Starting phenix.real_space_refine on Tue Feb 3 20:03:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jy2_61885/02_2026/9jy2_61885.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jy2_61885/02_2026/9jy2_61885.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jy2_61885/02_2026/9jy2_61885.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jy2_61885/02_2026/9jy2_61885.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jy2_61885/02_2026/9jy2_61885.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jy2_61885/02_2026/9jy2_61885.map" } resolution = 3.24 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= 0.017 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 46 5.16 5 C 4201 2.51 5 N 1035 2.21 5 O 1233 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 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: 6515 Number of models: 1 Model: "" Number of chains: 12 Chain: "a" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 251 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "b" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 237 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "d" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 817 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "e" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 959 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "f" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 933 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain breaks: 1 Chain: "g" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 907 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "m" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 285 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "n" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 310 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "A" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 807 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 100} Chain: "B" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 953 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.56, per 1000 atoms: 0.24 Number of scatterers: 6515 At special positions: 0 Unit cell: (99.704, 102.176, 126.896, 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 46 16.00 O 1233 8.00 N 1035 7.00 C 4201 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS d 37 " - pdb=" SG CYS d 73 " distance=2.03 Simple disulfide: pdb=" SG CYS d 93 " - pdb=" SG CYS d 96 " distance=2.02 Simple disulfide: pdb=" SG CYS e 49 " - pdb=" SG CYS e 98 " distance=2.03 Simple disulfide: pdb=" SG CYS f 49 " - pdb=" SG CYS f 98 " distance=2.03 Simple disulfide: pdb=" SG CYS f 119 " - pdb=" SG CYS f 122 " distance=2.03 Simple disulfide: pdb=" SG CYS g 46 " - pdb=" SG CYS g 87 " distance=2.03 Simple disulfide: pdb=" SG CYS g 104 " - pdb=" SG CYS g 107 " distance=2.04 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " 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 Links applied NAG-ASN " NAG d 201 " - " ASN d 74 " " NAG d 202 " - " ASN d 38 " Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 189.4 milliseconds 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1516 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 15 sheets defined 32.4% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'a' and resid 29 through 54 removed outlier: 3.648A pdb=" N LEU a 35 " --> pdb=" O LEU a 31 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP a 36 " --> pdb=" O CYS a 32 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE a 38 " --> pdb=" O LEU a 34 " (cutoff:3.500A) Processing helix chain 'b' and resid 28 through 55 Processing helix chain 'd' and resid 64 through 66 No H-bonds generated for 'chain 'd' and resid 64 through 66' Processing helix chain 'd' and resid 100 through 126 Processing helix chain 'e' and resid 88 through 93 removed outlier: 3.783A pdb=" N SER e 93 " --> pdb=" O GLU e 89 " (cutoff:3.500A) Processing helix chain 'e' and resid 126 through 153 removed outlier: 3.501A pdb=" N LYS e 153 " --> pdb=" O TYR e 149 " (cutoff:3.500A) Processing helix chain 'f' and resid 126 through 154 removed outlier: 3.566A pdb=" N ASN f 154 " --> pdb=" O TYR f 150 " (cutoff:3.500A) Processing helix chain 'g' and resid 76 through 80 Processing helix chain 'g' and resid 111 through 140 removed outlier: 3.792A pdb=" N ASP g 140 " --> pdb=" O ILE g 136 " (cutoff:3.500A) Processing helix chain 'm' and resid 256 through 289 Processing helix chain 'n' and resid 252 through 288 Processing helix chain 'B' and resid 28 through 30 No H-bonds generated for 'chain 'B' and resid 28 through 30' Processing helix chain 'B' and resid 62 through 65 removed outlier: 3.726A pdb=" N LYS B 65 " --> pdb=" O GLN B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 62 through 65' Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.538A pdb=" N SER B 91 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'd' and resid 26 through 29 removed outlier: 3.526A pdb=" N LEU d 29 " --> pdb=" O ARG d 32 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N VAL d 33 " --> pdb=" O LEU d 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'd' and resid 41 through 46 removed outlier: 6.172A pdb=" N ILE d 70 " --> pdb=" O VAL d 44 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLY d 46 " --> pdb=" O ARG d 68 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ARG d 68 " --> pdb=" O GLY d 46 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N PHE e 110 " --> pdb=" O CYS e 98 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N CYS e 98 " --> pdb=" O PHE e 110 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N TRP e 59 " --> pdb=" O ILE e 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'd' and resid 96 through 98 removed outlier: 3.579A pdb=" N MET e 123 " --> pdb=" O VAL d 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'e' and resid 37 through 41 Processing sheet with id=AA5, first strand: chain 'f' and resid 37 through 41 Processing sheet with id=AA6, first strand: chain 'f' and resid 64 through 66 removed outlier: 3.980A pdb=" N TRP f 59 " --> pdb=" O ILE f 66 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'f' and resid 112 through 116 removed outlier: 5.865A pdb=" N TYR f 113 " --> pdb=" O TYR g 100 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ARG g 102 " --> pdb=" O TYR f 113 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ARG f 115 " --> pdb=" O ARG g 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'f' and resid 122 through 124 removed outlier: 3.990A pdb=" N MET f 123 " --> pdb=" O ILE g 108 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE g 108 " --> pdb=" O MET f 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'g' and resid 31 through 34 removed outlier: 3.977A pdb=" N GLY g 75 " --> pdb=" O VAL g 42 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU g 44 " --> pdb=" O ASN g 73 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ASN g 73 " --> pdb=" O LEU g 44 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'g' and resid 60 through 63 removed outlier: 7.284A pdb=" N TRP g 55 " --> pdb=" O ILE g 62 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N CYS g 87 " --> pdb=" O SER g 94 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 4 through 6 removed outlier: 3.895A pdb=" N ASP A 70 " --> pdb=" O SER A 67 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 53 through 54 removed outlier: 6.720A pdb=" N TRP A 35 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N TYR A 49 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU A 33 " --> pdb=" O TYR A 49 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 3 through 6 removed outlier: 3.517A pdb=" N GLN B 3 " --> pdb=" O SER B 25 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 58 through 60 removed outlier: 5.019A pdb=" N LEU B 45 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N SER B 40 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N TRP B 47 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LYS B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL B 111 " --> pdb=" O ARG B 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 58 through 60 removed outlier: 5.019A pdb=" N LEU B 45 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N SER B 40 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N TRP B 47 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LYS B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) 354 hydrogen bonds defined for protein. 984 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: 0.96 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2013 1.34 - 1.46: 1653 1.46 - 1.59: 2917 1.59 - 1.71: 0 1.71 - 1.83: 65 Bond restraints: 6648 Sorted by residual: bond pdb=" CG LEU g 129 " pdb=" CD1 LEU g 129 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.80e+00 bond pdb=" CA ARG g 102 " pdb=" CB ARG g 102 " ideal model delta sigma weight residual 1.530 1.556 -0.026 1.69e-02 3.50e+03 2.34e+00 bond pdb=" SD MET m 261 " pdb=" CE MET m 261 " ideal model delta sigma weight residual 1.791 1.758 0.033 2.50e-02 1.60e+03 1.79e+00 bond pdb=" CA ILE d 24 " pdb=" CB ILE d 24 " ideal model delta sigma weight residual 1.537 1.520 0.017 1.29e-02 6.01e+03 1.76e+00 bond pdb=" CB ARG g 102 " pdb=" CG ARG g 102 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.62e+00 ... (remaining 6643 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 8818 2.25 - 4.50: 169 4.50 - 6.75: 19 6.75 - 9.01: 3 9.01 - 11.26: 2 Bond angle restraints: 9011 Sorted by residual: angle pdb=" CB MET g 103 " pdb=" CG MET g 103 " pdb=" SD MET g 103 " ideal model delta sigma weight residual 112.70 123.87 -11.17 3.00e+00 1.11e-01 1.39e+01 angle pdb=" N ILE d 55 " pdb=" CA ILE d 55 " pdb=" C ILE d 55 " ideal model delta sigma weight residual 110.21 106.11 4.10 1.13e+00 7.83e-01 1.32e+01 angle pdb=" CA MET m 261 " pdb=" CB MET m 261 " pdb=" CG MET m 261 " ideal model delta sigma weight residual 114.10 106.98 7.12 2.00e+00 2.50e-01 1.27e+01 angle pdb=" C GLU g 67 " pdb=" N ASP g 68 " pdb=" CA ASP g 68 " ideal model delta sigma weight residual 121.54 127.97 -6.43 1.91e+00 2.74e-01 1.13e+01 angle pdb=" CG MET m 271 " pdb=" SD MET m 271 " pdb=" CE MET m 271 " ideal model delta sigma weight residual 100.90 108.19 -7.29 2.20e+00 2.07e-01 1.10e+01 ... (remaining 9006 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 3343 17.72 - 35.44: 516 35.44 - 53.15: 147 53.15 - 70.87: 9 70.87 - 88.59: 8 Dihedral angle restraints: 4023 sinusoidal: 1649 harmonic: 2374 Sorted by residual: dihedral pdb=" CA MET g 103 " pdb=" C MET g 103 " pdb=" N CYS g 104 " pdb=" CA CYS g 104 " ideal model delta harmonic sigma weight residual 180.00 -155.87 -24.13 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CB CYS f 119 " pdb=" SG CYS f 119 " pdb=" SG CYS f 122 " pdb=" CB CYS f 122 " ideal model delta sinusoidal sigma weight residual -86.00 -125.00 39.00 1 1.00e+01 1.00e-02 2.14e+01 dihedral pdb=" CB CYS g 104 " pdb=" SG CYS g 104 " pdb=" SG CYS g 107 " pdb=" CB CYS g 107 " ideal model delta sinusoidal sigma weight residual 93.00 56.10 36.90 1 1.00e+01 1.00e-02 1.92e+01 ... (remaining 4020 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 838 0.053 - 0.106: 177 0.106 - 0.158: 24 0.158 - 0.211: 1 0.211 - 0.264: 1 Chirality restraints: 1041 Sorted by residual: chirality pdb=" C1 NAG d 202 " pdb=" ND2 ASN d 38 " pdb=" C2 NAG d 202 " pdb=" O5 NAG d 202 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CB ILE a 41 " pdb=" CA ILE a 41 " pdb=" CG1 ILE a 41 " pdb=" CG2 ILE a 41 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.92e-01 chirality pdb=" CA ASN e 121 " pdb=" N ASN e 121 " pdb=" C ASN e 121 " pdb=" CB ASN e 121 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.22e-01 ... (remaining 1038 not shown) Planarity restraints: 1110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 34 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.46e+00 pdb=" CG ASN A 34 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN A 34 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN A 34 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE a 50 " 0.003 2.00e-02 2.50e+03 1.51e-02 3.99e+00 pdb=" CG PHE a 50 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE a 50 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE a 50 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE a 50 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE a 50 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE a 50 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL d 35 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.83e+00 pdb=" C VAL d 35 " -0.029 2.00e-02 2.50e+03 pdb=" O VAL d 35 " 0.011 2.00e-02 2.50e+03 pdb=" N ASN d 36 " 0.010 2.00e-02 2.50e+03 ... (remaining 1107 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 87 2.59 - 3.17: 5589 3.17 - 3.75: 10220 3.75 - 4.32: 13815 4.32 - 4.90: 22943 Nonbonded interactions: 52654 Sorted by model distance: nonbonded pdb=" OD1 ASN d 38 " pdb=" OG1 THR d 76 " model vdw 2.018 3.040 nonbonded pdb=" NH1 ARG f 117 " pdb=" O CYS g 104 " model vdw 2.155 3.120 nonbonded pdb=" NE2 GLN A 89 " pdb=" O GLN A 90 " model vdw 2.208 3.120 nonbonded pdb=" OE1 GLN g 105 " pdb=" NE2 GLN n 256 " model vdw 2.238 3.120 nonbonded pdb=" NH2 ARG e 101 " pdb=" OG1 THR B 33 " model vdw 2.249 3.120 ... (remaining 52649 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'a' and resid 27 through 55) selection = (chain 'b' and resid 27 through 55) } ncs_group { reference = (chain 'e' and (resid 33 through 69 or resid 74 through 153)) selection = (chain 'f' and resid 33 through 153) } 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: 11.610 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.730 Find NCS groups from input model: 0.040 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 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 0.055 6659 Z= 0.242 Angle : 0.795 11.257 9035 Z= 0.423 Chirality : 0.045 0.264 1041 Planarity : 0.004 0.045 1108 Dihedral : 17.642 88.590 2480 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 5.40 % Allowed : 35.32 % Favored : 59.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.66 (0.29), residues: 796 helix: 2.32 (0.30), residues: 240 sheet: 0.26 (0.35), residues: 230 loop : -0.84 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG f 117 TYR 0.028 0.002 TYR n 276 PHE 0.029 0.003 PHE a 50 TRP 0.016 0.002 TRP f 59 HIS 0.005 0.003 HIS f 61 Details of bonding type rmsd covalent geometry : bond 0.00533 ( 6648) covalent geometry : angle 0.78326 ( 9011) SS BOND : bond 0.00386 ( 9) SS BOND : angle 1.28992 ( 18) hydrogen bonds : bond 0.16334 ( 341) hydrogen bonds : angle 6.98354 ( 984) link_NAG-ASN : bond 0.01911 ( 2) link_NAG-ASN : angle 5.13331 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 177 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 59 ASP cc_start: 0.7675 (p0) cc_final: 0.7394 (p0) REVERT: d 77 ASP cc_start: 0.7741 (m-30) cc_final: 0.7361 (m-30) REVERT: d 83 GLU cc_start: 0.7882 (pp20) cc_final: 0.7650 (pp20) REVERT: d 111 ASP cc_start: 0.7880 (t0) cc_final: 0.6452 (t70) REVERT: e 64 LYS cc_start: 0.8433 (ttmm) cc_final: 0.7982 (ttpp) REVERT: e 117 ARG cc_start: 0.7712 (ttp80) cc_final: 0.6958 (ttm170) REVERT: e 119 CYS cc_start: 0.8093 (t) cc_final: 0.7545 (m) REVERT: e 121 ASN cc_start: 0.6782 (m110) cc_final: 0.6473 (m110) REVERT: e 128 MET cc_start: 0.7242 (tpp) cc_final: 0.6997 (tpp) REVERT: f 123 MET cc_start: 0.7426 (pmm) cc_final: 0.6488 (ttm) REVERT: n 286 ARG cc_start: 0.5107 (mmm160) cc_final: 0.4214 (mtm180) REVERT: B 60 TYR cc_start: 0.8576 (m-80) cc_final: 0.7849 (m-80) outliers start: 39 outliers final: 21 residues processed: 203 average time/residue: 0.0638 time to fit residues: 17.5455 Evaluate side-chains 180 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 76 THR Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 97 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 107 ASP Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 123 MET Chi-restraints excluded: chain f residue 52 TYR Chi-restraints excluded: chain g residue 33 VAL Chi-restraints excluded: chain g residue 111 ASN Chi-restraints excluded: chain m residue 258 LYS Chi-restraints excluded: chain m residue 277 VAL Chi-restraints excluded: chain n residue 254 LEU Chi-restraints excluded: chain n residue 283 CYS Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 65 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 0.4980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.0980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 65 ASN f 33 GLN B 5 GLN B 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.231423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.175930 restraints weight = 8016.856| |-----------------------------------------------------------------------------| r_work (start): 0.4085 rms_B_bonded: 2.94 r_work: 0.3755 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6659 Z= 0.166 Angle : 0.656 10.612 9035 Z= 0.337 Chirality : 0.043 0.198 1041 Planarity : 0.004 0.046 1108 Dihedral : 7.602 58.010 1026 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 8.45 % Allowed : 29.92 % Favored : 61.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.30), residues: 796 helix: 2.82 (0.31), residues: 238 sheet: 0.34 (0.36), residues: 212 loop : -0.64 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG g 82 TYR 0.022 0.002 TYR g 34 PHE 0.029 0.002 PHE a 50 TRP 0.011 0.001 TRP d 43 HIS 0.005 0.001 HIS g 29 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 6648) covalent geometry : angle 0.63811 ( 9011) SS BOND : bond 0.00262 ( 9) SS BOND : angle 0.99643 ( 18) hydrogen bonds : bond 0.04004 ( 341) hydrogen bonds : angle 4.81528 ( 984) link_NAG-ASN : bond 0.01444 ( 2) link_NAG-ASN : angle 5.80485 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 161 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 26 LEU cc_start: 0.6048 (OUTLIER) cc_final: 0.5816 (mp) REVERT: b 51 LEU cc_start: 0.4525 (OUTLIER) cc_final: 0.4169 (mp) REVERT: d 111 ASP cc_start: 0.7341 (t0) cc_final: 0.7028 (t70) REVERT: e 117 ARG cc_start: 0.8018 (ttp80) cc_final: 0.7298 (ttp-170) REVERT: e 121 ASN cc_start: 0.6725 (m110) cc_final: 0.6418 (m110) REVERT: e 128 MET cc_start: 0.7237 (tpp) cc_final: 0.6957 (tpp) REVERT: f 33 GLN cc_start: 0.4698 (OUTLIER) cc_final: 0.4377 (pt0) REVERT: f 64 LYS cc_start: 0.8652 (mtpp) cc_final: 0.7763 (pttm) REVERT: f 81 HIS cc_start: 0.8881 (m90) cc_final: 0.8496 (m90) REVERT: f 123 MET cc_start: 0.7339 (pmm) cc_final: 0.6361 (ttm) REVERT: f 128 MET cc_start: 0.7768 (mpp) cc_final: 0.5804 (tpt) REVERT: g 74 LEU cc_start: 0.5612 (OUTLIER) cc_final: 0.5117 (pp) REVERT: g 84 MET cc_start: 0.3806 (tpt) cc_final: 0.1253 (ptp) REVERT: m 260 ASN cc_start: 0.7844 (m-40) cc_final: 0.7169 (m110) REVERT: m 270 ARG cc_start: 0.7918 (mtp180) cc_final: 0.7699 (mtp180) REVERT: n 286 ARG cc_start: 0.5170 (mmm160) cc_final: 0.4757 (mmp80) REVERT: B 63 LYS cc_start: 0.9027 (mptt) cc_final: 0.8790 (mptt) REVERT: B 65 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7103 (tttp) outliers start: 61 outliers final: 34 residues processed: 196 average time/residue: 0.0782 time to fit residues: 20.5215 Evaluate side-chains 190 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 151 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 38 ILE Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 76 THR Chi-restraints excluded: chain d residue 79 TYR Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 92 MET Chi-restraints excluded: chain d residue 125 PHE Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 61 HIS Chi-restraints excluded: chain e residue 93 SER Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain f residue 33 GLN Chi-restraints excluded: chain f residue 52 TYR Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 133 ILE Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain g residue 123 ILE Chi-restraints excluded: chain m residue 258 LYS Chi-restraints excluded: chain m residue 259 VAL Chi-restraints excluded: chain m residue 262 MET Chi-restraints excluded: chain n residue 261 SER Chi-restraints excluded: chain n residue 265 MET Chi-restraints excluded: chain n residue 271 LEU Chi-restraints excluded: chain n residue 282 CYS Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 84 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 41 optimal weight: 5.9990 chunk 35 optimal weight: 0.0970 chunk 29 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 7 optimal weight: 0.0980 chunk 40 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 121 ASN f 33 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.229266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.172820 restraints weight = 7929.812| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 3.02 r_work: 0.3704 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6659 Z= 0.154 Angle : 0.621 10.732 9035 Z= 0.318 Chirality : 0.043 0.201 1041 Planarity : 0.004 0.047 1108 Dihedral : 6.711 59.636 1006 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 8.45 % Allowed : 29.50 % Favored : 62.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.30), residues: 796 helix: 2.86 (0.30), residues: 238 sheet: 0.20 (0.35), residues: 220 loop : -0.58 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG d 32 TYR 0.017 0.002 TYR B 108 PHE 0.017 0.002 PHE f 87 TRP 0.010 0.001 TRP d 43 HIS 0.005 0.001 HIS f 81 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 6648) covalent geometry : angle 0.60241 ( 9011) SS BOND : bond 0.00275 ( 9) SS BOND : angle 0.76272 ( 18) hydrogen bonds : bond 0.03714 ( 341) hydrogen bonds : angle 4.52352 ( 984) link_NAG-ASN : bond 0.01309 ( 2) link_NAG-ASN : angle 5.84175 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 155 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 51 LEU cc_start: 0.4837 (OUTLIER) cc_final: 0.4394 (mp) REVERT: e 90 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8086 (mm) REVERT: e 117 ARG cc_start: 0.8006 (ttp80) cc_final: 0.7246 (ttp-170) REVERT: e 119 CYS cc_start: 0.7129 (m) cc_final: 0.6843 (m) REVERT: f 64 LYS cc_start: 0.8575 (mtpp) cc_final: 0.7694 (pttm) REVERT: f 117 ARG cc_start: 0.7263 (ptt-90) cc_final: 0.7008 (ptt-90) REVERT: f 123 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.6357 (ttm) REVERT: f 128 MET cc_start: 0.7750 (mpp) cc_final: 0.5782 (tpt) REVERT: m 260 ASN cc_start: 0.7894 (m-40) cc_final: 0.7411 (m-40) REVERT: m 270 ARG cc_start: 0.7841 (mtp180) cc_final: 0.7636 (mtp180) REVERT: n 286 ARG cc_start: 0.5205 (mmm160) cc_final: 0.4795 (mmp80) REVERT: B 40 SER cc_start: 0.8020 (OUTLIER) cc_final: 0.7820 (m) REVERT: B 63 LYS cc_start: 0.9058 (mptt) cc_final: 0.8822 (mptt) REVERT: B 65 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7334 (ttmm) outliers start: 61 outliers final: 40 residues processed: 190 average time/residue: 0.0811 time to fit residues: 20.6792 Evaluate side-chains 194 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 149 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 76 THR Chi-restraints excluded: chain d residue 79 TYR Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 92 MET Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 125 PHE Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 84 LEU Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 93 SER Chi-restraints excluded: chain e residue 107 ASP Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain f residue 52 TYR Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 123 MET Chi-restraints excluded: chain f residue 133 ILE Chi-restraints excluded: chain g residue 123 ILE Chi-restraints excluded: chain m residue 258 LYS Chi-restraints excluded: chain m residue 259 VAL Chi-restraints excluded: chain m residue 262 MET Chi-restraints excluded: chain m residue 275 LYS Chi-restraints excluded: chain n residue 265 MET Chi-restraints excluded: chain n residue 271 LEU Chi-restraints excluded: chain n residue 282 CYS Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 110 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 5 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 56 optimal weight: 20.0000 chunk 40 optimal weight: 8.9990 chunk 17 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** n 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.227303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.167946 restraints weight = 7883.758| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 3.01 r_work: 0.3716 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6659 Z= 0.186 Angle : 0.629 10.347 9035 Z= 0.321 Chirality : 0.043 0.205 1041 Planarity : 0.004 0.044 1108 Dihedral : 6.618 59.647 1006 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 8.86 % Allowed : 30.47 % Favored : 60.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.30), residues: 796 helix: 2.90 (0.30), residues: 236 sheet: -0.03 (0.37), residues: 212 loop : -0.43 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG m 270 TYR 0.019 0.002 TYR B 108 PHE 0.030 0.002 PHE a 50 TRP 0.014 0.002 TRP d 43 HIS 0.003 0.001 HIS g 29 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 6648) covalent geometry : angle 0.61117 ( 9011) SS BOND : bond 0.00320 ( 9) SS BOND : angle 0.81026 ( 18) hydrogen bonds : bond 0.03721 ( 341) hydrogen bonds : angle 4.42483 ( 984) link_NAG-ASN : bond 0.01202 ( 2) link_NAG-ASN : angle 5.68763 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 156 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: b 51 LEU cc_start: 0.4734 (OUTLIER) cc_final: 0.4414 (mp) REVERT: d 123 PHE cc_start: 0.4264 (OUTLIER) cc_final: 0.3140 (t80) REVERT: e 36 TYR cc_start: 0.8807 (m-80) cc_final: 0.7807 (m-80) REVERT: e 90 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8092 (mm) REVERT: e 117 ARG cc_start: 0.8040 (ttp80) cc_final: 0.7342 (ttm170) REVERT: e 119 CYS cc_start: 0.7283 (m) cc_final: 0.7006 (m) REVERT: f 52 TYR cc_start: 0.2926 (OUTLIER) cc_final: 0.2550 (m-80) REVERT: f 64 LYS cc_start: 0.8649 (mtpp) cc_final: 0.8268 (tmtt) REVERT: f 123 MET cc_start: 0.7310 (OUTLIER) cc_final: 0.6487 (ttm) REVERT: f 128 MET cc_start: 0.7768 (mpp) cc_final: 0.5803 (tpt) REVERT: g 38 GLU cc_start: 0.4594 (OUTLIER) cc_final: 0.3736 (mt-10) REVERT: g 74 LEU cc_start: 0.5640 (OUTLIER) cc_final: 0.5195 (pp) REVERT: g 84 MET cc_start: 0.3188 (tpt) cc_final: 0.0972 (ptp) REVERT: m 258 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7725 (mttp) REVERT: m 260 ASN cc_start: 0.8042 (m-40) cc_final: 0.7580 (m-40) REVERT: m 270 ARG cc_start: 0.7964 (mtp180) cc_final: 0.7740 (mtp180) REVERT: n 286 ARG cc_start: 0.5281 (mmm160) cc_final: 0.4715 (ttt180) REVERT: B 65 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7410 (ttmm) outliers start: 64 outliers final: 42 residues processed: 192 average time/residue: 0.0722 time to fit residues: 18.8688 Evaluate side-chains 206 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 155 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 79 TYR Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 92 MET Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain d residue 125 PHE Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 61 HIS Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 93 SER Chi-restraints excluded: chain e residue 107 ASP Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain f residue 44 THR Chi-restraints excluded: chain f residue 52 TYR Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 123 MET Chi-restraints excluded: chain f residue 133 ILE Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 38 GLU Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain g residue 123 ILE Chi-restraints excluded: chain m residue 258 LYS Chi-restraints excluded: chain m residue 259 VAL Chi-restraints excluded: chain m residue 262 MET Chi-restraints excluded: chain m residue 275 LYS Chi-restraints excluded: chain n residue 261 SER Chi-restraints excluded: chain n residue 265 MET Chi-restraints excluded: chain n residue 271 LEU Chi-restraints excluded: chain n residue 282 CYS Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 110 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 35 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 58 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** n 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.229008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.160975 restraints weight = 8018.654| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.95 r_work: 0.3688 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 6659 Z= 0.165 Angle : 0.616 9.709 9035 Z= 0.312 Chirality : 0.042 0.202 1041 Planarity : 0.003 0.042 1108 Dihedral : 6.217 58.106 1005 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 9.00 % Allowed : 30.06 % Favored : 60.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.30), residues: 796 helix: 2.89 (0.30), residues: 236 sheet: 0.21 (0.36), residues: 223 loop : -0.48 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG m 270 TYR 0.017 0.002 TYR B 108 PHE 0.024 0.002 PHE a 50 TRP 0.013 0.001 TRP d 43 HIS 0.003 0.001 HIS d 89 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 6648) covalent geometry : angle 0.59971 ( 9011) SS BOND : bond 0.00276 ( 9) SS BOND : angle 0.72232 ( 18) hydrogen bonds : bond 0.03624 ( 341) hydrogen bonds : angle 4.36953 ( 984) link_NAG-ASN : bond 0.01038 ( 2) link_NAG-ASN : angle 5.48072 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 155 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: b 51 LEU cc_start: 0.4912 (OUTLIER) cc_final: 0.4672 (mp) REVERT: d 123 PHE cc_start: 0.4310 (OUTLIER) cc_final: 0.3236 (t80) REVERT: e 36 TYR cc_start: 0.8815 (m-80) cc_final: 0.8056 (m-80) REVERT: e 90 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8112 (mm) REVERT: e 117 ARG cc_start: 0.7998 (ttp80) cc_final: 0.7238 (ttp-170) REVERT: f 52 TYR cc_start: 0.2860 (OUTLIER) cc_final: 0.2433 (m-80) REVERT: f 123 MET cc_start: 0.7272 (OUTLIER) cc_final: 0.6465 (ttm) REVERT: f 128 MET cc_start: 0.7833 (mpp) cc_final: 0.5796 (tpt) REVERT: g 38 GLU cc_start: 0.4646 (OUTLIER) cc_final: 0.3775 (mt-10) REVERT: g 74 LEU cc_start: 0.5670 (OUTLIER) cc_final: 0.5215 (pp) REVERT: g 84 MET cc_start: 0.3246 (tpt) cc_final: 0.1058 (ptp) REVERT: m 258 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7666 (mttp) REVERT: m 260 ASN cc_start: 0.8057 (m-40) cc_final: 0.7613 (m-40) REVERT: n 286 ARG cc_start: 0.5467 (mmm160) cc_final: 0.4909 (ttp80) REVERT: B 44 ASN cc_start: 0.7346 (t0) cc_final: 0.6635 (p0) REVERT: B 65 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7382 (ttmm) outliers start: 65 outliers final: 44 residues processed: 194 average time/residue: 0.0764 time to fit residues: 20.0536 Evaluate side-chains 204 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 151 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 65 LEU Chi-restraints excluded: chain d residue 79 TYR Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 92 MET Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain d residue 125 PHE Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 61 HIS Chi-restraints excluded: chain e residue 84 LEU Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 93 SER Chi-restraints excluded: chain e residue 107 ASP Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain f residue 52 TYR Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 123 MET Chi-restraints excluded: chain f residue 133 ILE Chi-restraints excluded: chain g residue 33 VAL Chi-restraints excluded: chain g residue 38 GLU Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain g residue 123 ILE Chi-restraints excluded: chain m residue 258 LYS Chi-restraints excluded: chain m residue 259 VAL Chi-restraints excluded: chain m residue 262 MET Chi-restraints excluded: chain m residue 275 LYS Chi-restraints excluded: chain n residue 261 SER Chi-restraints excluded: chain n residue 265 MET Chi-restraints excluded: chain n residue 271 LEU Chi-restraints excluded: chain n residue 282 CYS Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 110 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 5 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 39 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN ** B 35 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 = 0.4622 r_free = 0.4622 target = 0.227849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.154718 restraints weight = 8019.676| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 3.07 r_work: 0.3672 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6659 Z= 0.176 Angle : 0.632 8.965 9035 Z= 0.316 Chirality : 0.043 0.209 1041 Planarity : 0.003 0.040 1108 Dihedral : 6.036 53.864 1005 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 8.31 % Allowed : 29.92 % Favored : 61.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.30), residues: 796 helix: 3.00 (0.30), residues: 236 sheet: 0.14 (0.35), residues: 223 loop : -0.51 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG m 270 TYR 0.018 0.002 TYR B 94 PHE 0.026 0.002 PHE a 50 TRP 0.009 0.001 TRP B 47 HIS 0.003 0.001 HIS g 29 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 6648) covalent geometry : angle 0.61717 ( 9011) SS BOND : bond 0.00360 ( 9) SS BOND : angle 0.78880 ( 18) hydrogen bonds : bond 0.03594 ( 341) hydrogen bonds : angle 4.31300 ( 984) link_NAG-ASN : bond 0.00986 ( 2) link_NAG-ASN : angle 5.17923 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 160 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: d 123 PHE cc_start: 0.4143 (OUTLIER) cc_final: 0.3071 (t80) REVERT: e 36 TYR cc_start: 0.8836 (m-80) cc_final: 0.7827 (m-10) REVERT: e 90 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8128 (mm) REVERT: e 117 ARG cc_start: 0.7987 (ttp80) cc_final: 0.7153 (ttp-170) REVERT: f 52 TYR cc_start: 0.3069 (OUTLIER) cc_final: 0.1602 (m-80) REVERT: f 123 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.6530 (ttm) REVERT: f 128 MET cc_start: 0.7850 (mpp) cc_final: 0.5836 (tpt) REVERT: g 38 GLU cc_start: 0.4776 (OUTLIER) cc_final: 0.3837 (mt-10) REVERT: g 74 LEU cc_start: 0.5697 (OUTLIER) cc_final: 0.5251 (pp) REVERT: g 84 MET cc_start: 0.3079 (tpt) cc_final: 0.0960 (ptp) REVERT: m 260 ASN cc_start: 0.7991 (m-40) cc_final: 0.7524 (m-40) REVERT: n 286 ARG cc_start: 0.5482 (mmm160) cc_final: 0.4920 (ttt-90) REVERT: B 44 ASN cc_start: 0.7244 (t0) cc_final: 0.6505 (p0) REVERT: B 65 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7438 (ttmm) REVERT: B 67 LYS cc_start: 0.8732 (tppt) cc_final: 0.8522 (tppt) outliers start: 60 outliers final: 45 residues processed: 193 average time/residue: 0.0781 time to fit residues: 20.2418 Evaluate side-chains 206 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 154 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 31 LEU Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 79 TYR Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 92 MET Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain d residue 125 PHE Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 46 ILE Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 61 HIS Chi-restraints excluded: chain e residue 84 LEU Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 93 SER Chi-restraints excluded: chain e residue 107 ASP Chi-restraints excluded: chain f residue 52 TYR Chi-restraints excluded: chain f residue 92 GLN Chi-restraints excluded: chain f residue 123 MET Chi-restraints excluded: chain f residue 133 ILE Chi-restraints excluded: chain g residue 38 GLU Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain g residue 101 TYR Chi-restraints excluded: chain g residue 123 ILE Chi-restraints excluded: chain m residue 259 VAL Chi-restraints excluded: chain m residue 262 MET Chi-restraints excluded: chain m residue 266 VAL Chi-restraints excluded: chain m residue 275 LYS Chi-restraints excluded: chain n residue 261 SER Chi-restraints excluded: chain n residue 265 MET Chi-restraints excluded: chain n residue 271 LEU Chi-restraints excluded: chain n residue 282 CYS Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 110 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 25 optimal weight: 0.6980 chunk 66 optimal weight: 0.0370 chunk 7 optimal weight: 0.9980 chunk 30 optimal weight: 0.0980 chunk 0 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 65 optimal weight: 0.0770 chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 overall best weight: 0.3016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: n 256 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.228268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.157259 restraints weight = 7913.631| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 3.52 r_work: 0.3612 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6659 Z= 0.124 Angle : 0.593 8.461 9035 Z= 0.298 Chirality : 0.041 0.202 1041 Planarity : 0.003 0.040 1108 Dihedral : 5.470 50.973 999 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 7.06 % Allowed : 31.58 % Favored : 61.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.30), residues: 796 helix: 3.18 (0.30), residues: 238 sheet: 0.03 (0.36), residues: 217 loop : -0.47 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG m 270 TYR 0.012 0.001 TYR B 94 PHE 0.015 0.001 PHE a 50 TRP 0.008 0.001 TRP f 59 HIS 0.003 0.001 HIS g 29 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 6648) covalent geometry : angle 0.57927 ( 9011) SS BOND : bond 0.00210 ( 9) SS BOND : angle 0.65002 ( 18) hydrogen bonds : bond 0.03355 ( 341) hydrogen bonds : angle 4.14373 ( 984) link_NAG-ASN : bond 0.00881 ( 2) link_NAG-ASN : angle 4.86673 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 152 time to evaluate : 0.274 Fit side-chains REVERT: d 123 PHE cc_start: 0.4274 (OUTLIER) cc_final: 0.3301 (t80) REVERT: e 90 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8145 (mm) REVERT: e 117 ARG cc_start: 0.7939 (ttp80) cc_final: 0.7044 (ttp-170) REVERT: f 52 TYR cc_start: 0.2952 (OUTLIER) cc_final: 0.1315 (m-80) REVERT: f 99 TYR cc_start: 0.4911 (p90) cc_final: 0.4413 (p90) REVERT: f 123 MET cc_start: 0.7161 (OUTLIER) cc_final: 0.6340 (ttm) REVERT: f 128 MET cc_start: 0.7775 (mpp) cc_final: 0.5716 (tpt) REVERT: g 38 GLU cc_start: 0.4815 (OUTLIER) cc_final: 0.3696 (mt-10) REVERT: g 74 LEU cc_start: 0.5529 (OUTLIER) cc_final: 0.5092 (pp) REVERT: g 84 MET cc_start: 0.2928 (tpt) cc_final: 0.0876 (ptp) REVERT: m 260 ASN cc_start: 0.7852 (m-40) cc_final: 0.7379 (m-40) REVERT: n 286 ARG cc_start: 0.5453 (mmm160) cc_final: 0.4873 (ttt-90) REVERT: B 44 ASN cc_start: 0.7069 (t0) cc_final: 0.6351 (p0) REVERT: B 65 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7436 (ttmm) outliers start: 51 outliers final: 39 residues processed: 178 average time/residue: 0.0752 time to fit residues: 18.2073 Evaluate side-chains 196 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 150 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 31 LEU Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 76 THR Chi-restraints excluded: chain d residue 79 TYR Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 92 MET Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain d residue 125 PHE Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 61 HIS Chi-restraints excluded: chain e residue 84 LEU Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 93 SER Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain f residue 52 TYR Chi-restraints excluded: chain f residue 92 GLN Chi-restraints excluded: chain f residue 123 MET Chi-restraints excluded: chain g residue 33 VAL Chi-restraints excluded: chain g residue 38 GLU Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain m residue 262 MET Chi-restraints excluded: chain m residue 266 VAL Chi-restraints excluded: chain m residue 275 LYS Chi-restraints excluded: chain n residue 261 SER Chi-restraints excluded: chain n residue 265 MET Chi-restraints excluded: chain n residue 271 LEU Chi-restraints excluded: chain n residue 282 CYS Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 110 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 34 optimal weight: 0.8980 chunk 17 optimal weight: 0.0050 chunk 28 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 35 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 = 0.4572 r_free = 0.4572 target = 0.225857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.167576 restraints weight = 7998.878| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 3.02 r_work: 0.3634 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6659 Z= 0.171 Angle : 0.633 8.443 9035 Z= 0.322 Chirality : 0.043 0.209 1041 Planarity : 0.003 0.039 1108 Dihedral : 5.544 48.808 999 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 8.03 % Allowed : 30.06 % Favored : 61.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.30), residues: 796 helix: 2.89 (0.30), residues: 238 sheet: 0.03 (0.36), residues: 216 loop : -0.46 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG m 270 TYR 0.016 0.001 TYR B 94 PHE 0.009 0.001 PHE e 87 TRP 0.008 0.001 TRP B 112 HIS 0.003 0.001 HIS g 29 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 6648) covalent geometry : angle 0.62092 ( 9011) SS BOND : bond 0.00316 ( 9) SS BOND : angle 0.81002 ( 18) hydrogen bonds : bond 0.03560 ( 341) hydrogen bonds : angle 4.24654 ( 984) link_NAG-ASN : bond 0.00867 ( 2) link_NAG-ASN : angle 4.69940 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 148 time to evaluate : 0.256 Fit side-chains REVERT: d 123 PHE cc_start: 0.4171 (OUTLIER) cc_final: 0.3096 (t80) REVERT: e 90 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8127 (mm) REVERT: e 117 ARG cc_start: 0.7936 (ttp80) cc_final: 0.7197 (ttm170) REVERT: f 52 TYR cc_start: 0.2930 (OUTLIER) cc_final: 0.1214 (m-80) REVERT: f 123 MET cc_start: 0.7195 (OUTLIER) cc_final: 0.6436 (ttm) REVERT: g 38 GLU cc_start: 0.4861 (OUTLIER) cc_final: 0.4015 (mt-10) REVERT: g 74 LEU cc_start: 0.5662 (OUTLIER) cc_final: 0.5169 (pp) REVERT: g 84 MET cc_start: 0.3011 (tpt) cc_final: 0.0895 (ptp) REVERT: m 260 ASN cc_start: 0.7971 (m-40) cc_final: 0.7528 (m-40) REVERT: n 254 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8186 (tp) REVERT: n 286 ARG cc_start: 0.5485 (mmm160) cc_final: 0.4903 (ttt-90) REVERT: B 18 MET cc_start: 0.7888 (tpt) cc_final: 0.7643 (tpp) REVERT: B 44 ASN cc_start: 0.7192 (t0) cc_final: 0.6501 (p0) REVERT: B 65 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7445 (ttmm) outliers start: 58 outliers final: 40 residues processed: 180 average time/residue: 0.0660 time to fit residues: 16.6650 Evaluate side-chains 197 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 149 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 31 LEU Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 79 TYR Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 92 MET Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 49 CYS Chi-restraints excluded: chain e residue 61 HIS Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 93 SER Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain f residue 52 TYR Chi-restraints excluded: chain f residue 92 GLN Chi-restraints excluded: chain f residue 123 MET Chi-restraints excluded: chain f residue 134 VAL Chi-restraints excluded: chain g residue 38 GLU Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain g residue 99 VAL Chi-restraints excluded: chain m residue 262 MET Chi-restraints excluded: chain m residue 266 VAL Chi-restraints excluded: chain m residue 275 LYS Chi-restraints excluded: chain n residue 254 LEU Chi-restraints excluded: chain n residue 261 SER Chi-restraints excluded: chain n residue 265 MET Chi-restraints excluded: chain n residue 271 LEU Chi-restraints excluded: chain n residue 274 VAL Chi-restraints excluded: chain n residue 282 CYS Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 110 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 34 optimal weight: 2.9990 chunk 18 optimal weight: 0.0040 chunk 33 optimal weight: 7.9990 chunk 40 optimal weight: 0.0670 chunk 36 optimal weight: 0.0980 chunk 44 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 64 optimal weight: 0.1980 chunk 15 optimal weight: 0.7980 overall best weight: 0.2330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.229324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.155695 restraints weight = 8009.550| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 2.81 r_work: 0.3688 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6659 Z= 0.116 Angle : 0.595 8.799 9035 Z= 0.300 Chirality : 0.041 0.211 1041 Planarity : 0.003 0.039 1108 Dihedral : 5.279 51.611 999 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 6.37 % Allowed : 31.99 % Favored : 61.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.96 (0.30), residues: 796 helix: 2.86 (0.30), residues: 244 sheet: -0.05 (0.36), residues: 224 loop : -0.56 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG m 270 TYR 0.011 0.001 TYR B 108 PHE 0.010 0.001 PHE d 125 TRP 0.008 0.001 TRP f 59 HIS 0.002 0.001 HIS g 29 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 6648) covalent geometry : angle 0.58428 ( 9011) SS BOND : bond 0.00181 ( 9) SS BOND : angle 0.59897 ( 18) hydrogen bonds : bond 0.03332 ( 341) hydrogen bonds : angle 4.11712 ( 984) link_NAG-ASN : bond 0.00827 ( 2) link_NAG-ASN : angle 4.35380 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 155 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: d 123 PHE cc_start: 0.4241 (OUTLIER) cc_final: 0.3243 (t80) REVERT: e 90 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8092 (mm) REVERT: e 117 ARG cc_start: 0.7900 (ttp80) cc_final: 0.7120 (ttm170) REVERT: f 52 TYR cc_start: 0.2837 (OUTLIER) cc_final: 0.1214 (m-80) REVERT: f 123 MET cc_start: 0.7214 (OUTLIER) cc_final: 0.6264 (ttm) REVERT: f 128 MET cc_start: 0.7470 (mpp) cc_final: 0.5345 (tpt) REVERT: g 38 GLU cc_start: 0.4733 (OUTLIER) cc_final: 0.3892 (mt-10) REVERT: g 74 LEU cc_start: 0.5527 (OUTLIER) cc_final: 0.5067 (pp) REVERT: g 84 MET cc_start: 0.2897 (tpt) cc_final: 0.0759 (ptp) REVERT: m 260 ASN cc_start: 0.7816 (m-40) cc_final: 0.7372 (m-40) REVERT: m 261 MET cc_start: 0.6417 (tpt) cc_final: 0.5913 (tpt) REVERT: n 254 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8224 (tp) REVERT: n 286 ARG cc_start: 0.5571 (mmm160) cc_final: 0.4712 (mtt180) REVERT: B 44 ASN cc_start: 0.7028 (t0) cc_final: 0.6439 (p0) REVERT: B 65 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7460 (ttmm) outliers start: 46 outliers final: 33 residues processed: 178 average time/residue: 0.0650 time to fit residues: 15.7477 Evaluate side-chains 192 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 31 LEU Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 76 THR Chi-restraints excluded: chain d residue 79 TYR Chi-restraints excluded: chain d residue 92 MET Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 49 CYS Chi-restraints excluded: chain e residue 61 HIS Chi-restraints excluded: chain e residue 84 LEU Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 93 SER Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain f residue 52 TYR Chi-restraints excluded: chain f residue 92 GLN Chi-restraints excluded: chain f residue 123 MET Chi-restraints excluded: chain g residue 38 GLU Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain g residue 99 VAL Chi-restraints excluded: chain m residue 262 MET Chi-restraints excluded: chain m residue 275 LYS Chi-restraints excluded: chain n residue 254 LEU Chi-restraints excluded: chain n residue 261 SER Chi-restraints excluded: chain n residue 265 MET Chi-restraints excluded: chain n residue 271 LEU Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 110 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 9.9990 chunk 4 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 8 optimal weight: 0.0870 chunk 35 optimal weight: 0.3980 chunk 73 optimal weight: 0.5980 chunk 75 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 36 optimal weight: 0.0670 overall best weight: 0.2696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.229165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.157014 restraints weight = 7849.976| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 3.13 r_work: 0.3650 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6659 Z= 0.121 Angle : 0.607 8.820 9035 Z= 0.306 Chirality : 0.042 0.216 1041 Planarity : 0.003 0.040 1108 Dihedral : 5.025 50.114 996 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 6.23 % Allowed : 32.13 % Favored : 61.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.99 (0.30), residues: 796 helix: 2.90 (0.30), residues: 244 sheet: -0.09 (0.36), residues: 224 loop : -0.50 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG d 32 TYR 0.012 0.001 TYR n 264 PHE 0.011 0.001 PHE d 125 TRP 0.008 0.001 TRP f 59 HIS 0.003 0.001 HIS g 29 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 6648) covalent geometry : angle 0.59808 ( 9011) SS BOND : bond 0.00178 ( 9) SS BOND : angle 0.60619 ( 18) hydrogen bonds : bond 0.03360 ( 341) hydrogen bonds : angle 4.04442 ( 984) link_NAG-ASN : bond 0.00803 ( 2) link_NAG-ASN : angle 4.15756 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 157 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: d 123 PHE cc_start: 0.4257 (OUTLIER) cc_final: 0.3295 (t80) REVERT: e 90 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8093 (mm) REVERT: e 117 ARG cc_start: 0.7945 (ttp80) cc_final: 0.7098 (ttm170) REVERT: f 52 TYR cc_start: 0.2782 (OUTLIER) cc_final: 0.1213 (m-80) REVERT: f 88 SER cc_start: 0.5533 (m) cc_final: 0.5201 (t) REVERT: f 123 MET cc_start: 0.7124 (OUTLIER) cc_final: 0.6180 (ttm) REVERT: f 128 MET cc_start: 0.7364 (mpp) cc_final: 0.5197 (tpt) REVERT: g 38 GLU cc_start: 0.4888 (OUTLIER) cc_final: 0.3916 (mt-10) REVERT: g 74 LEU cc_start: 0.5451 (OUTLIER) cc_final: 0.5016 (pp) REVERT: g 84 MET cc_start: 0.2847 (tpt) cc_final: 0.0681 (ptp) REVERT: m 260 ASN cc_start: 0.7845 (m-40) cc_final: 0.7401 (m-40) REVERT: m 261 MET cc_start: 0.6452 (tpt) cc_final: 0.5956 (tpt) REVERT: n 254 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8216 (tp) REVERT: n 286 ARG cc_start: 0.5494 (mmm160) cc_final: 0.4946 (ttt-90) REVERT: B 18 MET cc_start: 0.7275 (tpp) cc_final: 0.6976 (ttt) REVERT: B 43 LYS cc_start: 0.7083 (tttt) cc_final: 0.6690 (ttpp) REVERT: B 44 ASN cc_start: 0.6920 (t0) cc_final: 0.6351 (p0) REVERT: B 65 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7498 (ttmm) outliers start: 45 outliers final: 35 residues processed: 181 average time/residue: 0.0625 time to fit residues: 15.3613 Evaluate side-chains 197 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 154 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 31 LEU Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 76 THR Chi-restraints excluded: chain d residue 79 TYR Chi-restraints excluded: chain d residue 92 MET Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 49 CYS Chi-restraints excluded: chain e residue 61 HIS Chi-restraints excluded: chain e residue 84 LEU Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 93 SER Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain f residue 52 TYR Chi-restraints excluded: chain f residue 92 GLN Chi-restraints excluded: chain f residue 123 MET Chi-restraints excluded: chain g residue 38 GLU Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain g residue 99 VAL Chi-restraints excluded: chain m residue 262 MET Chi-restraints excluded: chain m residue 275 LYS Chi-restraints excluded: chain n residue 254 LEU Chi-restraints excluded: chain n residue 261 SER Chi-restraints excluded: chain n residue 265 MET Chi-restraints excluded: chain n residue 271 LEU Chi-restraints excluded: chain n residue 282 CYS Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 110 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 66 optimal weight: 0.0570 chunk 23 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 3 optimal weight: 0.2980 chunk 58 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 21 optimal weight: 0.0980 overall best weight: 0.3498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.228611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.156849 restraints weight = 7975.616| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 3.35 r_work: 0.3634 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6659 Z= 0.127 Angle : 0.609 8.776 9035 Z= 0.305 Chirality : 0.042 0.215 1041 Planarity : 0.003 0.040 1108 Dihedral : 5.008 49.751 996 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 6.23 % Allowed : 32.27 % Favored : 61.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.99 (0.30), residues: 796 helix: 2.88 (0.30), residues: 244 sheet: -0.05 (0.36), residues: 223 loop : -0.51 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG m 270 TYR 0.011 0.001 TYR B 108 PHE 0.012 0.001 PHE d 125 TRP 0.008 0.001 TRP f 59 HIS 0.003 0.001 HIS g 29 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 6648) covalent geometry : angle 0.60030 ( 9011) SS BOND : bond 0.00198 ( 9) SS BOND : angle 0.61556 ( 18) hydrogen bonds : bond 0.03379 ( 341) hydrogen bonds : angle 4.00885 ( 984) link_NAG-ASN : bond 0.00812 ( 2) link_NAG-ASN : angle 4.07723 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2297.56 seconds wall clock time: 39 minutes 59.59 seconds (2399.59 seconds total)