Starting phenix.real_space_refine on Tue Feb 3 19:02:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kyd_62645/02_2026/9kyd_62645.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kyd_62645/02_2026/9kyd_62645.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kyd_62645/02_2026/9kyd_62645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kyd_62645/02_2026/9kyd_62645.map" model { file = "/net/cci-nas-00/data/ceres_data/9kyd_62645/02_2026/9kyd_62645.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kyd_62645/02_2026/9kyd_62645.cif" } resolution = 3.05 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= 0.138 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 4113 2.51 5 N 1056 2.21 5 O 1246 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6440 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1780 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 11, 'TRANS': 213} Chain: "C" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 932 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain: "D" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 932 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain: "E" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 932 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain: "F" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 932 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain: "G" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 932 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Time building chain proxies: 1.66, per 1000 atoms: 0.26 Number of scatterers: 6440 At special positions: 0 Unit cell: (80.08, 83.2, 95.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 25 16.00 O 1246 8.00 N 1056 7.00 C 4113 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 32 " - pdb=" SG CYS C 49 " distance=2.03 Simple disulfide: pdb=" SG CYS C 107 " - pdb=" SG CYS C 113 " distance=2.03 Simple disulfide: pdb=" SG CYS D 32 " - pdb=" SG CYS D 49 " distance=2.03 Simple disulfide: pdb=" SG CYS D 107 " - pdb=" SG CYS D 113 " distance=2.03 Simple disulfide: pdb=" SG CYS E 32 " - pdb=" SG CYS E 49 " distance=2.03 Simple disulfide: pdb=" SG CYS E 107 " - pdb=" SG CYS E 113 " distance=2.03 Simple disulfide: pdb=" SG CYS F 32 " - pdb=" SG CYS F 49 " distance=2.03 Simple disulfide: pdb=" SG CYS F 107 " - pdb=" SG CYS F 113 " distance=2.03 Simple disulfide: pdb=" SG CYS G 32 " - pdb=" SG CYS G 49 " distance=2.03 Simple disulfide: pdb=" SG CYS G 107 " - pdb=" SG CYS G 113 " 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: 0.43 Conformation dependent library (CDL) restraints added in 349.4 milliseconds 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1522 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 9 sheets defined 22.4% alpha, 35.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'B' and resid 16 through 21 Processing helix chain 'B' and resid 34 through 39 removed outlier: 3.757A pdb=" N ILE B 38 " --> pdb=" O LEU B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 71 removed outlier: 4.006A pdb=" N THR B 62 " --> pdb=" O ASP B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 97 through 104 Processing helix chain 'B' and resid 108 through 113 Processing helix chain 'B' and resid 128 through 130 No H-bonds generated for 'chain 'B' and resid 128 through 130' Processing helix chain 'B' and resid 196 through 200 Processing helix chain 'B' and resid 219 through 228 Processing helix chain 'C' and resid 57 through 59 No H-bonds generated for 'chain 'C' and resid 57 through 59' Processing helix chain 'C' and resid 60 through 75 Processing helix chain 'C' and resid 89 through 94 Processing helix chain 'D' and resid 57 through 59 No H-bonds generated for 'chain 'D' and resid 57 through 59' Processing helix chain 'D' and resid 60 through 74 removed outlier: 4.105A pdb=" N GLU D 66 " --> pdb=" O LYS D 62 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN D 67 " --> pdb=" O VAL D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 96 Processing helix chain 'E' and resid 60 through 74 removed outlier: 3.506A pdb=" N GLN E 67 " --> pdb=" O VAL E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 96 Processing helix chain 'F' and resid 2 through 6 removed outlier: 4.592A pdb=" N TYR F 6 " --> pdb=" O THR F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 74 Processing helix chain 'F' and resid 89 through 94 Processing helix chain 'G' and resid 60 through 74 Processing helix chain 'G' and resid 89 through 96 Processing sheet with id=AA1, first strand: chain 'B' and resid 9 through 13 removed outlier: 3.859A pdb=" N LYS B 134 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N GLN B 133 " --> pdb=" O ILE B 154 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ILE B 154 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ALA B 135 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER B 152 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ALA B 137 " --> pdb=" O GLY B 150 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA3, first strand: chain 'B' and resid 186 through 187 Processing sheet with id=AA4, first strand: chain 'G' and resid 9 through 10 removed outlier: 6.640A pdb=" N TYR G 81 " --> pdb=" O VAL G 102 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL G 102 " --> pdb=" O TYR G 81 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N VAL G 102 " --> pdb=" O GLN C 24 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN C 24 " --> pdb=" O VAL G 102 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N HIS C 14 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N VAL C 78 " --> pdb=" O HIS C 14 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY C 103 " --> pdb=" O TYR C 81 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ASP C 83 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LEU C 101 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ILE C 47 " --> pdb=" O ASN C 99 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU C 101 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N CYS C 49 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N GLY C 103 " --> pdb=" O CYS C 49 " (cutoff:3.500A) removed outlier: 12.955A pdb=" N VAL C 51 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 17.481A pdb=" N SER C 105 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL C 36 " --> pdb=" O ILE C 17 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ILE C 17 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 10 through 19 removed outlier: 6.558A pdb=" N LYS D 34 " --> pdb=" O SER D 18 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU D 101 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N CYS D 49 " --> pdb=" O LEU D 101 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N GLY D 103 " --> pdb=" O CYS D 49 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LEU D 101 " --> pdb=" O ASP D 83 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ASP D 83 " --> pdb=" O LEU D 101 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY D 103 " --> pdb=" O TYR D 81 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE D 80 " --> pdb=" O SER D 13 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N SER D 13 " --> pdb=" O ILE D 80 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR D 82 " --> pdb=" O TYR D 11 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N TYR D 11 " --> pdb=" O TYR D 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 46 through 51 removed outlier: 5.988A pdb=" N GLY E 28 " --> pdb=" O GLN E 24 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLN E 24 " --> pdb=" O GLY E 28 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N TYR E 30 " --> pdb=" O VAL E 22 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL E 22 " --> pdb=" O TYR E 30 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N CYS E 32 " --> pdb=" O PHE E 20 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N PHE E 20 " --> pdb=" O CYS E 32 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LYS E 34 " --> pdb=" O SER E 18 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N VAL E 78 " --> pdb=" O HIS E 14 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N VAL E 102 " --> pdb=" O GLN F 24 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN F 24 " --> pdb=" O VAL E 102 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N PHE F 20 " --> pdb=" O SER E 106 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ILE F 17 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL F 36 " --> pdb=" O ILE F 17 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 46 through 51 removed outlier: 5.988A pdb=" N GLY E 28 " --> pdb=" O GLN E 24 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLN E 24 " --> pdb=" O GLY E 28 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N TYR E 30 " --> pdb=" O VAL E 22 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL E 22 " --> pdb=" O TYR E 30 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N CYS E 32 " --> pdb=" O PHE E 20 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N PHE E 20 " --> pdb=" O CYS E 32 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LYS E 34 " --> pdb=" O SER E 18 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N VAL E 78 " --> pdb=" O HIS E 14 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N VAL E 102 " --> pdb=" O GLN F 24 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN F 24 " --> pdb=" O VAL E 102 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N PHE F 20 " --> pdb=" O SER E 106 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N VAL F 78 " --> pdb=" O HIS F 14 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 15 through 16 Processing sheet with id=AA9, first strand: chain 'G' and resid 15 through 16 232 hydrogen bonds defined for protein. 633 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: 0.99 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2057 1.35 - 1.47: 1839 1.47 - 1.59: 2698 1.59 - 1.71: 0 1.71 - 1.83: 27 Bond restraints: 6621 Sorted by residual: bond pdb=" C LEU C 104 " pdb=" N SER C 105 " ideal model delta sigma weight residual 1.330 1.259 0.071 1.39e-02 5.18e+03 2.60e+01 bond pdb=" C ARG B 220 " pdb=" N PRO B 221 " ideal model delta sigma weight residual 1.335 1.355 -0.020 1.36e-02 5.41e+03 2.09e+00 bond pdb=" C VAL E 102 " pdb=" O VAL E 102 " ideal model delta sigma weight residual 1.241 1.229 0.012 1.06e-02 8.90e+03 1.27e+00 bond pdb=" C THR B 94 " pdb=" N PRO B 95 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.02e+00 bond pdb=" CA ASP B 185 " pdb=" C ASP B 185 " ideal model delta sigma weight residual 1.532 1.523 0.009 9.60e-03 1.09e+04 9.02e-01 ... (remaining 6616 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 8868 2.09 - 4.17: 123 4.17 - 6.26: 21 6.26 - 8.34: 3 8.34 - 10.43: 1 Bond angle restraints: 9016 Sorted by residual: angle pdb=" N CYS B 194 " pdb=" CA CYS B 194 " pdb=" C CYS B 194 " ideal model delta sigma weight residual 113.72 106.06 7.66 1.30e+00 5.92e-01 3.48e+01 angle pdb=" C ASN B 179 " pdb=" CA ASN B 179 " pdb=" CB ASN B 179 " ideal model delta sigma weight residual 116.63 110.46 6.17 1.16e+00 7.43e-01 2.83e+01 angle pdb=" N ILE B 184 " pdb=" CA ILE B 184 " pdb=" C ILE B 184 " ideal model delta sigma weight residual 112.96 109.02 3.94 1.00e+00 1.00e+00 1.55e+01 angle pdb=" CA ASN B 179 " pdb=" C ASN B 179 " pdb=" N THR B 180 " ideal model delta sigma weight residual 119.63 116.64 2.99 8.10e-01 1.52e+00 1.36e+01 angle pdb=" CA LEU B 34 " pdb=" CB LEU B 34 " pdb=" CG LEU B 34 " ideal model delta sigma weight residual 116.30 126.73 -10.43 3.50e+00 8.16e-02 8.88e+00 ... (remaining 9011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 3268 17.74 - 35.48: 416 35.48 - 53.22: 133 53.22 - 70.96: 20 70.96 - 88.70: 11 Dihedral angle restraints: 3848 sinusoidal: 1460 harmonic: 2388 Sorted by residual: dihedral pdb=" CA MET B 214 " pdb=" C MET B 214 " pdb=" N PRO B 215 " pdb=" CA PRO B 215 " ideal model delta harmonic sigma weight residual 180.00 157.93 22.07 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" SG CYS E 32 " pdb=" CB CYS E 49 " pdb=" SG CYS E 49 " pdb=" CA CYS E 49 " ideal model delta sinusoidal sigma weight residual 79.00 6.66 72.34 1 2.00e+01 2.50e-03 1.67e+01 dihedral pdb=" SG CYS F 107 " pdb=" CB CYS F 113 " pdb=" SG CYS F 113 " pdb=" CA CYS F 113 " ideal model delta sinusoidal sigma weight residual 79.00 6.70 72.30 1 2.00e+01 2.50e-03 1.67e+01 ... (remaining 3845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 699 0.046 - 0.092: 203 0.092 - 0.138: 58 0.138 - 0.184: 4 0.184 - 0.230: 1 Chirality restraints: 965 Sorted by residual: chirality pdb=" CB ILE B 197 " pdb=" CA ILE B 197 " pdb=" CG1 ILE B 197 " pdb=" CG2 ILE B 197 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA ILE B 154 " pdb=" N ILE B 154 " pdb=" C ILE B 154 " pdb=" CB ILE B 154 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.54e-01 chirality pdb=" CA ARG B 220 " pdb=" N ARG B 220 " pdb=" C ARG B 220 " pdb=" CB ARG B 220 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.32e-01 ... (remaining 962 not shown) Planarity restraints: 1167 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 16 " 0.029 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO B 17 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 17 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 17 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 90 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.22e+00 pdb=" N PRO C 91 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 91 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 91 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER C 105 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.53e+00 pdb=" C SER C 105 " -0.027 2.00e-02 2.50e+03 pdb=" O SER C 105 " 0.010 2.00e-02 2.50e+03 pdb=" N SER C 106 " 0.009 2.00e-02 2.50e+03 ... (remaining 1164 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 699 2.75 - 3.28: 6511 3.28 - 3.82: 11296 3.82 - 4.36: 14006 4.36 - 4.90: 24165 Nonbonded interactions: 56677 Sorted by model distance: nonbonded pdb=" OG SER D 108 " pdb=" OE2 GLU E 19 " model vdw 2.208 3.040 nonbonded pdb=" OG SER E 105 " pdb=" O PHE E 114 " model vdw 2.208 3.040 nonbonded pdb=" NH1 ARG B 220 " pdb=" O VAL C 73 " model vdw 2.210 3.120 nonbonded pdb=" O ARG B 32 " pdb=" OH TYR B 52 " model vdw 2.210 3.040 nonbonded pdb=" NE2 GLN B 118 " pdb=" O LEU B 190 " model vdw 2.217 3.120 ... (remaining 56672 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 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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 individual isotropic 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: 0.510 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: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.020 Find NCS groups from input model: 0.080 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 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 : 0.004 0.071 6632 Z= 0.164 Angle : 0.642 10.431 9038 Z= 0.369 Chirality : 0.046 0.230 965 Planarity : 0.004 0.045 1167 Dihedral : 17.725 88.702 2293 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 3.40 % Allowed : 26.38 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.27), residues: 808 helix: -2.06 (0.34), residues: 183 sheet: -1.65 (0.33), residues: 218 loop : -2.01 (0.28), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 220 TYR 0.020 0.001 TYR F 6 PHE 0.008 0.001 PHE E 20 TRP 0.009 0.001 TRP C 87 HIS 0.005 0.001 HIS D 21 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 6621) covalent geometry : angle 0.64092 ( 9016) SS BOND : bond 0.00226 ( 11) SS BOND : angle 0.96122 ( 22) hydrogen bonds : bond 0.19680 ( 209) hydrogen bonds : angle 9.24643 ( 633) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: B 111 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.6723 (mp0) REVERT: F 54 GLU cc_start: 0.7235 (mt-10) cc_final: 0.6972 (mp0) REVERT: G 54 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7640 (tt0) outliers start: 24 outliers final: 19 residues processed: 88 average time/residue: 0.0611 time to fit residues: 8.0760 Evaluate side-chains 90 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain G residue 8 ASN Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 104 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 GLN E 84 HIS F 76 GLN G 85 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.191715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.161465 restraints weight = 6736.378| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 2.41 r_work: 0.3749 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6632 Z= 0.138 Angle : 0.577 8.135 9038 Z= 0.307 Chirality : 0.047 0.168 965 Planarity : 0.004 0.046 1167 Dihedral : 7.135 59.473 928 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 4.11 % Allowed : 23.83 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.28), residues: 808 helix: -1.15 (0.39), residues: 183 sheet: -1.44 (0.33), residues: 218 loop : -1.96 (0.28), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 220 TYR 0.020 0.001 TYR F 6 PHE 0.012 0.001 PHE B 195 TRP 0.008 0.001 TRP C 87 HIS 0.004 0.000 HIS D 21 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 6621) covalent geometry : angle 0.57650 ( 9016) SS BOND : bond 0.00174 ( 11) SS BOND : angle 0.86721 ( 22) hydrogen bonds : bond 0.04023 ( 209) hydrogen bonds : angle 6.30280 ( 633) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 77 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 66 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7625 (mt-10) REVERT: G 94 ASN cc_start: 0.7926 (m-40) cc_final: 0.7397 (m110) outliers start: 29 outliers final: 15 residues processed: 101 average time/residue: 0.0668 time to fit residues: 9.7391 Evaluate side-chains 90 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain E residue 34 LYS Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 66 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 73 optimal weight: 0.2980 chunk 75 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 4 optimal weight: 0.0040 chunk 19 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.192744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.162553 restraints weight = 6676.472| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 2.40 r_work: 0.3804 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6632 Z= 0.125 Angle : 0.553 6.770 9038 Z= 0.293 Chirality : 0.046 0.209 965 Planarity : 0.004 0.040 1167 Dihedral : 5.568 57.206 904 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 4.96 % Allowed : 23.55 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.28), residues: 808 helix: -1.00 (0.39), residues: 183 sheet: -1.28 (0.34), residues: 218 loop : -1.92 (0.28), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 220 TYR 0.021 0.001 TYR F 6 PHE 0.009 0.001 PHE E 96 TRP 0.008 0.001 TRP C 87 HIS 0.004 0.001 HIS D 21 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 6621) covalent geometry : angle 0.55213 ( 9016) SS BOND : bond 0.00164 ( 11) SS BOND : angle 0.79192 ( 22) hydrogen bonds : bond 0.03557 ( 209) hydrogen bonds : angle 5.90755 ( 633) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 76 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 111 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.6757 (mp0) REVERT: B 213 LYS cc_start: 0.6922 (OUTLIER) cc_final: 0.6547 (mmtt) REVERT: E 66 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7298 (mp0) REVERT: G 24 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.8120 (tt0) REVERT: G 94 ASN cc_start: 0.7823 (m-40) cc_final: 0.7386 (m-40) outliers start: 35 outliers final: 19 residues processed: 105 average time/residue: 0.0636 time to fit residues: 9.7196 Evaluate side-chains 92 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain E residue 34 LYS Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 104 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 27 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 76 optimal weight: 0.0980 chunk 62 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 1 optimal weight: 0.0370 chunk 47 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 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 = 0.4295 r_free = 0.4295 target = 0.194510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.164214 restraints weight = 6753.290| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 2.43 r_work: 0.3777 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6632 Z= 0.115 Angle : 0.548 9.966 9038 Z= 0.287 Chirality : 0.046 0.175 965 Planarity : 0.004 0.043 1167 Dihedral : 5.210 57.017 901 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 4.68 % Allowed : 23.40 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.28), residues: 808 helix: -0.97 (0.39), residues: 183 sheet: -1.08 (0.34), residues: 218 loop : -1.95 (0.28), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 11 TYR 0.021 0.001 TYR F 6 PHE 0.009 0.001 PHE G 31 TRP 0.009 0.001 TRP C 87 HIS 0.003 0.000 HIS D 21 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 6621) covalent geometry : angle 0.54749 ( 9016) SS BOND : bond 0.00153 ( 11) SS BOND : angle 0.73051 ( 22) hydrogen bonds : bond 0.03382 ( 209) hydrogen bonds : angle 5.70183 ( 633) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 72 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 111 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.6768 (mp0) REVERT: E 66 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: F 1 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.7590 (pp20) REVERT: G 24 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8195 (tt0) outliers start: 33 outliers final: 18 residues processed: 101 average time/residue: 0.0627 time to fit residues: 9.2115 Evaluate side-chains 93 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain F residue 1 GLU Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 104 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 70 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 14 optimal weight: 0.0970 chunk 68 optimal weight: 0.8980 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 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 = 0.4234 r_free = 0.4234 target = 0.188153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.157408 restraints weight = 6851.781| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 2.44 r_work: 0.3758 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6632 Z= 0.181 Angle : 0.585 8.306 9038 Z= 0.309 Chirality : 0.047 0.191 965 Planarity : 0.004 0.043 1167 Dihedral : 5.011 44.493 899 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 4.54 % Allowed : 23.12 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.28), residues: 808 helix: -1.08 (0.38), residues: 183 sheet: -1.17 (0.34), residues: 213 loop : -1.83 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 11 TYR 0.021 0.002 TYR B 69 PHE 0.012 0.001 PHE B 187 TRP 0.004 0.001 TRP E 87 HIS 0.003 0.001 HIS D 21 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 6621) covalent geometry : angle 0.58422 ( 9016) SS BOND : bond 0.00281 ( 11) SS BOND : angle 0.89219 ( 22) hydrogen bonds : bond 0.03642 ( 209) hydrogen bonds : angle 5.83297 ( 633) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 70 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: B 11 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.6804 (ttt-90) REVERT: B 111 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.6646 (mp0) REVERT: E 66 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7456 (mt-10) REVERT: G 24 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8161 (tt0) REVERT: G 94 ASN cc_start: 0.7987 (m-40) cc_final: 0.7422 (m110) outliers start: 32 outliers final: 21 residues processed: 97 average time/residue: 0.0612 time to fit residues: 8.6263 Evaluate side-chains 92 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 67 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain E residue 34 LYS Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 104 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 2 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 65 optimal weight: 0.0570 chunk 72 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 60 optimal weight: 0.2980 chunk 67 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 ASN E 8 ASN G 85 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.192068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.161897 restraints weight = 6764.210| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 2.41 r_work: 0.3807 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6632 Z= 0.121 Angle : 0.546 7.404 9038 Z= 0.288 Chirality : 0.046 0.186 965 Planarity : 0.004 0.035 1167 Dihedral : 4.839 44.314 899 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 3.83 % Allowed : 23.69 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.28), residues: 808 helix: -1.08 (0.38), residues: 189 sheet: -1.18 (0.34), residues: 218 loop : -1.83 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 11 TYR 0.022 0.001 TYR B 69 PHE 0.010 0.001 PHE G 31 TRP 0.020 0.001 TRP G 2 HIS 0.003 0.001 HIS D 21 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 6621) covalent geometry : angle 0.54536 ( 9016) SS BOND : bond 0.00170 ( 11) SS BOND : angle 0.74707 ( 22) hydrogen bonds : bond 0.03288 ( 209) hydrogen bonds : angle 5.64281 ( 633) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 70 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: B 11 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.6909 (ttt-90) REVERT: B 111 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.6622 (mp0) REVERT: E 66 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7392 (mt-10) REVERT: F 1 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.7463 (pp20) REVERT: G 24 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8165 (tt0) REVERT: G 94 ASN cc_start: 0.7908 (m-40) cc_final: 0.7398 (m110) outliers start: 27 outliers final: 19 residues processed: 91 average time/residue: 0.0689 time to fit residues: 8.8590 Evaluate side-chains 90 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain E residue 34 LYS Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain F residue 1 GLU Chi-restraints excluded: chain F residue 6 TYR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 104 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 71 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 49 optimal weight: 0.1980 chunk 45 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 17 optimal weight: 0.3980 chunk 18 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 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 = 0.4291 r_free = 0.4291 target = 0.193194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.163971 restraints weight = 6694.470| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 2.31 r_work: 0.3797 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6632 Z= 0.121 Angle : 0.541 6.711 9038 Z= 0.286 Chirality : 0.046 0.172 965 Planarity : 0.004 0.038 1167 Dihedral : 4.750 44.698 899 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 3.55 % Allowed : 24.40 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.28), residues: 808 helix: -0.97 (0.39), residues: 183 sheet: -1.09 (0.33), residues: 218 loop : -1.87 (0.28), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 51 TYR 0.020 0.001 TYR F 6 PHE 0.009 0.001 PHE G 31 TRP 0.010 0.001 TRP G 2 HIS 0.003 0.000 HIS D 21 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 6621) covalent geometry : angle 0.54086 ( 9016) SS BOND : bond 0.00174 ( 11) SS BOND : angle 0.73379 ( 22) hydrogen bonds : bond 0.03244 ( 209) hydrogen bonds : angle 5.53615 ( 633) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 111 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.6657 (mp0) REVERT: E 66 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7342 (mt-10) REVERT: F 1 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.7378 (pp20) REVERT: F 81 TYR cc_start: 0.8318 (m-80) cc_final: 0.8011 (m-80) REVERT: G 24 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8167 (tt0) outliers start: 25 outliers final: 18 residues processed: 92 average time/residue: 0.0720 time to fit residues: 9.4969 Evaluate side-chains 90 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain E residue 34 LYS Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain F residue 1 GLU Chi-restraints excluded: chain F residue 6 TYR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 104 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 30 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 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 = 0.4261 r_free = 0.4261 target = 0.190872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.160588 restraints weight = 6762.484| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.41 r_work: 0.3793 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6632 Z= 0.135 Angle : 0.551 6.764 9038 Z= 0.291 Chirality : 0.046 0.162 965 Planarity : 0.004 0.034 1167 Dihedral : 4.726 45.030 898 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 3.69 % Allowed : 24.26 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.28), residues: 808 helix: -0.98 (0.39), residues: 183 sheet: -1.08 (0.34), residues: 218 loop : -1.84 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 11 TYR 0.021 0.001 TYR B 69 PHE 0.009 0.001 PHE G 31 TRP 0.009 0.001 TRP G 2 HIS 0.003 0.001 HIS D 21 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 6621) covalent geometry : angle 0.55023 ( 9016) SS BOND : bond 0.00205 ( 11) SS BOND : angle 0.76217 ( 22) hydrogen bonds : bond 0.03282 ( 209) hydrogen bonds : angle 5.53696 ( 633) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 68 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: B 111 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.6587 (mp0) REVERT: B 208 LYS cc_start: 0.2892 (OUTLIER) cc_final: 0.1185 (tptt) REVERT: D 9 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8287 (mp) REVERT: E 66 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7321 (mt-10) REVERT: F 1 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.7322 (pp20) REVERT: G 24 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8158 (tt0) outliers start: 26 outliers final: 15 residues processed: 90 average time/residue: 0.0734 time to fit residues: 9.3125 Evaluate side-chains 89 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain E residue 34 LYS Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain F residue 1 GLU Chi-restraints excluded: chain F residue 6 TYR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 104 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 62 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.191070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.159942 restraints weight = 6877.259| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 2.49 r_work: 0.3709 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6632 Z= 0.154 Angle : 0.565 6.817 9038 Z= 0.298 Chirality : 0.047 0.168 965 Planarity : 0.004 0.036 1167 Dihedral : 4.803 45.281 898 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 3.69 % Allowed : 24.54 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.28), residues: 808 helix: -1.03 (0.39), residues: 183 sheet: -1.12 (0.34), residues: 218 loop : -1.86 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 22 TYR 0.023 0.001 TYR B 69 PHE 0.009 0.001 PHE G 31 TRP 0.009 0.001 TRP G 2 HIS 0.003 0.001 HIS D 21 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 6621) covalent geometry : angle 0.56409 ( 9016) SS BOND : bond 0.00232 ( 11) SS BOND : angle 0.80631 ( 22) hydrogen bonds : bond 0.03377 ( 209) hydrogen bonds : angle 5.59615 ( 633) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 65 time to evaluate : 0.240 Fit side-chains REVERT: B 11 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.6832 (ttt-90) REVERT: B 111 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.6881 (mp0) REVERT: B 208 LYS cc_start: 0.2882 (OUTLIER) cc_final: 0.1179 (tptt) REVERT: D 9 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8311 (mp) REVERT: E 34 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8172 (ttpp) REVERT: E 66 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7437 (mt-10) REVERT: F 1 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.7460 (pp20) REVERT: F 81 TYR cc_start: 0.8282 (m-80) cc_final: 0.7932 (m-80) REVERT: G 24 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8246 (tt0) REVERT: G 94 ASN cc_start: 0.8038 (m-40) cc_final: 0.7539 (m110) outliers start: 26 outliers final: 15 residues processed: 86 average time/residue: 0.0628 time to fit residues: 7.7062 Evaluate side-chains 88 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain E residue 34 LYS Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain F residue 1 GLU Chi-restraints excluded: chain F residue 6 TYR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 31 optimal weight: 0.5980 chunk 16 optimal weight: 0.0970 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 ASN E 8 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.193778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.163109 restraints weight = 6699.148| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 2.45 r_work: 0.3758 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6632 Z= 0.119 Angle : 0.539 6.694 9038 Z= 0.284 Chirality : 0.046 0.153 965 Planarity : 0.004 0.037 1167 Dihedral : 4.700 44.963 898 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 3.26 % Allowed : 24.68 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.28), residues: 808 helix: -0.96 (0.39), residues: 183 sheet: -1.08 (0.34), residues: 218 loop : -1.79 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 22 TYR 0.022 0.001 TYR B 69 PHE 0.010 0.001 PHE G 31 TRP 0.009 0.001 TRP G 2 HIS 0.003 0.000 HIS D 21 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 6621) covalent geometry : angle 0.53827 ( 9016) SS BOND : bond 0.00156 ( 11) SS BOND : angle 0.71675 ( 22) hydrogen bonds : bond 0.03152 ( 209) hydrogen bonds : angle 5.46481 ( 633) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 111 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.6760 (mp0) REVERT: D 9 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8269 (mp) REVERT: E 34 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8087 (ttpp) REVERT: E 66 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7366 (mt-10) REVERT: F 1 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.7299 (pp20) REVERT: G 24 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8162 (tt0) REVERT: G 94 ASN cc_start: 0.8026 (m-40) cc_final: 0.7515 (m110) outliers start: 23 outliers final: 16 residues processed: 87 average time/residue: 0.0625 time to fit residues: 7.6557 Evaluate side-chains 89 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain E residue 34 LYS Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain F residue 1 GLU Chi-restraints excluded: chain F residue 6 TYR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 9 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 53 optimal weight: 0.0980 chunk 33 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 56 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 HIS ** E 53 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 = 0.4237 r_free = 0.4237 target = 0.188809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.157741 restraints weight = 6819.159| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 2.47 r_work: 0.3691 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6632 Z= 0.181 Angle : 0.583 6.864 9038 Z= 0.308 Chirality : 0.048 0.185 965 Planarity : 0.004 0.041 1167 Dihedral : 4.888 45.455 898 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 3.40 % Allowed : 24.54 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.28), residues: 808 helix: -1.06 (0.39), residues: 183 sheet: -1.14 (0.35), residues: 213 loop : -1.71 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 22 TYR 0.026 0.002 TYR B 69 PHE 0.010 0.001 PHE B 25 TRP 0.008 0.001 TRP G 2 HIS 0.003 0.001 HIS D 21 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 6621) covalent geometry : angle 0.58203 ( 9016) SS BOND : bond 0.00283 ( 11) SS BOND : angle 0.88384 ( 22) hydrogen bonds : bond 0.03509 ( 209) hydrogen bonds : angle 5.65060 ( 633) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1461.95 seconds wall clock time: 25 minutes 55.49 seconds (1555.49 seconds total)