8.053 8412 Z= 0.314 Chirality : 0.045 0.158 1058 Planarity : 0.003 0.032 1103 Dihedral : 6.177 56.669 841 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.08 % Allowed : 17.58 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 are not related in a simple way. whole: 1.53 (0.30), residues: 796 helix: -3.53 (0.69), residues: 24 sheet: 1.78 (0.29), residues: 304 loop : 0.87 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR A 35 PHE 0.007 0.002 PHE E 71 TRP 0.003 0.001 TRP E 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.25 ( 6140) covalent geometry : angle 0.60229 / 0.31 ( 8402) SS BOND : bond 0.00273 / 0.16 ( 5) SS BOND : angle 1.30154 / 0.74 ( 10) hydrogen bonds : bond 0.03429 / 2.32 ( 248) hydrogen bonds : angle 6.30544 / 4.43 ( 783) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 66 time to evaluate : 0.131 Fit side-chains revert: symmetry clash REVERT: C 139 ASP cc_start: 0.8197 (p0) cc_final: 0.7790 (p0) REVERT: C 144 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7715 (pttt) REVERT: D 86 LYS cc_start: 0.8428 (mtpp) cc_final: 0.8017 (mttm) REVERT: D 139 ASP cc_start: 0.8391 (p0) cc_final: 0.8102 (p0) REVERT: D 144 LYS cc_start: 0.8801 (ttmt) cc_final: 0.8490 (ttpp) REVERT: E 20 ASP cc_start: 0.7716 (m-30) cc_final: 0.6928 (t0) REVERT: E 35 TYR cc_start: 0.6338 (m-80) cc_final: 0.4610 (t80) REVERT: E 37 ASP cc_start: 0.7618 (t0) cc_final: 0.7205 (t0) REVERT: E 59 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.7784 (mt-10) REVERT: E 60 LYS cc_start: 0.8108 (mttt) cc_final: 0.6996 (mmtt) REVERT: E 127 LYS cc_start: 0.9384 (mtmm) cc_final: 0.8913 (mtpp) REVERT: E 139 ASP cc_start: 0.8638 (p0) cc_final: 0.8177 (p0) REVERT: B 139 ASP cc_start: 0.7914 (p0) cc_final: 0.7304 (p0) outliers start: 29 outliers final: 21 residues processed: 88 average time/residue: 0.0632 time to fit residues: 7.2130 Evaluate side-chains 80 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 57 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 138 CYS Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 162 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 54 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 108 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.084018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.066511 restraints weight = 16656.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.068937 restraints weight = 8713.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.070594 restraints weight = 5537.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.071640 restraints weight = 3943.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.072442 restraints weight = 3074.238| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6145 Z= 0.202 Angle : 0.566 7.797 8412 Z= 0.296 Chirality : 0.045 0.146 1058 Planarity : 0.003 0.026 1103 Dihedral : 5.593 56.089 833 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.94 % Allowed : 18.42 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 are not related in a simple way. whole: 1.93 (0.31), residues: 796 helix: None (None), residues: 0 sheet: 1.77 (0.29), residues: 312 loop : 1.09 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.001 TYR D 35 PHE 0.008 0.001 PHE E 71 TRP 0.003 0.001 TRP C 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 ( 6140) covalent geometry : angle 0.56370 / 0.29 ( 8402) SS BOND : bond 0.00343 / 0.19 ( 5) SS BOND : angle 1.65610 / 0.90 ( 10) hydrogen bonds : bond 0.02868 / 1.93 ( 248) hydrogen bonds : angle 6.05166 / 4.27 ( 783) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 65 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: C 133 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7608 (pp20) REVERT: C 139 ASP cc_start: 0.8250 (p0) cc_final: 0.7641 (p0) REVERT: D 86 LYS cc_start: 0.8416 (mtpp) cc_final: 0.7997 (mttm) REVERT: D 139 ASP cc_start: 0.8438 (p0) cc_final: 0.8151 (p0) REVERT: D 144 LYS cc_start: 0.8826 (ttmt) cc_final: 0.8469 (ttpp) REVERT: D 152 ASN cc_start: 0.8878 (OUTLIER) cc_final: 0.8590 (t0) REVERT: E 20 ASP cc_start: 0.7621 (m-30) cc_final: 0.6701 (t0) REVERT: E 35 TYR cc_start: 0.6362 (m-80) cc_final: 0.4608 (t80) REVERT: E 37 ASP cc_start: 0.7658 (t0) cc_final: 0.7445 (t0) REVERT: E 60 LYS cc_start: 0.7977 (mttt) cc_final: 0.6817 (mmtt) REVERT: E 127 LYS cc_start: 0.9324 (mtmm) cc_final: 0.8858 (mtpp) REVERT: B 139 ASP cc_start: 0.8024 (p0) cc_final: 0.7395 (p0) REVERT: A 145 LYS cc_start: 0.9229 (tppt) cc_final: 0.8930 (tptt) outliers start: 28 outliers final: 19 residues processed: 87 average time/residue: 0.0677 time to fit residues: 7.6514 Evaluate side-chains 84 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain D residue 138 CYS Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 162 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 70 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 108 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.083930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.066333 restraints weight = 16497.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.068783 restraints weight = 8561.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.070471 restraints weight = 5411.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.071622 restraints weight = 3850.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.072353 restraints weight = 2981.253| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6145 Z= 0.150 Angle : 0.525 7.611 8412 Z= 0.276 Chirality : 0.044 0.141 1058 Planarity : 0.003 0.024 1103 Dihedral : 5.213 44.623 833 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.09 % Allowed : 20.68 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 are not related in a simple way. whole: 2.07 (0.31), residues: 796 helix: None (None), residues: 0 sheet: 1.87 (0.28), residues: 312 loop : 1.18 (0.31), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.001 TYR D 35 PHE 0.007 0.001 PHE E 71 TRP 0.002 0.000 TRP B 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 6140) covalent geometry : angle 0.52376 / 0.28 ( 8402) SS BOND : bond 0.00304 / 0.17 ( 5) SS BOND : angle 1.13979 / 0.67 ( 10) hydrogen bonds : bond 0.02481 / 1.68 ( 248) hydrogen bonds : angle 5.76298 / 4.08 ( 783) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.141 Fit side-chains revert: symmetry clash REVERT: C 139 ASP cc_start: 0.7982 (p0) cc_final: 0.7613 (p0) REVERT: D 86 LYS cc_start: 0.8415 (mtpp) cc_final: 0.8019 (mttm) REVERT: D 139 ASP cc_start: 0.8436 (p0) cc_final: 0.8085 (p0) REVERT: D 144 LYS cc_start: 0.8843 (ttmt) cc_final: 0.8464 (ttpp) REVERT: E 20 ASP cc_start: 0.7666 (m-30) cc_final: 0.6509 (t0) REVERT: E 35 TYR cc_start: 0.6350 (m-80) cc_final: 0.4570 (t80) REVERT: E 37 ASP cc_start: 0.7695 (t0) cc_final: 0.7304 (t0) REVERT: E 59 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.7885 (mt-10) REVERT: E 127 LYS cc_start: 0.9367 (mtmm) cc_final: 0.8910 (mtpp) REVERT: B 139 ASP cc_start: 0.7934 (p0) cc_final: 0.7304 (p0) REVERT: A 104 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8176 (mp) REVERT: A 139 ASP cc_start: 0.8193 (p0) cc_final: 0.7698 (p0) outliers start: 22 outliers final: 13 residues processed: 85 average time/residue: 0.0558 time to fit residues: 6.2666 Evaluate side-chains 73 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 110 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 65 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 9 optimal weight: 0.0270 chunk 5 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 overall best weight: 1.6042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 108 GLN D 108 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.081376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.063748 restraints weight = 17137.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.066087 restraints weight = 9101.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.067723 restraints weight = 5873.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.068861 restraints weight = 4239.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.069658 restraints weight = 3308.296| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6145 Z= 0.242 Angle : 0.583 7.790 8412 Z= 0.302 Chirality : 0.045 0.146 1058 Planarity : 0.003 0.024 1103 Dihedral : 4.952 37.411 830 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.22 % Allowed : 19.55 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 are not related in a simple way. whole: 1.89 (0.31), residues: 796 helix: None (None), residues: 0 sheet: 1.75 (0.28), residues: 312 loop : 1.06 (0.31), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.001 TYR D 35 PHE 0.008 0.002 PHE E 71 TRP 0.002 0.001 TRP B 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.24 ( 6140) covalent geometry : angle 0.57927 / 0.30 ( 8402) SS BOND : bond 0.00168 / 0.10 ( 5) SS BOND : angle 1.95347 / 1.06 ( 10) hydrogen bonds : bond 0.02536 / 1.70 ( 248) hydrogen bonds : angle 5.81811 / 4.12 ( 783) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 60 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 133 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7657 (pp20) REVERT: C 139 ASP cc_start: 0.8156 (p0) cc_final: 0.7705 (p0) REVERT: D 86 LYS cc_start: 0.8418 (mtpp) cc_final: 0.7977 (mttm) REVERT: D 139 ASP cc_start: 0.8445 (p0) cc_final: 0.8129 (p0) REVERT: E 35 TYR cc_start: 0.6150 (m-80) cc_final: 0.4398 (t80) REVERT: E 37 ASP cc_start: 0.7775 (t0) cc_final: 0.7322 (t0) REVERT: E 59 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.7865 (mt-10) REVERT: E 127 LYS cc_start: 0.9367 (mtmm) cc_final: 0.8901 (mtpp) REVERT: B 139 ASP cc_start: 0.8038 (p0) cc_final: 0.7439 (p0) REVERT: B 152 ASN cc_start: 0.9172 (OUTLIER) cc_final: 0.8961 (t0) REVERT: A 104 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8206 (mp) REVERT: A 139 ASP cc_start: 0.8238 (p0) cc_final: 0.7763 (p0) outliers start: 30 outliers final: 18 residues processed: 86 average time/residue: 0.0659 time to fit residues: 7.5091 Evaluate side-chains 78 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 56 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 162 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 50 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.079996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.062156 restraints weight = 16959.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.064433 restraints weight = 9199.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.066033 restraints weight = 6003.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.067133 restraints weight = 4381.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.067916 restraints weight = 3450.861| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 6145 Z= 0.300 Angle : 0.634 7.847 8412 Z= 0.327 Chirality : 0.045 0.146 1058 Planarity : 0.003 0.025 1103 Dihedral : 5.155 38.844 830 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.78 % Allowed : 19.83 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 are not related in a simple way. whole: 1.66 (0.30), residues: 796 helix: None (None), residues: 0 sheet: 1.54 (0.28), residues: 312 loop : 0.94 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.001 TYR D 35 PHE 0.009 0.002 PHE C 125 TRP 0.003 0.001 TRP B 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00667 / 0.30 ( 6140) covalent geometry : angle 0.63156 / 0.33 ( 8402) SS BOND : bond 0.00240 / 0.15 ( 5) SS BOND : angle 1.72925 / 0.94 ( 10) hydrogen bonds : bond 0.02600 / 1.75 ( 248) hydrogen bonds : angle 5.90205 / 4.18 ( 783) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 62 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 133 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7713 (pp20) REVERT: C 139 ASP cc_start: 0.8162 (p0) cc_final: 0.7731 (p0) REVERT: D 49 GLN cc_start: 0.8799 (tm-30) cc_final: 0.8597 (tm-30) REVERT: D 86 LYS cc_start: 0.8440 (mtpp) cc_final: 0.7942 (mttm) REVERT: D 139 ASP cc_start: 0.8483 (p0) cc_final: 0.8175 (p0) REVERT: E 35 TYR cc_start: 0.6148 (m-80) cc_final: 0.4373 (t80) REVERT: E 37 ASP cc_start: 0.7780 (t0) cc_final: 0.7386 (t0) REVERT: E 59 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.7862 (mt-10) REVERT: E 127 LYS cc_start: 0.9371 (mtmm) cc_final: 0.8899 (mtpp) REVERT: E 133 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.6364 (tm-30) REVERT: E 139 ASP cc_start: 0.8718 (p0) cc_final: 0.8319 (p0) REVERT: B 139 ASP cc_start: 0.8051 (p0) cc_final: 0.7439 (p0) REVERT: A 104 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8256 (mp) REVERT: A 139 ASP cc_start: 0.8255 (p0) cc_final: 0.7810 (p0) REVERT: A 144 LYS cc_start: 0.8661 (ttmm) cc_final: 0.8313 (ttmt) outliers start: 34 outliers final: 23 residues processed: 90 average time/residue: 0.0631 time to fit residues: 7.4715 Evaluate side-chains 86 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 59 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 99 CYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 162 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 21 optimal weight: 0.8980 chunk 41 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN A 108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.082256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.064514 restraints weight = 16860.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.066864 restraints weight = 8991.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.068504 restraints weight = 5784.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.069620 restraints weight = 4172.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.070358 restraints weight = 3262.331| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6145 Z= 0.158 Angle : 0.559 7.382 8412 Z= 0.294 Chirality : 0.044 0.139 1058 Planarity : 0.003 0.034 1103 Dihedral : 4.946 38.593 830 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.80 % Allowed : 20.96 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 are not related in a simple way. whole: 1.80 (0.30), residues: 796 helix: None (None), residues: 0 sheet: 1.60 (0.28), residues: 310 loop : 1.06 (0.31), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYR D 35 PHE 0.008 0.001 PHE E 71 TRP 0.003 0.001 TRP C 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 ( 6140) covalent geometry : angle 0.55733 / 0.29 ( 8402) SS BOND : bond 0.00236 / 0.15 ( 5) SS BOND : angle 1.41305 / 0.78 ( 10) hydrogen bonds : bond 0.02209 / 1.49 ( 248) hydrogen bonds : angle 5.70727 / 4.05 ( 783) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 63 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 20 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.7270 (m-30) REVERT: D 86 LYS cc_start: 0.8369 (mtpp) cc_final: 0.7890 (mttm) REVERT: D 139 ASP cc_start: 0.8515 (p0) cc_final: 0.8208 (p0) REVERT: E 35 TYR cc_start: 0.6073 (m-80) cc_final: 0.4235 (t80) REVERT: E 37 ASP cc_start: 0.7684 (t0) cc_final: 0.7325 (t0) REVERT: E 59 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.7746 (mt-10) REVERT: E 127 LYS cc_start: 0.9302 (mtmm) cc_final: 0.8847 (mtpp) REVERT: E 133 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.6283 (tm-30) REVERT: E 139 ASP cc_start: 0.8777 (p0) cc_final: 0.8400 (p0) REVERT: B 139 ASP cc_start: 0.8157 (p0) cc_final: 0.7570 (p0) REVERT: A 104 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8167 (mp) REVERT: A 139 ASP cc_start: 0.8365 (p0) cc_final: 0.7881 (p0) outliers start: 27 outliers final: 16 residues processed: 85 average time/residue: 0.0686 time to fit residues: 7.6349 Evaluate side-chains 76 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 99 CYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 162 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 10 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 71 optimal weight: 0.2980 chunk 5 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 40 optimal weight: 0.0060 chunk 59 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 108 GLN D 49 GLN D 108 GLN D 110 ASN E 106 ASN A 108 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.083721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.066303 restraints weight = 16801.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.068652 restraints weight = 8783.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.070295 restraints weight = 5598.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.071424 restraints weight = 4006.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.072147 restraints weight = 3106.156| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6145 Z= 0.130 Angle : 0.553 7.700 8412 Z= 0.289 Chirality : 0.044 0.141 1058 Planarity : 0.003 0.033 1103 Dihedral : 4.879 37.656 830 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.53 % Allowed : 21.94 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 are not related in a simple way. whole: 1.87 (0.30), residues: 796 helix: None (None), residues: 0 sheet: 1.64 (0.28), residues: 310 loop : 1.13 (0.31), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR D 35 PHE 0.008 0.001 PHE E 71 TRP 0.002 0.000 TRP C 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 6140) covalent geometry : angle 0.55132 / 0.29 ( 8402) SS BOND : bond 0.00177 / 0.11 ( 5) SS BOND : angle 1.23603 / 0.67 ( 10) hydrogen bonds : bond 0.02075 / 1.39 ( 248) hydrogen bonds : angle 5.51873 / 3.93 ( 783) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 20 ASP cc_start: 0.7362 (OUTLIER) cc_final: 0.7133 (m-30) REVERT: D 86 LYS cc_start: 0.8384 (mtpp) cc_final: 0.7944 (mttm) REVERT: D 139 ASP cc_start: 0.8434 (p0) cc_final: 0.8111 (p0) REVERT: E 35 TYR cc_start: 0.6116 (m-80) cc_final: 0.4201 (t80) REVERT: E 37 ASP cc_start: 0.7772 (t0) cc_final: 0.7473 (t0) REVERT: E 59 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.7831 (mt-10) REVERT: E 127 LYS cc_start: 0.9347 (mtmm) cc_final: 0.8902 (mtpp) REVERT: E 133 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6382 (tm-30) REVERT: A 104 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8216 (mp) REVERT: A 139 ASP cc_start: 0.8292 (p0) cc_final: 0.7798 (p0) REVERT: A 144 LYS cc_start: 0.8256 (ttmt) cc_final: 0.7955 (ptpt) outliers start: 18 outliers final: 12 residues processed: 74 average time/residue: 0.0720 time to fit residues: 6.9651 Evaluate side-chains 79 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 99 CYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 104 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 74 optimal weight: 0.2980 chunk 71 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 40 optimal weight: 0.0970 chunk 11 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 49 GLN E 106 ASN B 143 ASN A 108 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.084621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.067023 restraints weight = 16773.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.069472 restraints weight = 8596.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.071126 restraints weight = 5418.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.072285 restraints weight = 3875.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.073044 restraints weight = 2988.409| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6145 Z= 0.129 Angle : 0.532 7.557 8412 Z= 0.280 Chirality : 0.044 0.136 1058 Planarity : 0.003 0.037 1103 Dihedral : 4.805 36.430 830 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.52 % Allowed : 21.10 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 are not related in a simple way. whole: 1.96 (0.30), residues: 796 helix: None (None), residues: 0 sheet: 1.67 (0.27), residues: 310 loop : 1.20 (0.31), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR B 35 PHE 0.008 0.001 PHE E 71 TRP 0.002 0.000 TRP C 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 6140) covalent geometry : angle 0.53079 / 0.28 ( 8402) SS BOND : bond 0.00201 / 0.12 ( 5) SS BOND : angle 1.17421 / 0.64 ( 10) hydrogen bonds : bond 0.02039 / 1.37 ( 248) hydrogen bonds : angle 5.44897 / 3.87 ( 783) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 65 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 20 ASP cc_start: 0.7340 (OUTLIER) cc_final: 0.7135 (m-30) REVERT: C 133 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7636 (pp20) REVERT: C 139 ASP cc_start: 0.8247 (p0) cc_final: 0.7648 (p0) REVERT: D 139 ASP cc_start: 0.8429 (p0) cc_final: 0.8102 (p0) REVERT: E 35 TYR cc_start: 0.6127 (m-80) cc_final: 0.4219 (t80) REVERT: E 37 ASP cc_start: 0.7778 (t0) cc_final: 0.7500 (t0) REVERT: E 59 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.7848 (mt-10) REVERT: E 127 LYS cc_start: 0.9348 (mtmm) cc_final: 0.8905 (mtpp) REVERT: E 133 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6403 (tm-30) REVERT: B 139 ASP cc_start: 0.7997 (p0) cc_final: 0.7392 (p0) REVERT: A 104 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8222 (mp) REVERT: A 139 ASP cc_start: 0.8272 (p0) cc_final: 0.7779 (p0) REVERT: A 144 LYS cc_start: 0.8207 (ttmt) cc_final: 0.7940 (ptpt) outliers start: 25 outliers final: 15 residues processed: 85 average time/residue: 0.0680 time to fit residues: 7.5902 Evaluate side-chains 77 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 99 CYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 162 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 73 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 67 optimal weight: 0.2980 chunk 65 optimal weight: 0.9990 chunk 78 optimal weight: 0.4980 chunk 4 optimal weight: 0.0970 chunk 76 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 108 GLN D 108 GLN D 152 ASN ** E 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.084940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.067321 restraints weight = 16557.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.069797 restraints weight = 8512.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.071488 restraints weight = 5342.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.072552 restraints weight = 3799.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.073386 restraints weight = 2968.412| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6145 Z= 0.131 Angle : 0.567 7.523 8412 Z= 0.297 Chirality : 0.044 0.138 1058 Planarity : 0.003 0.037 1103 Dihedral : 4.763 35.248 830 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.81 % Allowed : 21.66 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 are not related in a simple way. whole: 2.00 (0.31), residues: 796 helix: None (None), residues: 0 sheet: 1.72 (0.27), residues: 310 loop : 1.22 (0.31), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR B 35 PHE 0.008 0.001 PHE E 71 TRP 0.002 0.000 TRP C 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 6140) covalent geometry : angle 0.56577 / 0.30 ( 8402) SS BOND : bond 0.00214 / 0.13 ( 5) SS BOND : angle 1.12455 / 0.61 ( 10) hydrogen bonds : bond 0.02002 / 1.34 ( 248) hydrogen bonds : angle 5.38073 / 3.82 ( 783) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 133 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7579 (pp20) REVERT: C 139 ASP cc_start: 0.8290 (p0) cc_final: 0.7688 (p0) REVERT: D 34 GLN cc_start: 0.8708 (pm20) cc_final: 0.8330 (pm20) REVERT: D 139 ASP cc_start: 0.8491 (p0) cc_final: 0.8223 (p0) REVERT: E 35 TYR cc_start: 0.6108 (m-80) cc_final: 0.4235 (t80) REVERT: E 37 ASP cc_start: 0.7725 (t0) cc_final: 0.7472 (t0) REVERT: E 59 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.7828 (mt-10) REVERT: E 127 LYS cc_start: 0.9304 (mtmm) cc_final: 0.8872 (mtpp) REVERT: E 133 GLU cc_start: 0.6823 (OUTLIER) cc_final: 0.6344 (tm-30) REVERT: A 139 ASP cc_start: 0.8351 (p0) cc_final: 0.7845 (p0) REVERT: A 144 LYS cc_start: 0.8201 (ttmt) cc_final: 0.7942 (ptpt) outliers start: 20 outliers final: 16 residues processed: 76 average time/residue: 0.0741 time to fit residues: 7.3059 Evaluate side-chains 77 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 99 CYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 162 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 2 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 0.1980 chunk 29 optimal weight: 0.2980 chunk 30 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.085231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.067771 restraints weight = 16720.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.070231 restraints weight = 8548.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.071904 restraints weight = 5372.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.073069 restraints weight = 3806.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.073857 restraints weight = 2920.305| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 6145 Z= 0.184 Angle : 1.003 59.199 8412 Z= 0.603 Chirality : 0.051 0.868 1058 Planarity : 0.004 0.082 1103 Dihedral : 4.763 35.230 830 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.81 % Allowed : 21.38 % Favored : 75.81 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 14.29 % 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 are not related in a simple way. whole: 1.95 (0.30), residues: 796 helix: None (None), residues: 0 sheet: 1.72 (0.27), residues: 310 loop : 1.17 (0.31), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR B 35 PHE 0.008 0.001 PHE E 71 TRP 0.002 0.000 TRP C 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.18 ( 6140) covalent geometry : angle 1.00310 / 0.60 ( 8402) SS BOND : bond 0.00219 / 0.13 ( 5) SS BOND : angle 1.13110 / 0.61 ( 10) hydrogen bonds : bond 0.02008 / 1.34 ( 248) hydrogen bonds : angle 5.37963 / 3.82 ( 783) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1050.31 seconds wall clock time: 18 minutes 45.34 seconds (1125.34 seconds total)