Starting phenix.real_space_refine on Thu Jul 2 03:16:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sj2_54935/07_2026/9sj2_54935.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sj2_54935/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9sj2_54935/07_2026/9sj2_54935.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sj2_54935/07_2026/9sj2_54935.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9sj2_54935/07_2026/9sj2_54935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sj2_54935/07_2026/9sj2_54935.map" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Time building chain proxies: 1.01, per 1000 atoms: 0.17 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: 0.31 Conformation dependent library (CDL) restraints added in 146.2 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: 0.76 Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 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 3.250 nonbonded pdb=" OD1 ASP C 46 " pdb="CA CA C 202 " model vdw 2.175 3.250 nonbonded pdb=" OE2 GLU D 4 " pdb="CA CA C 201 " model vdw 2.184 3.250 nonbonded pdb=" OD1 ASP B 18 " pdb="CA CA B 203 " model vdw 2.215 3.250 nonbonded pdb=" OE2 GLU C 4 " pdb="CA CA B 201 " model vdw 2.221 3.250 ... (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: 3.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.190 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.000 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:0.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.840 ------------------------------------------------------------------------------- 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 : 0.159 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: 0.0800 time to fit residues: 6.9908 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 : 0.142 ------------------------------------------------------------------------------- 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: 0.7980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 0.0010 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- 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** A 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.086130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.068716 restraints weight = 16618.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.071237 restraints weight = 8267.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.072961 restraints weight = 5014.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.074123 restraints weight = 3466.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.074919 restraints weight = 2620.346| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1028 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= 0.155 Angle : 0.553 8.079 8412 Z= 0.295 Chirality : 0.045 0.158 1058 Planarity : 0.003 0.031 1103 Dihedral : 6.083 59.399 841 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.25 % Allowed : 18.57 % Favored : 79.18 % 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: 1.51 (0.31), residues: 796 helix: -3.05 (0.91), residues: 24 sheet: 1.59 (0.29), residues: 317 loop : 0.95 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.001 TYR A 35 PHE 0.007 0.001 PHE E 71 TRP 0.001 0.000 TRP C 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 6140) covalent geometry : angle 0.55151 / 0.29 ( 8402) SS BOND : bond 0.00205 / 0.13 ( 5) SS BOND : angle 1.16448 / 0.66 ( 10) hydrogen bonds : bond 0.03319 / 2.27 ( 248) hydrogen bonds : angle 6.36560 / 4.47 ( 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 73 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 139 ASP cc_start: 0.8424 (p0) cc_final: 0.8171 (p0) REVERT: E 20 ASP cc_start: 0.7588 (m-30) cc_final: 0.6773 (t0) REVERT: E 35 TYR cc_start: 0.6417 (m-80) cc_final: 0.4677 (t80) REVERT: E 60 LYS cc_start: 0.8020 (mttt) cc_final: 0.6933 (mmtt) REVERT: E 127 LYS cc_start: 0.9357 (mtmm) cc_final: 0.8893 (mtpp) REVERT: E 139 ASP cc_start: 0.8637 (p0) cc_final: 0.8157 (p0) outliers start: 16 outliers final: 12 residues processed: 68 average time/residue: 0.0766 time to fit residues: 6.6688 Evaluate side-chains 62 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 138 CYS 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 D residue 153 ILE Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 138 CYS Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 153 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 54 optimal weight: 3.9990 chunk 77 optimal weight: 0.0570 chunk 61 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.6902 ------------------------------------------------------------------------------- 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 = 0.3676 r_free = 0.3676 target = 0.086056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.068955 restraints weight = 16551.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.071444 restraints weight = 8137.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.073141 restraints weight = 4930.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.074304 restraints weight = 3403.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.075068 restraints weight = 2573.170| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6145 Z= 0.136 Angle : 0.513 7.473 8412 Z= 0.271 Chirality : 0.044 0.140 1058 Planarity : 0.003 0.025 1103 Dihedral : 5.378 54.024 832 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.23 % Allowed : 18.00 % Favored : 78.76 % 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: 1.97 (0.31), residues: 796 helix: None (None), residues: 0 sheet: 1.78 (0.28), residues: 317 loop : 1.12 (0.31), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.001 TYR D 35 PHE 0.007 0.001 PHE E 71 TRP 0.001 0.000 TRP C 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 ( 6140) covalent geometry : angle 0.50994 / 0.27 ( 8402) SS BOND : bond 0.00479 / 0.26 ( 5) SS BOND : angle 1.79398 / 0.96 ( 10) hydrogen bonds : bond 0.02799 / 1.89 ( 248) hydrogen bonds : angle 5.81037 / 4.11 ( 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 77 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 54 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 103 LYS cc_start: 0.8794 (mtmm) cc_final: 0.8592 (mtmm) REVERT: E 20 ASP cc_start: 0.7528 (m-30) cc_final: 0.6716 (t0) REVERT: E 35 TYR cc_start: 0.6372 (m-80) cc_final: 0.4576 (t80) REVERT: E 37 ASP cc_start: 0.7573 (t0) cc_final: 0.7132 (t0) REVERT: E 59 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.7856 (mt-10) REVERT: E 60 LYS cc_start: 0.8044 (mttt) cc_final: 0.6867 (mmtt) REVERT: E 127 LYS cc_start: 0.9369 (mtmm) cc_final: 0.8930 (mtpp) outliers start: 23 outliers final: 12 residues processed: 72 average time/residue: 0.0712 time to fit residues: 6.6584 Evaluate side-chains 62 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 THR 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 D residue 153 ILE Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain B residue 104 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 70 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 0.0870 chunk 20 optimal weight: 4.9990 chunk 59 optimal weight: 0.0870 chunk 23 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 overall best weight: 1.3540 ------------------------------------------------------------------------------- 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** A 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.084087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.066941 restraints weight = 16814.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.069414 restraints weight = 8306.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.071096 restraints weight = 5075.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.072242 restraints weight = 3525.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.073015 restraints weight = 2682.005| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6145 Z= 0.208 Angle : 0.562 7.710 8412 Z= 0.290 Chirality : 0.045 0.146 1058 Planarity : 0.003 0.023 1103 Dihedral : 4.893 25.103 828 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.36 % Allowed : 18.57 % Favored : 77.07 % 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 (0.31), residues: 796 helix: None (None), residues: 0 sheet: 1.72 (0.28), residues: 312 loop : 1.16 (0.31), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 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 0.00463 / 0.21 ( 6140) covalent geometry : angle 0.55919 / 0.29 ( 8402) SS BOND : bond 0.00250 / 0.14 ( 5) SS BOND : angle 1.61606 / 0.88 ( 10) hydrogen bonds : bond 0.02605 / 1.74 ( 248) hydrogen bonds : angle 5.65172 / 4.01 ( 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 88 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 57 time to evaluate : 0.175 Fit side-chains revert: symmetry clash REVERT: D 49 GLN cc_start: 0.8686 (tm-30) cc_final: 0.8404 (tm-30) REVERT: D 86 LYS cc_start: 0.8387 (mtpp) cc_final: 0.7962 (mttm) REVERT: D 103 LYS cc_start: 0.8808 (mtmm) cc_final: 0.8604 (mtmm) REVERT: D 139 ASP cc_start: 0.8381 (p0) cc_final: 0.8089 (p0) REVERT: E 20 ASP cc_start: 0.7570 (m-30) cc_final: 0.6718 (t0) REVERT: E 35 TYR cc_start: 0.6377 (m-80) cc_final: 0.4579 (t80) REVERT: E 37 ASP cc_start: 0.7651 (t0) cc_final: 0.7230 (t0) REVERT: E 59 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.7829 (mt-10) REVERT: E 60 LYS cc_start: 0.8038 (mttt) cc_final: 0.6906 (mtpt) REVERT: E 127 LYS cc_start: 0.9370 (mtmm) cc_final: 0.8917 (mtpp) outliers start: 31 outliers final: 23 residues processed: 82 average time/residue: 0.0672 time to fit residues: 7.1256 Evaluate side-chains 75 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 51 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 138 CYS 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 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 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 153 ILE Chi-restraints excluded: chain A residue 162 VAL 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: 0.7980 chunk 75 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 4 optimal weight: 0.0980 chunk 39 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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** ** E 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.085168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.067262 restraints weight = 16755.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.069844 restraints weight = 8378.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.071586 restraints weight = 5160.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.072788 restraints weight = 3611.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.073486 restraints weight = 2760.599| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6145 Z= 0.124 Angle : 0.514 8.502 8412 Z= 0.267 Chirality : 0.044 0.136 1058 Planarity : 0.003 0.023 1103 Dihedral : 4.692 28.751 828 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.67 % Allowed : 20.25 % Favored : 77.07 % 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 (0.28), residues: 312 loop : 1.22 (0.31), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.001 TYR D 35 PHE 0.007 0.001 PHE E 71 TRP 0.003 0.000 TRP C 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 6140) covalent geometry : angle 0.51246 / 0.27 ( 8402) SS BOND : bond 0.00245 / 0.13 ( 5) SS BOND : angle 1.31170 / 0.72 ( 10) hydrogen bonds : bond 0.02294 / 1.53 ( 248) hydrogen bonds : angle 5.49984 / 3.93 ( 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 76 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: D 34 GLN cc_start: 0.8670 (pm20) cc_final: 0.8457 (pm20) REVERT: D 35 TYR cc_start: 0.8605 (m-80) cc_final: 0.8398 (m-10) REVERT: D 49 GLN cc_start: 0.8869 (tm-30) cc_final: 0.8667 (tm-30) REVERT: E 35 TYR cc_start: 0.6395 (m-80) cc_final: 0.4674 (t80) REVERT: E 37 ASP cc_start: 0.7596 (t0) cc_final: 0.7220 (t0) REVERT: E 59 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.7818 (mt-10) REVERT: E 127 LYS cc_start: 0.9306 (mtmm) cc_final: 0.8868 (mtpp) REVERT: B 139 ASP cc_start: 0.8120 (p0) cc_final: 0.7512 (p0) REVERT: A 145 LYS cc_start: 0.9172 (tppt) cc_final: 0.8920 (tptt) outliers start: 19 outliers final: 11 residues processed: 71 average time/residue: 0.0651 time to fit residues: 6.0776 Evaluate side-chains 61 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain D residue 138 CYS 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 50 optimal weight: 0.0980 chunk 25 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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** E 49 GLN ** E 68 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 = 0.3591 r_free = 0.3591 target = 0.082326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.064472 restraints weight = 16660.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.066924 restraints weight = 8418.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.068613 restraints weight = 5246.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.069798 restraints weight = 3703.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.070579 restraints weight = 2848.681| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2081 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= 0.238 Angle : 0.573 7.543 8412 Z= 0.297 Chirality : 0.044 0.145 1058 Planarity : 0.003 0.023 1103 Dihedral : 4.740 22.901 827 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.94 % Allowed : 19.83 % 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: 1.86 (0.31), residues: 796 helix: None (None), residues: 0 sheet: 1.61 (0.28), residues: 312 loop : 1.13 (0.31), 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 B 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.24 ( 6140) covalent geometry : angle 0.57068 / 0.30 ( 8402) SS BOND : bond 0.00163 / 0.09 ( 5) SS BOND : angle 1.48590 / 0.81 ( 10) hydrogen bonds : bond 0.02446 / 1.62 ( 248) hydrogen bonds : angle 5.57775 / 3.97 ( 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 79 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 51 time to evaluate : 0.157 Fit side-chains REVERT: C 133 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7623 (pp20) REVERT: D 86 LYS cc_start: 0.8385 (mtpp) cc_final: 0.7952 (mttm) REVERT: D 139 ASP cc_start: 0.8478 (p0) cc_final: 0.8167 (p0) REVERT: E 35 TYR cc_start: 0.6256 (m-80) cc_final: 0.4500 (t80) REVERT: E 37 ASP cc_start: 0.7733 (t0) cc_final: 0.7289 (t0) REVERT: E 59 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.7858 (mt-10) REVERT: E 127 LYS cc_start: 0.9348 (mtmm) cc_final: 0.8901 (mtpp) outliers start: 28 outliers final: 21 residues processed: 74 average time/residue: 0.0735 time to fit residues: 7.0894 Evaluate side-chains 72 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 49 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 ILE 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 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 153 ILE Chi-restraints excluded: chain E residue 59 GLU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 21 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 54 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 77 optimal weight: 0.0030 chunk 20 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 108 GLN D 110 ASN ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 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 = 0.3636 r_free = 0.3636 target = 0.084514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.066746 restraints weight = 16526.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.069283 restraints weight = 8255.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.071018 restraints weight = 5093.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.072149 restraints weight = 3568.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.072994 restraints weight = 2755.517| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6145 Z= 0.129 Angle : 0.527 7.600 8412 Z= 0.274 Chirality : 0.044 0.135 1058 Planarity : 0.003 0.035 1103 Dihedral : 4.589 22.252 827 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.38 % Allowed : 19.69 % 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: 1.89 (0.31), residues: 796 helix: None (None), residues: 0 sheet: 1.60 (0.28), residues: 312 loop : 1.18 (0.31), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.001 TYR D 35 PHE 0.007 0.001 PHE E 71 TRP 0.003 0.001 TRP D 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 ( 6140) covalent geometry : angle 0.52417 / 0.27 ( 8402) SS BOND : bond 0.00229 / 0.14 ( 5) SS BOND : angle 1.60872 / 0.89 ( 10) hydrogen bonds : bond 0.02137 / 1.42 ( 248) hydrogen bonds : angle 5.46204 / 3.91 ( 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 79 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 55 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 139 ASP cc_start: 0.8527 (p0) cc_final: 0.8227 (p0) REVERT: E 35 TYR cc_start: 0.6260 (m-80) cc_final: 0.4568 (t80) REVERT: E 37 ASP cc_start: 0.7656 (t0) cc_final: 0.7265 (t0) REVERT: E 59 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.7847 (mt-10) REVERT: E 127 LYS cc_start: 0.9315 (mtmm) cc_final: 0.8872 (mtpp) REVERT: B 54 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8263 (tt) outliers start: 24 outliers final: 14 residues processed: 76 average time/residue: 0.0636 time to fit residues: 6.3651 Evaluate side-chains 68 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.206 ------------------------------------------------------------------------------- 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 153 ILE Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 100 VAL 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 54 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 110 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 162 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 10 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 71 optimal weight: 0.0010 chunk 5 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 0.1980 chunk 59 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 108 GLN ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN A 108 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.085046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.067430 restraints weight = 16517.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.069973 restraints weight = 8218.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.071720 restraints weight = 5048.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.072893 restraints weight = 3525.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.073692 restraints weight = 2684.951| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6145 Z= 0.124 Angle : 0.522 7.376 8412 Z= 0.271 Chirality : 0.044 0.135 1058 Planarity : 0.003 0.036 1103 Dihedral : 4.507 20.652 827 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.09 % Allowed : 19.55 % Favored : 77.36 % 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: 1.95 (0.31), residues: 796 helix: None (None), residues: 0 sheet: 1.64 (0.28), residues: 312 loop : 1.22 (0.31), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR D 35 PHE 0.007 0.001 PHE E 71 TRP 0.002 0.000 TRP C 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 6140) covalent geometry : angle 0.52026 / 0.27 ( 8402) SS BOND : bond 0.00186 / 0.11 ( 5) SS BOND : angle 1.42436 / 0.79 ( 10) hydrogen bonds : bond 0.02028 / 1.37 ( 248) hydrogen bonds : angle 5.31026 / 3.79 ( 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 76 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 54 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: C 133 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7527 (pp20) REVERT: D 139 ASP cc_start: 0.8514 (p0) cc_final: 0.8207 (p0) REVERT: E 35 TYR cc_start: 0.6252 (m-80) cc_final: 0.4539 (t80) REVERT: E 37 ASP cc_start: 0.7667 (t0) cc_final: 0.7355 (t0) REVERT: E 59 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.7892 (mt-10) REVERT: E 127 LYS cc_start: 0.9310 (mtmm) cc_final: 0.8870 (mtpp) REVERT: B 139 ASP cc_start: 0.8086 (p0) cc_final: 0.7465 (p0) outliers start: 22 outliers final: 16 residues processed: 74 average time/residue: 0.0616 time to fit residues: 6.0511 Evaluate side-chains 67 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.193 ------------------------------------------------------------------------------- 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 133 GLU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain D residue 100 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 74 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 13 optimal weight: 0.0670 chunk 30 optimal weight: 0.0970 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.083858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.065965 restraints weight = 16853.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.068480 restraints weight = 8457.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.070232 restraints weight = 5224.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.071415 restraints weight = 3663.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.072198 restraints weight = 2803.826| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6145 Z= 0.143 Angle : 0.536 7.213 8412 Z= 0.279 Chirality : 0.044 0.137 1058 Planarity : 0.003 0.037 1103 Dihedral : 4.524 20.236 827 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.67 % Allowed : 19.83 % Favored : 77.50 % 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: 1.65 (0.28), residues: 312 loop : 1.19 (0.31), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 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 0.00323 / 0.14 ( 6140) covalent geometry : angle 0.53476 / 0.28 ( 8402) SS BOND : bond 0.00193 / 0.12 ( 5) SS BOND : angle 1.35596 / 0.74 ( 10) hydrogen bonds : bond 0.02065 / 1.37 ( 248) hydrogen bonds : angle 5.31963 / 3.79 ( 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 70 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 51 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: C 133 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7512 (pp20) REVERT: D 86 LYS cc_start: 0.8290 (mtpp) cc_final: 0.7884 (mttm) REVERT: D 119 GLN cc_start: 0.8750 (mp10) cc_final: 0.8488 (mp10) REVERT: D 139 ASP cc_start: 0.8549 (p0) cc_final: 0.8245 (p0) REVERT: E 35 TYR cc_start: 0.6212 (m-80) cc_final: 0.4478 (t80) REVERT: E 37 ASP cc_start: 0.7662 (t0) cc_final: 0.7348 (t0) REVERT: E 59 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.7867 (mt-10) REVERT: E 127 LYS cc_start: 0.9288 (mtmm) cc_final: 0.8842 (mtpp) outliers start: 19 outliers final: 16 residues processed: 66 average time/residue: 0.0759 time to fit residues: 6.5298 Evaluate side-chains 68 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.191 ------------------------------------------------------------------------------- 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 133 GLU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain D residue 100 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 73 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 30 optimal weight: 0.0270 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 overall best weight: 1.1440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.082532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.064560 restraints weight = 16780.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.067022 restraints weight = 8519.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.068750 restraints weight = 5322.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.069934 restraints weight = 3753.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.070688 restraints weight = 2892.701| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6145 Z= 0.188 Angle : 0.561 7.225 8412 Z= 0.290 Chirality : 0.044 0.139 1058 Planarity : 0.003 0.037 1103 Dihedral : 4.636 19.742 827 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.81 % Allowed : 19.69 % Favored : 77.50 % 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: 1.86 (0.31), residues: 796 helix: None (None), residues: 0 sheet: 1.58 (0.28), residues: 312 loop : 1.16 (0.31), residues: 484 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 0.003 0.001 TRP B 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 ( 6140) covalent geometry : angle 0.55948 / 0.29 ( 8402) SS BOND : bond 0.00231 / 0.15 ( 5) SS BOND : angle 1.44340 / 0.78 ( 10) hydrogen bonds : bond 0.02155 / 1.42 ( 248) hydrogen bonds : angle 5.36319 / 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 75 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 55 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 133 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7536 (pp20) REVERT: D 119 GLN cc_start: 0.8768 (mp10) cc_final: 0.8487 (mp10) REVERT: D 139 ASP cc_start: 0.8560 (p0) cc_final: 0.8266 (p0) REVERT: E 35 TYR cc_start: 0.6127 (m-80) cc_final: 0.4325 (t80) REVERT: E 37 ASP cc_start: 0.7708 (t0) cc_final: 0.7377 (t0) REVERT: E 59 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.7879 (mt-10) REVERT: E 127 LYS cc_start: 0.9300 (mtmm) cc_final: 0.8855 (mtpp) REVERT: B 139 ASP cc_start: 0.8157 (p0) cc_final: 0.7546 (p0) outliers start: 20 outliers final: 18 residues processed: 71 average time/residue: 0.0746 time to fit residues: 6.9582 Evaluate side-chains 70 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 50 time to evaluate : 0.151 ------------------------------------------------------------------------------- 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 133 GLU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain D residue 100 VAL 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 46 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 2 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 6 optimal weight: 0.1980 chunk 29 optimal weight: 0.0070 chunk 30 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.085261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.067539 restraints weight = 16620.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.070083 restraints weight = 8231.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.071838 restraints weight = 5055.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.072983 restraints weight = 3523.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.073794 restraints weight = 2714.700| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6145 Z= 0.127 Angle : 0.557 7.192 8412 Z= 0.291 Chirality : 0.044 0.148 1058 Planarity : 0.003 0.037 1103 Dihedral : 4.597 20.661 827 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.81 % Allowed : 20.11 % Favored : 77.07 % 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: 1.63 (0.28), residues: 312 loop : 1.20 (0.31), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR B 35 PHE 0.007 0.001 PHE E 71 TRP 0.003 0.000 TRP C 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 6140) covalent geometry : angle 0.55560 / 0.29 ( 8402) SS BOND : bond 0.00215 / 0.13 ( 5) SS BOND : angle 1.26227 / 0.69 ( 10) hydrogen bonds : bond 0.02024 / 1.34 ( 248) hydrogen bonds : angle 5.33866 / 3.81 ( 783) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1069.92 seconds wall clock time: 19 minutes 8.41 seconds (1148.41 seconds total)