Starting phenix.real_space_refine on Tue Aug 4 15:28:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w9y_65793/08_2026/9w9y_65793.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w9y_65793/08_2026/9w9y_65793.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w9y_65793/08_2026/9w9y_65793.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w9y_65793/08_2026/9w9y_65793.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w9y_65793/08_2026/9w9y_65793.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w9y_65793/08_2026/9w9y_65793.map" } resolution = 2.27 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= 0.004 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 6 5.16 5 C 2802 2.51 5 N 729 2.21 5 O 804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4341 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 714 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain breaks: 1 Chain: "C" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 733 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain breaks: 1 Chain: "A" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 714 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain breaks: 1 Chain: "D" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 733 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain breaks: 1 Chain: "E" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 714 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain breaks: 1 Chain: "F" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 733 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain breaks: 1 Time building chain proxies: 1.17, per 1000 atoms: 0.27 Number of scatterers: 4341 At special positions: 0 Unit cell: (130.2, 127.41, 35.34, 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 6 16.00 O 804 8.00 N 729 7.00 C 2802 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.32 Conformation dependent library (CDL) restraints added in 158.9 milliseconds 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1056 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 25 sheets defined 0.0% alpha, 43.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 6.454A pdb=" N MET B 13 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N VAL A 16 " --> pdb=" O MET B 13 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LYS B 15 " --> pdb=" O VAL A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 20 removed outlier: 6.316A pdb=" N ALA B 19 " --> pdb=" O VAL A 20 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 27 removed outlier: 6.597A pdb=" N ILE B 26 " --> pdb=" O ASN E 27 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 31 through 32 removed outlier: 6.221A pdb=" N HIS B 31 " --> pdb=" O VAL A 32 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 62 through 65 removed outlier: 6.473A pdb=" N GLU B 63 " --> pdb=" O PHE A 64 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 71 through 73 removed outlier: 6.236A pdb=" N VAL B 71 " --> pdb=" O GLU A 72 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 76 through 80 removed outlier: 6.966A pdb=" N SER B 77 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N TYR A 78 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 9.518A pdb=" N LYS B 76 " --> pdb=" O SER E 77 " (cutoff:3.500A) removed outlier: 9.693A pdb=" N TRP E 79 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N TYR B 78 " --> pdb=" O TRP E 79 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.626A pdb=" N ARG B 83 " --> pdb=" O ILE E 84 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 91 through 99 removed outlier: 6.462A pdb=" N ALA B 91 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N VAL A 94 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL B 93 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N THR A 96 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N PHE B 95 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N ASN A 98 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA B 97 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 103 through 110 removed outlier: 6.681A pdb=" N ARG B 103 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N THR A 106 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR B 105 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ALA A 108 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE B 107 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU A 110 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ALA B 109 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU B 110 " --> pdb=" O ALA E 109 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 114 through 115 removed outlier: 6.823A pdb=" N TYR B 114 " --> pdb=" O SER E 115 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 118 through 122 removed outlier: 6.017A pdb=" N THR B 118 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL A 121 " --> pdb=" O THR B 118 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA B 120 " --> pdb=" O VAL A 121 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 12 through 16 removed outlier: 6.411A pdb=" N MET C 13 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N VAL D 16 " --> pdb=" O MET C 13 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LYS C 15 " --> pdb=" O VAL D 16 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 19 through 21 removed outlier: 6.653A pdb=" N VAL C 20 " --> pdb=" O ARG F 21 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 25 through 27 removed outlier: 6.694A pdb=" N ILE C 26 " --> pdb=" O ASN F 27 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 30 through 32 removed outlier: 6.585A pdb=" N VAL C 30 " --> pdb=" O HIS F 31 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 58 through 59 removed outlier: 6.787A pdb=" N LEU C 58 " --> pdb=" O THR F 59 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 63 through 65 removed outlier: 6.314A pdb=" N GLU C 63 " --> pdb=" O PHE D 64 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 69 through 73 removed outlier: 6.459A pdb=" N TYR C 69 " --> pdb=" O LYS D 70 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N GLU D 72 " --> pdb=" O TYR C 69 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL C 71 " --> pdb=" O GLU D 72 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 76 through 80 removed outlier: 6.967A pdb=" N SER C 77 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N TYR D 78 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 9.388A pdb=" N LYS C 76 " --> pdb=" O SER F 77 " (cutoff:3.500A) removed outlier: 9.556A pdb=" N TRP F 79 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N TYR C 78 " --> pdb=" O TRP F 79 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 83 through 84 removed outlier: 6.619A pdb=" N ARG C 83 " --> pdb=" O ILE F 84 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 92 through 99 removed outlier: 6.433A pdb=" N VAL C 93 " --> pdb=" O VAL D 94 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N THR D 96 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N PHE C 95 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ASN D 98 " --> pdb=" O PHE C 95 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ALA C 97 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 103 through 110 removed outlier: 9.072A pdb=" N ARG C 104 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 9.610A pdb=" N ILE D 107 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N THR C 106 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 9.490A pdb=" N ALA D 109 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ALA C 108 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ARG F 104 " --> pdb=" O ARG C 103 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N TYR C 105 " --> pdb=" O ARG F 104 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N THR F 106 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE C 107 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ALA F 108 " --> pdb=" O ILE C 107 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 114 through 115 removed outlier: 6.842A pdb=" N TYR C 114 " --> pdb=" O SER F 115 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 118 through 122 removed outlier: 5.955A pdb=" N THR C 118 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N VAL D 121 " --> pdb=" O THR C 118 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA C 120 " --> pdb=" O VAL D 121 " (cutoff:3.500A) 69 hydrogen bonds defined for protein. 207 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: 0.60 Time building geometry restraints manager: 0.43 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: 1368 1.34 - 1.46: 759 1.46 - 1.57: 2304 1.57 - 1.69: 0 1.69 - 1.80: 12 Bond restraints: 4443 Sorted by residual: bond pdb=" CG LEU E 12 " pdb=" CD1 LEU E 12 " ideal model delta sigma weight residual 1.521 1.424 0.097 3.30e-02 9.18e+02 8.60e+00 bond pdb=" CG LEU B 12 " pdb=" CD1 LEU B 12 " ideal model delta sigma weight residual 1.521 1.424 0.097 3.30e-02 9.18e+02 8.58e+00 bond pdb=" CG LEU A 12 " pdb=" CD1 LEU A 12 " ideal model delta sigma weight residual 1.521 1.424 0.097 3.30e-02 9.18e+02 8.57e+00 bond pdb=" CG LEU F 12 " pdb=" CD1 LEU F 12 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.76e+00 bond pdb=" CG LEU D 12 " pdb=" CD1 LEU D 12 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.76e+00 ... (remaining 4438 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 5906 2.06 - 4.13: 115 4.13 - 6.19: 12 6.19 - 8.26: 6 8.26 - 10.32: 3 Bond angle restraints: 6042 Sorted by residual: angle pdb=" CD1 LEU A 12 " pdb=" CG LEU A 12 " pdb=" CD2 LEU A 12 " ideal model delta sigma weight residual 110.80 102.97 7.83 2.20e+00 2.07e-01 1.27e+01 angle pdb=" CD1 LEU E 12 " pdb=" CG LEU E 12 " pdb=" CD2 LEU E 12 " ideal model delta sigma weight residual 110.80 102.99 7.81 2.20e+00 2.07e-01 1.26e+01 angle pdb=" CD1 LEU B 12 " pdb=" CG LEU B 12 " pdb=" CD2 LEU B 12 " ideal model delta sigma weight residual 110.80 102.99 7.81 2.20e+00 2.07e-01 1.26e+01 angle pdb=" CB LEU A 12 " pdb=" CG LEU A 12 " pdb=" CD2 LEU A 12 " ideal model delta sigma weight residual 110.70 100.38 10.32 3.00e+00 1.11e-01 1.18e+01 angle pdb=" CB LEU B 12 " pdb=" CG LEU B 12 " pdb=" CD2 LEU B 12 " ideal model delta sigma weight residual 110.70 100.38 10.32 3.00e+00 1.11e-01 1.18e+01 ... (remaining 6037 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.38: 2274 16.38 - 32.76: 255 32.76 - 49.14: 84 49.14 - 65.52: 24 65.52 - 81.90: 3 Dihedral angle restraints: 2640 sinusoidal: 1017 harmonic: 1623 Sorted by residual: dihedral pdb=" CA ILE A 26 " pdb=" C ILE A 26 " pdb=" N ASN A 27 " pdb=" CA ASN A 27 " ideal model delta harmonic sigma weight residual 180.00 161.99 18.01 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA ILE B 26 " pdb=" C ILE B 26 " pdb=" N ASN B 27 " pdb=" CA ASN B 27 " ideal model delta harmonic sigma weight residual 180.00 162.03 17.97 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ILE E 26 " pdb=" C ILE E 26 " pdb=" N ASN E 27 " pdb=" CA ASN E 27 " ideal model delta harmonic sigma weight residual 180.00 162.03 17.97 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 2637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 491 0.052 - 0.103: 143 0.103 - 0.155: 71 0.155 - 0.206: 0 0.206 - 0.258: 3 Chirality restraints: 708 Sorted by residual: chirality pdb=" CG LEU A 12 " pdb=" CB LEU A 12 " pdb=" CD1 LEU A 12 " pdb=" CD2 LEU A 12 " both_signs ideal model delta sigma weight residual False -2.59 -2.85 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CG LEU B 12 " pdb=" CB LEU B 12 " pdb=" CD1 LEU B 12 " pdb=" CD2 LEU B 12 " both_signs ideal model delta sigma weight residual False -2.59 -2.85 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CG LEU E 12 " pdb=" CB LEU E 12 " pdb=" CD1 LEU E 12 " pdb=" CD2 LEU E 12 " both_signs ideal model delta sigma weight residual False -2.59 -2.85 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 705 not shown) Planarity restraints: 747 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 83 " -0.180 9.50e-02 1.11e+02 8.08e-02 4.02e+00 pdb=" NE ARG C 83 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG C 83 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG C 83 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG C 83 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 83 " -0.179 9.50e-02 1.11e+02 8.03e-02 3.98e+00 pdb=" NE ARG F 83 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG F 83 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG F 83 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG F 83 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 83 " -0.179 9.50e-02 1.11e+02 8.01e-02 3.94e+00 pdb=" NE ARG D 83 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG D 83 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG D 83 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG D 83 " -0.007 2.00e-02 2.50e+03 ... (remaining 744 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 1088 2.82 - 3.34: 3348 3.34 - 3.86: 7487 3.86 - 4.38: 7995 4.38 - 4.90: 15575 Nonbonded interactions: 35493 Sorted by model distance: nonbonded pdb=" NH2 ARG B 21 " pdb=" OE1 GLU F 92 " model vdw 2.294 3.120 nonbonded pdb=" OE1 GLU C 92 " pdb=" NH2 ARG A 21 " model vdw 2.301 3.120 nonbonded pdb=" O SER A 112 " pdb=" OG SER A 112 " model vdw 2.325 3.040 nonbonded pdb=" O SER B 112 " pdb=" OG SER B 112 " model vdw 2.326 3.040 nonbonded pdb=" O SER E 112 " pdb=" OG SER E 112 " model vdw 2.326 3.040 ... (remaining 35488 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: 0.01 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'F' } 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: 4.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.900 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 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 : 0.005 0.097 4443 Z= 0.190 Angle : 0.772 10.323 6042 Z= 0.417 Chirality : 0.058 0.258 708 Planarity : 0.006 0.081 747 Dihedral : 16.620 81.899 1584 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 18.35 % Favored : 81.65 % 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: -2.81 (0.31), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 83 TYR 0.019 0.002 TYR F 114 PHE 0.019 0.002 PHE E 33 TRP 0.004 0.001 TRP F 79 HIS 0.005 0.001 HIS A 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.19 ( 4443) covalent geometry : angle 0.77179 / 0.42 ( 6042) hydrogen bonds : bond 0.13652 / 8.90 ( 69) hydrogen bonds : angle 8.22653 / 5.87 ( 207) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 83 ARG cc_start: 0.7486 (mtt90) cc_final: 0.7258 (mtm180) REVERT: A 13 MET cc_start: 0.8752 (ttt) cc_final: 0.8312 (ttp) REVERT: A 89 GLU cc_start: 0.6819 (mm-30) cc_final: 0.6460 (tm-30) REVERT: E 34 ARG cc_start: 0.8520 (ttt180) cc_final: 0.7785 (ptp-170) REVERT: E 89 GLU cc_start: 0.6518 (mm-30) cc_final: 0.5164 (pt0) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.9280 time to fit residues: 86.1552 Evaluate side-chains 88 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 31 HIS A 124 ASN D 31 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.124355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.103964 restraints weight = 5065.592| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.65 r_work: 0.3424 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4443 Z= 0.221 Angle : 0.670 6.457 6042 Z= 0.362 Chirality : 0.055 0.137 708 Planarity : 0.004 0.024 747 Dihedral : 5.738 20.184 597 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.90 % Allowed : 20.04 % Favored : 78.06 % 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: -2.69 (0.32), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 83 TYR 0.019 0.002 TYR B 114 PHE 0.017 0.002 PHE B 33 TRP 0.010 0.002 TRP C 79 HIS 0.006 0.002 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.22 ( 4443) covalent geometry : angle 0.67033 / 0.36 ( 6042) hydrogen bonds : bond 0.03454 / 2.12 ( 69) hydrogen bonds : angle 5.99137 / 4.28 ( 207) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.192 Fit side-chains REVERT: A 13 MET cc_start: 0.8774 (ttt) cc_final: 0.8410 (ttp) REVERT: A 34 ARG cc_start: 0.8511 (ttm-80) cc_final: 0.8239 (ttm-80) REVERT: A 83 ARG cc_start: 0.7782 (mtm-85) cc_final: 0.7220 (mtt90) REVERT: A 89 GLU cc_start: 0.7038 (mm-30) cc_final: 0.6640 (tm-30) REVERT: D 21 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8064 (ttt-90) REVERT: E 34 ARG cc_start: 0.8520 (ttt180) cc_final: 0.7771 (ptp-170) outliers start: 9 outliers final: 3 residues processed: 98 average time/residue: 0.7577 time to fit residues: 75.8298 Evaluate side-chains 94 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain D residue 21 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 37 optimal weight: 0.0000 chunk 4 optimal weight: 8.9990 chunk 26 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.128232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.107807 restraints weight = 4966.942| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.67 r_work: 0.3465 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4443 Z= 0.117 Angle : 0.554 5.951 6042 Z= 0.295 Chirality : 0.051 0.136 708 Planarity : 0.003 0.022 747 Dihedral : 5.299 18.722 597 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.90 % Allowed : 21.94 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.54 (0.32), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 34 TYR 0.014 0.001 TYR B 114 PHE 0.014 0.002 PHE B 33 TRP 0.003 0.001 TRP D 79 HIS 0.004 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 4443) covalent geometry : angle 0.55380 / 0.30 ( 6042) hydrogen bonds : bond 0.02483 / 1.60 ( 69) hydrogen bonds : angle 5.40591 / 3.89 ( 207) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.099 Fit side-chains REVERT: B 34 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7895 (ttm-80) REVERT: B 83 ARG cc_start: 0.7883 (mtt180) cc_final: 0.7518 (mtp85) REVERT: A 13 MET cc_start: 0.8773 (ttt) cc_final: 0.8401 (ttp) REVERT: A 83 ARG cc_start: 0.7897 (mtm-85) cc_final: 0.7457 (mtm-85) REVERT: E 34 ARG cc_start: 0.8478 (ttt180) cc_final: 0.7621 (ptp-170) REVERT: E 83 ARG cc_start: 0.8333 (mtm180) cc_final: 0.7743 (mtt90) outliers start: 9 outliers final: 2 residues processed: 93 average time/residue: 0.7410 time to fit residues: 70.3634 Evaluate side-chains 88 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain A residue 28 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 46 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.124513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.103976 restraints weight = 4954.384| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.65 r_work: 0.3410 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4443 Z= 0.180 Angle : 0.618 6.205 6042 Z= 0.332 Chirality : 0.052 0.137 708 Planarity : 0.003 0.023 747 Dihedral : 5.603 20.108 597 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.90 % Allowed : 21.73 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.32), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 83 TYR 0.018 0.002 TYR B 114 PHE 0.016 0.002 PHE B 33 TRP 0.005 0.001 TRP C 79 HIS 0.005 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 ( 4443) covalent geometry : angle 0.61785 / 0.33 ( 6042) hydrogen bonds : bond 0.02857 / 1.81 ( 69) hydrogen bonds : angle 5.57172 / 4.00 ( 207) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.167 Fit side-chains REVERT: B 13 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8197 (ttp) REVERT: A 13 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8432 (ttp) REVERT: E 34 ARG cc_start: 0.8460 (ttt180) cc_final: 0.7707 (ptp-170) outliers start: 9 outliers final: 4 residues processed: 92 average time/residue: 0.7083 time to fit residues: 66.5299 Evaluate side-chains 95 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain F residue 88 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 49 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 48 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.123902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.103625 restraints weight = 5056.809| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.65 r_work: 0.3397 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4443 Z= 0.218 Angle : 0.657 6.484 6042 Z= 0.355 Chirality : 0.054 0.139 708 Planarity : 0.003 0.023 747 Dihedral : 5.790 21.025 597 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.11 % Allowed : 21.31 % Favored : 76.58 % 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 (0.32), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 83 TYR 0.019 0.002 TYR B 114 PHE 0.017 0.002 PHE B 33 TRP 0.005 0.001 TRP F 79 HIS 0.006 0.002 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.22 ( 4443) covalent geometry : angle 0.65690 / 0.35 ( 6042) hydrogen bonds : bond 0.03002 / 1.88 ( 69) hydrogen bonds : angle 5.71349 / 4.10 ( 207) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.103 Fit side-chains REVERT: B 13 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.8216 (ttp) REVERT: A 13 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8441 (ttp) REVERT: D 21 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8084 (ttt-90) REVERT: E 34 ARG cc_start: 0.8496 (ttt180) cc_final: 0.7724 (ptp-170) outliers start: 10 outliers final: 4 residues processed: 93 average time/residue: 0.6948 time to fit residues: 65.9044 Evaluate side-chains 95 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain F residue 88 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 8 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 ASN ** E 31 HIS ** 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 = 0.3768 r_free = 0.3768 target = 0.123116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.103008 restraints weight = 5214.123| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.65 r_work: 0.3387 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 4443 Z= 0.236 Angle : 0.675 6.820 6042 Z= 0.365 Chirality : 0.055 0.140 708 Planarity : 0.004 0.028 747 Dihedral : 5.890 21.600 597 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.74 % Allowed : 20.04 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.52 (0.32), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 34 TYR 0.020 0.002 TYR B 114 PHE 0.017 0.002 PHE B 33 TRP 0.005 0.002 TRP F 79 HIS 0.007 0.002 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.24 ( 4443) covalent geometry : angle 0.67542 / 0.37 ( 6042) hydrogen bonds : bond 0.03060 / 1.91 ( 69) hydrogen bonds : angle 5.79244 / 4.15 ( 207) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.098 Fit side-chains REVERT: B 13 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8233 (ttp) REVERT: A 13 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8482 (ttp) REVERT: D 21 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8143 (ttt-90) REVERT: E 34 ARG cc_start: 0.8489 (ttt180) cc_final: 0.7724 (ptp-170) outliers start: 13 outliers final: 5 residues processed: 93 average time/residue: 0.7938 time to fit residues: 75.3698 Evaluate side-chains 97 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain F residue 88 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 2 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 34 optimal weight: 0.0270 chunk 11 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 overall best weight: 2.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.126261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.106151 restraints weight = 5006.240| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.65 r_work: 0.3447 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4443 Z= 0.141 Angle : 0.585 6.978 6042 Z= 0.313 Chirality : 0.051 0.135 708 Planarity : 0.003 0.023 747 Dihedral : 5.572 20.057 597 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.32 % Allowed : 20.68 % Favored : 77.00 % 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: -2.41 (0.32), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 34 TYR 0.016 0.002 TYR C 114 PHE 0.015 0.002 PHE B 33 TRP 0.003 0.001 TRP C 79 HIS 0.004 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 4443) covalent geometry : angle 0.58517 / 0.31 ( 6042) hydrogen bonds : bond 0.02402 / 1.53 ( 69) hydrogen bonds : angle 5.42887 / 3.91 ( 207) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.111 Fit side-chains REVERT: B 13 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8205 (ttp) REVERT: A 13 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8469 (ttp) REVERT: A 34 ARG cc_start: 0.8490 (ttm-80) cc_final: 0.8001 (ttm170) REVERT: E 34 ARG cc_start: 0.8481 (ttt180) cc_final: 0.7669 (ptp-170) outliers start: 11 outliers final: 4 residues processed: 93 average time/residue: 0.7477 time to fit residues: 71.0324 Evaluate side-chains 95 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain F residue 88 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 39 optimal weight: 0.3980 chunk 1 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 23 optimal weight: 0.2980 chunk 48 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.125703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.105415 restraints weight = 5013.675| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.66 r_work: 0.3440 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4443 Z= 0.154 Angle : 0.601 7.097 6042 Z= 0.320 Chirality : 0.051 0.137 708 Planarity : 0.003 0.023 747 Dihedral : 5.614 20.317 597 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.11 % Allowed : 20.68 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.41 (0.32), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 34 TYR 0.017 0.002 TYR B 114 PHE 0.016 0.002 PHE B 33 TRP 0.003 0.001 TRP C 79 HIS 0.004 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 ( 4443) covalent geometry : angle 0.60127 / 0.32 ( 6042) hydrogen bonds : bond 0.02476 / 1.57 ( 69) hydrogen bonds : angle 5.43021 / 3.91 ( 207) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.158 Fit side-chains REVERT: B 13 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8231 (ttp) REVERT: A 13 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8445 (ttp) REVERT: A 34 ARG cc_start: 0.8438 (ttm-80) cc_final: 0.7961 (ttm170) REVERT: E 34 ARG cc_start: 0.8494 (ttt180) cc_final: 0.7705 (ptp-170) outliers start: 10 outliers final: 4 residues processed: 93 average time/residue: 0.7366 time to fit residues: 69.9341 Evaluate side-chains 95 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain F residue 88 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 19 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 48 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.125215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.104947 restraints weight = 5058.391| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.66 r_work: 0.3434 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4443 Z= 0.164 Angle : 0.612 6.980 6042 Z= 0.326 Chirality : 0.052 0.136 708 Planarity : 0.003 0.022 747 Dihedral : 5.644 20.441 597 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.90 % Allowed : 20.89 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.42 (0.32), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 34 TYR 0.017 0.002 TYR B 114 PHE 0.016 0.002 PHE B 33 TRP 0.003 0.001 TRP C 79 HIS 0.005 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 ( 4443) covalent geometry : angle 0.61187 / 0.33 ( 6042) hydrogen bonds : bond 0.02508 / 1.58 ( 69) hydrogen bonds : angle 5.49697 / 3.95 ( 207) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.098 Fit side-chains REVERT: B 13 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8231 (ttp) REVERT: A 13 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8467 (ttp) REVERT: A 34 ARG cc_start: 0.8438 (ttm-80) cc_final: 0.7965 (ttm170) REVERT: E 34 ARG cc_start: 0.8496 (ttt180) cc_final: 0.7706 (ptp-170) outliers start: 9 outliers final: 5 residues processed: 92 average time/residue: 0.6765 time to fit residues: 63.5265 Evaluate side-chains 95 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain F residue 88 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 37 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 ASN ** E 31 HIS ** 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 = 0.3779 r_free = 0.3779 target = 0.123612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.103398 restraints weight = 5038.998| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.64 r_work: 0.3413 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4443 Z= 0.210 Angle : 0.659 7.073 6042 Z= 0.353 Chirality : 0.053 0.140 708 Planarity : 0.004 0.026 747 Dihedral : 5.814 21.313 597 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.90 % Allowed : 21.73 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.32), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 34 TYR 0.019 0.002 TYR B 114 PHE 0.018 0.002 PHE B 33 TRP 0.004 0.001 TRP F 79 HIS 0.006 0.002 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.21 ( 4443) covalent geometry : angle 0.65909 / 0.35 ( 6042) hydrogen bonds : bond 0.02823 / 1.76 ( 69) hydrogen bonds : angle 5.66698 / 4.06 ( 207) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.098 Fit side-chains REVERT: B 13 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8229 (ttp) REVERT: A 13 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8472 (ttp) REVERT: A 34 ARG cc_start: 0.8451 (ttm-80) cc_final: 0.7979 (ttm170) REVERT: E 34 ARG cc_start: 0.8471 (ttt180) cc_final: 0.7705 (ptp-170) outliers start: 9 outliers final: 5 residues processed: 93 average time/residue: 0.7075 time to fit residues: 67.1212 Evaluate side-chains 97 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain F residue 88 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 chunk 2 optimal weight: 9.9990 chunk 14 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 29 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.128736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.108753 restraints weight = 5003.100| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.65 r_work: 0.3490 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4443 Z= 0.107 Angle : 0.556 7.327 6042 Z= 0.293 Chirality : 0.050 0.132 708 Planarity : 0.003 0.023 747 Dihedral : 5.400 18.944 597 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.27 % Allowed : 22.57 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.33), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 34 TYR 0.014 0.001 TYR D 114 PHE 0.012 0.001 PHE B 33 TRP 0.002 0.001 TRP B 79 HIS 0.003 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 4443) covalent geometry : angle 0.55561 / 0.29 ( 6042) hydrogen bonds : bond 0.02096 / 1.32 ( 69) hydrogen bonds : angle 5.24129 / 3.76 ( 207) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2063.67 seconds wall clock time: 35 minutes 41.65 seconds (2141.65 seconds total)