Starting phenix.real_space_refine on Thu Oct 22 23:27:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/33cg_59342/10_2026/33cg_59342.cif Found real_map, /net/cci-nas-00/data/ceres_data/33cg_59342/10_2026/33cg_59342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/33cg_59342/10_2026/33cg_59342.map" default_real_map = "/net/cci-nas-00/data/ceres_data/33cg_59342/10_2026/33cg_59342.map" model { file = "/net/cci-nas-00/data/ceres_data/33cg_59342/10_2026/33cg_59342.cif" } default_model = "/net/cci-nas-00/data/ceres_data/33cg_59342/10_2026/33cg_59342.cif" } resolution = 2.2 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= 0.013 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 30 5.16 5 C 4177 2.51 5 N 1152 2.21 5 O 1308 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6667 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2256 Classifications: {'peptide': 277} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 264} Chain: "B" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 837 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 94} Chain: "C" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 80 Classifications: {'peptide': 10} Modifications used: {'COO': 1} Link IDs: {'TRANS': 9} Chain: "D" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 818 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 101} Chain: "E" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 914 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "F" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Chain: "G" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 1.41, per 1000 atoms: 0.21 Number of scatterers: 6667 At special positions: 0 Unit cell: (64.9782, 97.8684, 133.165, 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 30 16.00 O 1308 8.00 N 1152 7.00 C 4177 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 164 " distance=2.04 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 259 " distance=2.03 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 80 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.05 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 355.3 milliseconds 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1540 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 18 sheets defined 14.4% alpha, 48.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 51 through 55 Processing helix chain 'A' and resid 56 through 85 Processing helix chain 'A' and resid 137 through 150 Processing helix chain 'A' and resid 151 through 162 removed outlier: 3.589A pdb=" N TYR A 159 " --> pdb=" O GLN A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 253 through 255 No H-bonds generated for 'chain 'A' and resid 253 through 255' Processing helix chain 'D' and resid 30 through 32 No H-bonds generated for 'chain 'D' and resid 30 through 32' Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.770A pdb=" N PHE D 84 " --> pdb=" O PRO D 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.540A pdb=" N PHE F 83 " --> pdb=" O ALA F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.611A pdb=" N THR G 32 " --> pdb=" O VAL G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 65 Processing helix chain 'G' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 47 removed outlier: 6.795A pdb=" N GLY A 26 " --> pdb=" O PHE A 33 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ARG A 35 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA A 24 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ASP A 37 " --> pdb=" O PHE A 22 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N PHE A 22 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR A 94 " --> pdb=" O TYR A 118 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TYR A 118 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLN A 96 " --> pdb=" O TYR A 116 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N TYR A 116 " --> pdb=" O GLN A 96 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N MET A 98 " --> pdb=" O HIS A 114 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N HIS A 114 " --> pdb=" O MET A 98 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLY A 100 " --> pdb=" O GLY A 112 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLY A 112 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASP A 102 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N HIS A 114 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N TYR A 118 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ASP A 122 " --> pdb=" O TYR A 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 193 removed outlier: 3.520A pdb=" N HIS A 188 " --> pdb=" O TRP A 204 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N PHE A 241 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 186 through 193 removed outlier: 3.520A pdb=" N HIS A 188 " --> pdb=" O TRP A 204 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N PHE A 241 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 224 removed outlier: 4.724A pdb=" N TRP A 217 " --> pdb=" O GLN A 224 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 6 through 11 removed outlier: 5.708A pdb=" N PHE B 62 " --> pdb=" O GLY B 29 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 6 through 11 removed outlier: 5.708A pdb=" N PHE B 62 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER B 55 " --> pdb=" O TYR B 63 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 44 through 45 Processing sheet with id=AA8, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.576A pdb=" N SER D 22 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N THR D 70 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 9.789A pdb=" N GLN D 27 " --> pdb=" O SER D 68 " (cutoff:3.500A) removed outlier: 9.740A pdb=" N SER D 68 " --> pdb=" O GLN D 27 " (cutoff:3.500A) removed outlier: 11.301A pdb=" N VAL D 29 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 11.678A pdb=" N SER D 66 " --> pdb=" O VAL D 29 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.037A pdb=" N LEU D 11 " --> pdb=" O GLU D 107 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLN D 38 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N LEU D 47 " --> pdb=" O GLN D 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.037A pdb=" N LEU D 11 " --> pdb=" O GLU D 107 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR D 99 " --> pdb=" O GLN D 91 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.779A pdb=" N MET E 34 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N SER E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.860A pdb=" N ILE E 108 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.653A pdb=" N LYS F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.353A pdb=" N GLN F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AB8, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.458A pdb=" N ILE G 34 " --> pdb=" O ARG G 50 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ARG G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.781A pdb=" N TYR G 108 " --> pdb=" O ARG G 98 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE G 100 " --> pdb=" O MET G 106 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N MET G 106 " --> pdb=" O PHE G 100 " (cutoff:3.500A) 325 hydrogen bonds defined for protein. 807 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: 1.02 Time building geometry restraints manager: 0.69 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: 2168 1.34 - 1.46: 1741 1.46 - 1.58: 2858 1.58 - 1.70: 0 1.70 - 1.82: 44 Bond restraints: 6811 Sorted by residual: bond pdb=" N TYR G 60 " pdb=" CA TYR G 60 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.25e-02 6.40e+03 7.05e+00 bond pdb=" N GLU A 222 " pdb=" CA GLU A 222 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.27e-02 6.20e+03 6.29e+00 bond pdb=" N GLY C 1 " pdb=" CA GLY C 1 " ideal model delta sigma weight residual 1.451 1.489 -0.038 1.60e-02 3.91e+03 5.64e+00 bond pdb=" N GLN A 226 " pdb=" CA GLN A 226 " ideal model delta sigma weight residual 1.454 1.483 -0.029 1.31e-02 5.83e+03 4.98e+00 bond pdb=" N ASP A 223 " pdb=" CA ASP A 223 " ideal model delta sigma weight residual 1.462 1.489 -0.027 1.28e-02 6.10e+03 4.40e+00 ... (remaining 6806 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 8987 1.57 - 3.13: 198 3.13 - 4.70: 41 4.70 - 6.27: 5 6.27 - 7.83: 1 Bond angle restraints: 9232 Sorted by residual: angle pdb=" C ASP G 61 " pdb=" CA ASP G 61 " pdb=" CB ASP G 61 " ideal model delta sigma weight residual 109.62 115.72 -6.10 1.57e+00 4.06e-01 1.51e+01 angle pdb=" C TYR G 60 " pdb=" CA TYR G 60 " pdb=" CB TYR G 60 " ideal model delta sigma weight residual 109.38 101.55 7.83 2.03e+00 2.43e-01 1.49e+01 angle pdb=" CA GLU A 222 " pdb=" C GLU A 222 " pdb=" O GLU A 222 " ideal model delta sigma weight residual 121.36 116.85 4.51 1.20e+00 6.94e-01 1.41e+01 angle pdb=" CA GLU A 222 " pdb=" C GLU A 222 " pdb=" N ASP A 223 " ideal model delta sigma weight residual 115.51 119.75 -4.24 1.24e+00 6.50e-01 1.17e+01 angle pdb=" N ASP G 61 " pdb=" CA ASP G 61 " pdb=" C ASP G 61 " ideal model delta sigma weight residual 109.48 104.68 4.80 1.44e+00 4.82e-01 1.11e+01 ... (remaining 9227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 3645 17.62 - 35.23: 255 35.23 - 52.85: 78 52.85 - 70.46: 33 70.46 - 88.08: 12 Dihedral angle restraints: 4023 sinusoidal: 1606 harmonic: 2417 Sorted by residual: dihedral pdb=" CB CYS G 22 " pdb=" SG CYS G 22 " pdb=" SG CYS G 96 " pdb=" CB CYS G 96 " ideal model delta sinusoidal sigma weight residual 93.00 57.29 35.71 1 1.00e+01 1.00e-02 1.80e+01 dihedral pdb=" CA TYR A 27 " pdb=" C TYR A 27 " pdb=" N VAL A 28 " pdb=" CA VAL A 28 " ideal model delta harmonic sigma weight residual 180.00 160.27 19.73 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA PRO B 5 " pdb=" C PRO B 5 " pdb=" N LYS B 6 " pdb=" CA LYS B 6 " ideal model delta harmonic sigma weight residual 180.00 161.30 18.70 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 4020 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 544 0.028 - 0.056: 302 0.056 - 0.084: 51 0.084 - 0.112: 53 0.112 - 0.140: 21 Chirality restraints: 971 Sorted by residual: chirality pdb=" CA ILE D 59 " pdb=" N ILE D 59 " pdb=" C ILE D 59 " pdb=" CB ILE D 59 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA ILE F 21 " pdb=" N ILE F 21 " pdb=" C ILE F 21 " pdb=" CB ILE F 21 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.55e-01 chirality pdb=" CA ILE D 49 " pdb=" N ILE D 49 " pdb=" C ILE D 49 " pdb=" CB ILE D 49 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 968 not shown) Planarity restraints: 1192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP G 61 " 0.013 2.00e-02 2.50e+03 2.53e-02 6.38e+00 pdb=" C ASP G 61 " -0.044 2.00e-02 2.50e+03 pdb=" O ASP G 61 " 0.016 2.00e-02 2.50e+03 pdb=" N PRO G 62 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 40 " 0.134 9.50e-02 1.11e+02 6.00e-02 2.35e+00 pdb=" NE ARG G 40 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG G 40 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG G 40 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG G 40 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 60 " -0.018 2.00e-02 2.50e+03 1.02e-02 2.07e+00 pdb=" CG TYR G 60 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR G 60 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR G 60 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR G 60 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR G 60 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR G 60 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR G 60 " -0.007 2.00e-02 2.50e+03 ... (remaining 1189 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 747 2.75 - 3.29: 6098 3.29 - 3.83: 11756 3.83 - 4.36: 14719 4.36 - 4.90: 24325 Nonbonded interactions: 57645 Sorted by model distance: nonbonded pdb=" OG SER B 57 " pdb=" OD1 ASP B 59 " model vdw 2.219 3.040 nonbonded pdb=" NH2 ARG A 6 " pdb=" CE1 TYR A 113 " model vdw 2.227 3.420 nonbonded pdb=" OG SER F 12 " pdb=" OE2 GLU F 105 " model vdw 2.229 3.040 nonbonded pdb=" OD1 ASN E 35 " pdb=" OG SER E 50 " model vdw 2.260 3.040 nonbonded pdb=" O PRO D 96 " pdb=" O HOH D 301 " model vdw 2.283 3.040 ... (remaining 57640 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.550 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: 0.020 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.810 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: 0.010 Load rotamer database and sin/cos tables:5.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6818 Z= 0.173 Angle : 0.607 7.834 9246 Z= 0.354 Chirality : 0.042 0.140 971 Planarity : 0.004 0.060 1192 Dihedral : 15.408 88.079 2462 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.14 % Allowed : 9.68 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % 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: 1.21 (0.29), residues: 826 helix: 1.79 (0.60), residues: 73 sheet: 0.95 (0.26), residues: 364 loop : 0.61 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 40 TYR 0.021 0.002 TYR G 60 PHE 0.012 0.002 PHE B 56 TRP 0.013 0.002 TRP G 99 HIS 0.005 0.001 HIS A 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.17 ( 6811) covalent geometry : angle 0.60581 / 0.35 ( 9232) SS BOND : bond 0.00889 / 0.42 ( 7) SS BOND : angle 1.22901 / 0.77 ( 14) hydrogen bonds : bond 0.18746 / 13.04 ( 280) hydrogen bonds : angle 8.16661 / 5.84 ( 807) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 0.233 Fit side-chains REVERT: A 82 ARG cc_start: 0.7925 (ttp-110) cc_final: 0.7360 (ttp80) REVERT: A 166 GLU cc_start: 0.7829 (tt0) cc_final: 0.7295 (tm-30) REVERT: A 262 GLN cc_start: 0.7605 (mt0) cc_final: 0.6540 (tm130) REVERT: D 24 ARG cc_start: 0.7157 (ttm170) cc_final: 0.6823 (ttp80) REVERT: F 105 GLU cc_start: 0.7720 (pt0) cc_final: 0.6736 (tp30) REVERT: G 5 GLN cc_start: 0.7910 (pt0) cc_final: 0.7436 (mm-40) REVERT: G 19 LYS cc_start: 0.7924 (tttt) cc_final: 0.7625 (tttp) REVERT: G 42 LYS cc_start: 0.7564 (mttt) cc_final: 0.7095 (mmpt) outliers start: 1 outliers final: 1 residues processed: 143 average time/residue: 0.6821 time to fit residues: 101.4613 Evaluate side-chains 133 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 27 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74] chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 HIS A 114 HIS A 115 GLN A 188 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.165912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.128525 restraints weight = 5610.254| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.68 r_work: 0.3306 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6818 Z= 0.158 Angle : 0.607 6.958 9246 Z= 0.331 Chirality : 0.044 0.158 971 Planarity : 0.005 0.051 1192 Dihedral : 5.426 38.530 930 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.38 % Allowed : 11.08 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % 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: 1.26 (0.28), residues: 826 helix: 1.96 (0.60), residues: 75 sheet: 0.98 (0.26), residues: 360 loop : 0.62 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 40 TYR 0.020 0.002 TYR A 116 PHE 0.012 0.002 PHE E 29 TRP 0.014 0.002 TRP G 99 HIS 0.005 0.001 HIS A 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.16 ( 6811) covalent geometry : angle 0.60590 / 0.33 ( 9232) SS BOND : bond 0.00880 / 0.41 ( 7) SS BOND : angle 1.27592 / 0.79 ( 14) hydrogen bonds : bond 0.05314 / 3.58 ( 280) hydrogen bonds : angle 5.76705 / 4.05 ( 807) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.256 Fit side-chains REVERT: A 82 ARG cc_start: 0.8321 (ttp-110) cc_final: 0.7830 (ttp80) REVERT: A 138 MET cc_start: 0.7655 (OUTLIER) cc_final: 0.6761 (tpt) REVERT: A 166 GLU cc_start: 0.8484 (tt0) cc_final: 0.7899 (tm-30) REVERT: A 173 GLU cc_start: 0.7817 (tp30) cc_final: 0.7606 (mt-10) REVERT: A 262 GLN cc_start: 0.7979 (mt0) cc_final: 0.6800 (tm130) REVERT: B 75 LYS cc_start: 0.7162 (OUTLIER) cc_final: 0.6938 (pttm) REVERT: B 77 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7005 (tp30) REVERT: F 105 GLU cc_start: 0.8150 (pt0) cc_final: 0.7029 (tp30) REVERT: G 42 LYS cc_start: 0.8003 (mttt) cc_final: 0.7554 (mmpt) outliers start: 17 outliers final: 10 residues processed: 148 average time/residue: 0.6804 time to fit residues: 104.7780 Evaluate side-chains 147 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 109 LYS Chi-restraints excluded: chain F residue 11 GLN Chi-restraints excluded: chain F residue 70 LYS Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain G residue 27 PHE Chi-restraints excluded: chain G residue 78 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: [55, 70, 1, 21, 13, 46, 53, 29, 34, 51, 64] chunk 55 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN A 174 ASN A 188 HIS G 43 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.163931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.127029 restraints weight = 5511.464| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.55 r_work: 0.3271 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 6818 Z= 0.230 Angle : 0.682 7.267 9246 Z= 0.370 Chirality : 0.047 0.163 971 Planarity : 0.006 0.076 1192 Dihedral : 5.781 36.028 930 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.81 % Allowed : 12.06 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % 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 (0.28), residues: 826 helix: 1.75 (0.58), residues: 75 sheet: 0.94 (0.25), residues: 357 loop : 0.54 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 62 TYR 0.019 0.002 TYR A 116 PHE 0.017 0.003 PHE B 56 TRP 0.019 0.003 TRP G 99 HIS 0.006 0.001 HIS A 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.23 ( 6811) covalent geometry : angle 0.67967 / 0.37 ( 9232) SS BOND : bond 0.01288 / 0.62 ( 7) SS BOND : angle 1.58999 / 1.01 ( 14) hydrogen bonds : bond 0.05846 / 3.90 ( 280) hydrogen bonds : angle 5.81561 / 4.07 ( 807) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.269 Fit side-chains REVERT: A 72 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8130 (tt0) REVERT: A 82 ARG cc_start: 0.8417 (ttp-110) cc_final: 0.7926 (ttp80) REVERT: A 138 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.6908 (tpt) REVERT: A 262 GLN cc_start: 0.8089 (mt0) cc_final: 0.7888 (mt0) REVERT: B 77 GLU cc_start: 0.7456 (mm-30) cc_final: 0.7007 (tp30) REVERT: F 24 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8256 (mm) REVERT: F 105 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7077 (tp30) REVERT: G 5 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7510 (mm-40) REVERT: G 42 LYS cc_start: 0.8043 (mttt) cc_final: 0.7586 (mmpt) outliers start: 20 outliers final: 10 residues processed: 139 average time/residue: 0.6979 time to fit residues: 100.7922 Evaluate side-chains 144 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 109 LYS Chi-restraints excluded: chain F residue 11 GLN Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 70 LYS Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain G residue 5 GLN Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 27 PHE Chi-restraints excluded: chain G residue 78 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: [8, 75, 7, 47, 60, 37, 28, 13, 57, 69, 21] chunk 8 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 60 optimal weight: 0.0070 chunk 37 optimal weight: 0.9990 chunk 28 optimal weight: 0.0170 chunk 13 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.168862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.133397 restraints weight = 5657.238| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.49 r_work: 0.3338 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6818 Z= 0.113 Angle : 0.533 7.324 9246 Z= 0.289 Chirality : 0.042 0.138 971 Planarity : 0.004 0.043 1192 Dihedral : 5.175 35.871 930 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.24 % Allowed : 14.17 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % 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: 1.31 (0.29), residues: 826 helix: 2.05 (0.61), residues: 75 sheet: 1.00 (0.26), residues: 359 loop : 0.66 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 40 TYR 0.017 0.001 TYR A 116 PHE 0.009 0.002 PHE A 33 TRP 0.013 0.001 TRP A 60 HIS 0.003 0.001 HIS A 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 ( 6811) covalent geometry : angle 0.53194 / 0.29 ( 9232) SS BOND : bond 0.00639 / 0.30 ( 7) SS BOND : angle 1.06681 / 0.66 ( 14) hydrogen bonds : bond 0.04258 / 2.84 ( 280) hydrogen bonds : angle 5.24356 / 3.67 ( 807) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.256 Fit side-chains REVERT: A 82 ARG cc_start: 0.8170 (ttp-110) cc_final: 0.7723 (ttp80) REVERT: A 138 MET cc_start: 0.7514 (OUTLIER) cc_final: 0.6681 (tpt) REVERT: A 262 GLN cc_start: 0.8027 (mt0) cc_final: 0.6754 (tm130) REVERT: B 77 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7009 (tp30) REVERT: D 34 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8397 (tm) REVERT: E 54 ARG cc_start: 0.8425 (mmm-85) cc_final: 0.7597 (mtm110) REVERT: E 111 GLN cc_start: 0.8260 (mp10) cc_final: 0.7987 (pm20) REVERT: F 24 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8096 (mm) REVERT: F 70 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7512 (mtmm) REVERT: F 105 GLU cc_start: 0.8172 (pt0) cc_final: 0.6970 (tp30) REVERT: G 5 GLN cc_start: 0.8145 (pt0) cc_final: 0.7432 (mm-40) REVERT: G 42 LYS cc_start: 0.7995 (mttt) cc_final: 0.7539 (mmpt) outliers start: 16 outliers final: 7 residues processed: 146 average time/residue: 0.7103 time to fit residues: 107.7413 Evaluate side-chains 145 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain F residue 11 GLN Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 70 LYS Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 27 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: [64, 41, 43, 11, 79, 16, 19, 35, 40, 53, 13] chunk 64 optimal weight: 0.7980 chunk 41 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN A 188 HIS F 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.162444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.125083 restraints weight = 5639.305| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.74 r_work: 0.3235 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 6818 Z= 0.211 Angle : 0.657 9.458 9246 Z= 0.353 Chirality : 0.046 0.149 971 Planarity : 0.005 0.069 1192 Dihedral : 5.644 38.865 930 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.66 % Allowed : 13.88 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % 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: 1.26 (0.29), residues: 826 helix: 1.86 (0.59), residues: 75 sheet: 0.98 (0.25), residues: 357 loop : 0.64 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 21 TYR 0.018 0.002 TYR A 116 PHE 0.015 0.002 PHE B 56 TRP 0.018 0.002 TRP G 99 HIS 0.005 0.001 HIS A 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.21 ( 6811) covalent geometry : angle 0.65530 / 0.35 ( 9232) SS BOND : bond 0.01189 / 0.57 ( 7) SS BOND : angle 1.47848 / 0.93 ( 14) hydrogen bonds : bond 0.05444 / 3.62 ( 280) hydrogen bonds : angle 5.59861 / 3.92 ( 807) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.257 Fit side-chains REVERT: A 72 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8207 (tt0) REVERT: A 82 ARG cc_start: 0.8391 (ttp-110) cc_final: 0.7885 (ttp80) REVERT: A 138 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.6784 (tpt) REVERT: A 262 GLN cc_start: 0.8100 (mt0) cc_final: 0.7844 (mt0) REVERT: D 34 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8375 (tm) REVERT: F 24 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8229 (mm) REVERT: F 105 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.6960 (tp30) REVERT: G 5 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7459 (mm-40) REVERT: G 42 LYS cc_start: 0.7996 (mttt) cc_final: 0.7524 (mmpt) outliers start: 19 outliers final: 11 residues processed: 140 average time/residue: 0.7104 time to fit residues: 103.3714 Evaluate side-chains 152 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain F residue 11 GLN Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 70 LYS Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain G residue 5 GLN Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 27 PHE Chi-restraints excluded: chain G residue 78 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: [19, 6, 50, 1, 3, 2, 49, 61, 65, 64, 42] chunk 19 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 65 optimal weight: 0.0980 chunk 64 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS F 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.163368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.126297 restraints weight = 5605.704| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.71 r_work: 0.3245 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6818 Z= 0.170 Angle : 0.617 9.212 9246 Z= 0.329 Chirality : 0.044 0.144 971 Planarity : 0.005 0.058 1192 Dihedral : 5.523 39.301 930 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.38 % Allowed : 14.87 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % 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: 1.26 (0.29), residues: 826 helix: 1.92 (0.60), residues: 75 sheet: 0.98 (0.26), residues: 357 loop : 0.63 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 40 TYR 0.018 0.002 TYR A 116 PHE 0.013 0.002 PHE B 56 TRP 0.015 0.002 TRP G 99 HIS 0.004 0.001 HIS A 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 ( 6811) covalent geometry : angle 0.61551 / 0.33 ( 9232) SS BOND : bond 0.00990 / 0.48 ( 7) SS BOND : angle 1.37317 / 0.85 ( 14) hydrogen bonds : bond 0.05023 / 3.34 ( 280) hydrogen bonds : angle 5.45507 / 3.83 ( 807) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.263 Fit side-chains REVERT: A 82 ARG cc_start: 0.8323 (ttp-110) cc_final: 0.7814 (ttp80) REVERT: A 138 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.6718 (tpt) REVERT: A 262 GLN cc_start: 0.8105 (mt0) cc_final: 0.7840 (mt0) REVERT: D 34 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8389 (tm) REVERT: E 54 ARG cc_start: 0.8437 (mmm-85) cc_final: 0.7580 (mtm110) REVERT: E 77 ASN cc_start: 0.8431 (OUTLIER) cc_final: 0.8212 (m110) REVERT: E 111 GLN cc_start: 0.8267 (mp-120) cc_final: 0.8011 (pm20) REVERT: F 24 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8186 (mm) REVERT: F 105 GLU cc_start: 0.8181 (pt0) cc_final: 0.6938 (tp30) REVERT: G 5 GLN cc_start: 0.8160 (pt0) cc_final: 0.7442 (mm-40) REVERT: G 42 LYS cc_start: 0.7996 (mttt) cc_final: 0.7517 (mmpt) outliers start: 17 outliers final: 10 residues processed: 140 average time/residue: 0.7171 time to fit residues: 104.2952 Evaluate side-chains 146 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain F residue 11 GLN Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 70 LYS Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 27 PHE Chi-restraints excluded: chain G residue 78 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: [22, 57, 64, 77, 41, 44, 29, 56, 68, 70, 5] chunk 22 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 29 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS F 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.162777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.125538 restraints weight = 5557.748| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.72 r_work: 0.3243 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 6818 Z= 0.184 Angle : 0.640 9.158 9246 Z= 0.341 Chirality : 0.045 0.146 971 Planarity : 0.005 0.063 1192 Dihedral : 5.607 40.412 930 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.66 % Allowed : 14.73 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % 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: 1.22 (0.28), residues: 826 helix: 1.88 (0.59), residues: 75 sheet: 0.96 (0.26), residues: 357 loop : 0.59 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 40 TYR 0.018 0.002 TYR A 116 PHE 0.014 0.002 PHE B 56 TRP 0.016 0.002 TRP G 99 HIS 0.004 0.001 HIS A 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 ( 6811) covalent geometry : angle 0.63851 / 0.34 ( 9232) SS BOND : bond 0.01083 / 0.52 ( 7) SS BOND : angle 1.42471 / 0.89 ( 14) hydrogen bonds : bond 0.05174 / 3.43 ( 280) hydrogen bonds : angle 5.51119 / 3.86 ( 807) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.177 Fit side-chains REVERT: A 82 ARG cc_start: 0.8319 (ttp-110) cc_final: 0.7808 (ttp80) REVERT: A 138 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.6726 (tpt) REVERT: A 262 GLN cc_start: 0.8099 (mt0) cc_final: 0.7826 (mt0) REVERT: D 34 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8352 (tm) REVERT: E 54 ARG cc_start: 0.8432 (mmm-85) cc_final: 0.7593 (mtm110) REVERT: E 77 ASN cc_start: 0.8429 (OUTLIER) cc_final: 0.8204 (m110) REVERT: E 111 GLN cc_start: 0.8245 (mp-120) cc_final: 0.7962 (pm20) REVERT: F 24 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8213 (mm) REVERT: F 105 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.6940 (tp30) REVERT: G 5 GLN cc_start: 0.8142 (pt0) cc_final: 0.7453 (mm-40) REVERT: G 42 LYS cc_start: 0.7983 (mttt) cc_final: 0.7512 (mmpt) outliers start: 19 outliers final: 11 residues processed: 138 average time/residue: 0.6982 time to fit residues: 100.1403 Evaluate side-chains 147 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain F residue 11 GLN Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 70 LYS Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 27 PHE Chi-restraints excluded: chain G residue 78 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: [6, 79, 18, 62, 32, 53, 23, 46, 3, 8, 15] chunk 6 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS F 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.165245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.128393 restraints weight = 5618.208| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.72 r_work: 0.3270 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6818 Z= 0.134 Angle : 0.582 9.052 9246 Z= 0.308 Chirality : 0.043 0.140 971 Planarity : 0.005 0.047 1192 Dihedral : 5.336 40.897 930 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.10 % Allowed : 15.57 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % 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: 1.31 (0.29), residues: 826 helix: 2.06 (0.60), residues: 75 sheet: 0.97 (0.26), residues: 360 loop : 0.69 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 76 TYR 0.017 0.002 TYR A 116 PHE 0.010 0.002 PHE B 56 TRP 0.013 0.002 TRP A 60 HIS 0.004 0.001 HIS A 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 6811) covalent geometry : angle 0.58060 / 0.31 ( 9232) SS BOND : bond 0.00770 / 0.37 ( 7) SS BOND : angle 1.20877 / 0.74 ( 14) hydrogen bonds : bond 0.04553 / 3.02 ( 280) hydrogen bonds : angle 5.28792 / 3.71 ( 807) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.236 Fit side-chains REVERT: A 72 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8233 (tt0) REVERT: A 82 ARG cc_start: 0.8217 (ttp-110) cc_final: 0.7738 (ttp80) REVERT: A 138 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.6638 (tpt) REVERT: A 262 GLN cc_start: 0.8057 (mt0) cc_final: 0.6729 (tm130) REVERT: B 77 GLU cc_start: 0.7410 (mm-30) cc_final: 0.6939 (tp30) REVERT: D 34 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8316 (tm) REVERT: E 54 ARG cc_start: 0.8425 (mmm-85) cc_final: 0.7555 (mtm110) REVERT: E 77 ASN cc_start: 0.8414 (OUTLIER) cc_final: 0.8201 (m110) REVERT: E 111 GLN cc_start: 0.8265 (mp-120) cc_final: 0.7960 (pm20) REVERT: F 24 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8145 (mm) REVERT: F 105 GLU cc_start: 0.8171 (pt0) cc_final: 0.6929 (tp30) REVERT: G 5 GLN cc_start: 0.8129 (pt0) cc_final: 0.7445 (mm-40) REVERT: G 42 LYS cc_start: 0.7987 (mttt) cc_final: 0.7520 (mmpt) outliers start: 15 outliers final: 10 residues processed: 138 average time/residue: 0.6881 time to fit residues: 98.6273 Evaluate side-chains 148 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain F residue 11 GLN Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 70 LYS Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 27 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: [77, 75, 28, 7, 16, 49, 58, 63, 2, 6, 19] chunk 77 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS F 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.164098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.127044 restraints weight = 5600.743| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.72 r_work: 0.3253 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6818 Z= 0.169 Angle : 0.625 8.993 9246 Z= 0.332 Chirality : 0.044 0.146 971 Planarity : 0.005 0.058 1192 Dihedral : 5.511 42.099 930 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.38 % Allowed : 15.15 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % 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: 1.26 (0.29), residues: 826 helix: 1.99 (0.60), residues: 75 sheet: 0.94 (0.26), residues: 360 loop : 0.67 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 76 TYR 0.018 0.002 TYR A 116 PHE 0.013 0.002 PHE B 56 TRP 0.015 0.002 TRP G 99 HIS 0.004 0.001 HIS A 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 ( 6811) covalent geometry : angle 0.62356 / 0.33 ( 9232) SS BOND : bond 0.00985 / 0.47 ( 7) SS BOND : angle 1.33313 / 0.83 ( 14) hydrogen bonds : bond 0.04990 / 3.30 ( 280) hydrogen bonds : angle 5.43271 / 3.81 ( 807) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.237 Fit side-chains REVERT: A 72 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8227 (tt0) REVERT: A 82 ARG cc_start: 0.8270 (ttp-110) cc_final: 0.7776 (ttp80) REVERT: A 138 MET cc_start: 0.7623 (OUTLIER) cc_final: 0.6690 (tpt) REVERT: A 262 GLN cc_start: 0.8080 (mt0) cc_final: 0.7801 (mt0) REVERT: D 34 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8331 (tm) REVERT: E 54 ARG cc_start: 0.8428 (mmm-85) cc_final: 0.7551 (mtm110) REVERT: F 24 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8192 (mm) REVERT: F 105 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.6946 (tp30) REVERT: G 5 GLN cc_start: 0.8133 (pt0) cc_final: 0.7448 (mm-40) REVERT: G 42 LYS cc_start: 0.7989 (mttt) cc_final: 0.7510 (mmpt) outliers start: 17 outliers final: 12 residues processed: 138 average time/residue: 0.6923 time to fit residues: 99.1796 Evaluate side-chains 150 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain F residue 11 GLN Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 70 LYS Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 27 PHE Chi-restraints excluded: chain G residue 78 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: [68, 22, 32, 33, 39, 13, 21, 31, 64, 20, 52] chunk 68 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 39 optimal weight: 0.0470 chunk 13 optimal weight: 0.4980 chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS F 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.165905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.129290 restraints weight = 5622.509| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.73 r_work: 0.3287 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6818 Z= 0.123 Angle : 0.573 9.039 9246 Z= 0.302 Chirality : 0.043 0.139 971 Planarity : 0.005 0.055 1192 Dihedral : 5.234 42.226 930 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.10 % Allowed : 15.43 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % 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: 1.32 (0.29), residues: 826 helix: 2.11 (0.61), residues: 75 sheet: 0.95 (0.26), residues: 356 loop : 0.71 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 40 TYR 0.017 0.001 TYR A 116 PHE 0.010 0.002 PHE A 33 TRP 0.013 0.002 TRP A 60 HIS 0.003 0.001 HIS A 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 6811) covalent geometry : angle 0.57205 / 0.30 ( 9232) SS BOND : bond 0.00690 / 0.33 ( 7) SS BOND : angle 1.11759 / 0.68 ( 14) hydrogen bonds : bond 0.04333 / 2.86 ( 280) hydrogen bonds : angle 5.20898 / 3.65 ( 807) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.263 Fit side-chains REVERT: A 82 ARG cc_start: 0.8173 (ttp-110) cc_final: 0.7673 (ttp80) REVERT: A 138 MET cc_start: 0.7476 (OUTLIER) cc_final: 0.6596 (tpt) REVERT: A 262 GLN cc_start: 0.7978 (mt0) cc_final: 0.6665 (tm130) REVERT: B 77 GLU cc_start: 0.7390 (mm-30) cc_final: 0.6927 (tp30) REVERT: D 34 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8342 (tm) REVERT: E 12 VAL cc_start: 0.8473 (t) cc_final: 0.8164 (m) REVERT: E 54 ARG cc_start: 0.8415 (mmm-85) cc_final: 0.7542 (mtm110) REVERT: E 111 GLN cc_start: 0.8216 (mp-120) cc_final: 0.7942 (pm20) REVERT: F 24 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8103 (mm) REVERT: F 103 LYS cc_start: 0.8673 (tptt) cc_final: 0.8454 (tptp) REVERT: F 105 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.6902 (tp30) REVERT: G 5 GLN cc_start: 0.8127 (pt0) cc_final: 0.7404 (mm-40) REVERT: G 42 LYS cc_start: 0.7994 (mttt) cc_final: 0.7524 (mmpt) outliers start: 15 outliers final: 10 residues processed: 143 average time/residue: 0.6916 time to fit residues: 102.8321 Evaluate side-chains 148 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain F residue 11 GLN Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 70 LYS Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 27 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: [3, 79, 49, 57, 60, 59, 16, 37, 13, 18, 33] chunk 3 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 49 optimal weight: 0.0470 chunk 57 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 18 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.166237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.129391 restraints weight = 5617.237| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.73 r_work: 0.3288 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6818 Z= 0.121 Angle : 0.568 8.767 9246 Z= 0.301 Chirality : 0.042 0.138 971 Planarity : 0.005 0.056 1192 Dihedral : 5.198 42.820 930 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.96 % Allowed : 15.43 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % 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: 1.36 (0.29), residues: 826 helix: 2.16 (0.61), residues: 75 sheet: 0.96 (0.26), residues: 356 loop : 0.75 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 76 TYR 0.016 0.001 TYR A 116 PHE 0.010 0.002 PHE D 84 TRP 0.013 0.002 TRP A 60 HIS 0.004 0.001 HIS A 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 6811) covalent geometry : angle 0.56717 / 0.30 ( 9232) SS BOND : bond 0.00671 / 0.32 ( 7) SS BOND : angle 1.08701 / 0.66 ( 14) hydrogen bonds : bond 0.04281 / 2.83 ( 280) hydrogen bonds : angle 5.17524 / 3.63 ( 807) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3613.98 seconds wall clock time: 61 minutes 57.07 seconds (3717.07 seconds total)