Starting phenix.real_space_refine on Sat May 2 12:54:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i5e_52628/05_2026/9i5e_52628.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i5e_52628/05_2026/9i5e_52628.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9i5e_52628/05_2026/9i5e_52628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i5e_52628/05_2026/9i5e_52628.map" model { file = "/net/cci-nas-00/data/ceres_data/9i5e_52628/05_2026/9i5e_52628.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i5e_52628/05_2026/9i5e_52628.cif" } resolution = 3.77 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= 0.015 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: 8 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 24 5.16 5 Cl 2 4.86 5 C 3336 2.51 5 N 922 2.21 5 O 1048 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5340 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1644 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 4, 'TRANS': 199} Chain: "M" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 954 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "N" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 954 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "B" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1644 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 4, 'TRANS': 199} Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 72 Unusual residues: {' MG': 1, 'GDP': 1, 'M1X': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {' MG': 1, 'M1X': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.47, per 1000 atoms: 0.28 Number of scatterers: 5340 At special positions: 0 Unit cell: (145, 107.88, 58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Cl 2 17.00 S 24 16.00 P 4 15.00 Mg 2 11.99 F 2 9.00 O 1048 8.00 N 922 7.00 C 3336 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 93 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 93 " 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.42 Conformation dependent library (CDL) restraints added in 178.4 milliseconds 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1224 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 8 sheets defined 34.2% alpha, 28.4% 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 18 through 26 removed outlier: 3.698A pdb=" N GLN A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 72 removed outlier: 3.737A pdb=" N ASP A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 105 removed outlier: 3.691A pdb=" N ARG A 102 " --> pdb=" O GLU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 138 Processing helix chain 'A' and resid 151 through 204 removed outlier: 3.567A pdb=" N LYS A 203 " --> pdb=" O GLN A 199 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 88 removed outlier: 3.622A pdb=" N THR M 88 " --> pdb=" O PRO M 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 110 removed outlier: 4.162A pdb=" N TYR M 110 " --> pdb=" O ALA M 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 88 removed outlier: 3.755A pdb=" N THR N 88 " --> pdb=" O PRO N 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 26 removed outlier: 3.788A pdb=" N GLN B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 72 removed outlier: 3.774A pdb=" N ASP B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 105 removed outlier: 3.731A pdb=" N ARG B 102 " --> pdb=" O GLU B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 138 Processing helix chain 'B' and resid 151 through 204 removed outlier: 3.573A pdb=" N LYS B 203 " --> pdb=" O GLN B 199 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 46 removed outlier: 8.893A pdb=" N GLY A 77 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS A 5 " --> pdb=" O GLY A 77 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N LEU A 79 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL A 7 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N VAL A 81 " --> pdb=" O VAL A 7 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL A 9 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N ILE A 142 " --> pdb=" O MET A 111 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU A 113 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N THR A 144 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N GLY A 115 " --> pdb=" O THR A 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AA3, first strand: chain 'M' and resid 10 through 13 removed outlier: 3.724A pdb=" N MET M 34 " --> pdb=" O SER M 51 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ARG M 38 " --> pdb=" O PHE M 47 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N PHE M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 10 through 13 Processing sheet with id=AA5, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AA6, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.645A pdb=" N MET N 34 " --> pdb=" O SER N 51 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ARG N 38 " --> pdb=" O PHE N 47 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N PHE N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 10 through 13 Processing sheet with id=AA8, first strand: chain 'B' and resid 39 through 46 removed outlier: 8.871A pdb=" N GLY B 77 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS B 5 " --> pdb=" O GLY B 77 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N LEU B 79 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL B 7 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N VAL B 81 " --> pdb=" O VAL B 7 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL B 9 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N ILE B 142 " --> pdb=" O MET B 111 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU B 113 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR B 144 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N GLY B 115 " --> pdb=" O THR B 144 " (cutoff:3.500A) 285 hydrogen bonds defined for protein. 777 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: 1.03 Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 908 1.30 - 1.43: 1420 1.43 - 1.56: 3058 1.56 - 1.69: 18 1.69 - 1.81: 38 Bond restraints: 5442 Sorted by residual: bond pdb=" C37 M1X A 301 " pdb=" N33 M1X A 301 " ideal model delta sigma weight residual 1.448 1.176 0.272 2.00e-02 2.50e+03 1.85e+02 bond pdb=" C37 M1X B 303 " pdb=" N33 M1X B 303 " ideal model delta sigma weight residual 1.448 1.176 0.272 2.00e-02 2.50e+03 1.85e+02 bond pdb=" C32 M1X A 301 " pdb=" N33 M1X A 301 " ideal model delta sigma weight residual 1.470 1.244 0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C32 M1X B 303 " pdb=" N33 M1X B 303 " ideal model delta sigma weight residual 1.470 1.244 0.226 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C34 M1X A 301 " pdb=" C35 M1X A 301 " ideal model delta sigma weight residual 1.525 1.329 0.196 2.00e-02 2.50e+03 9.61e+01 ... (remaining 5437 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.96: 7364 11.96 - 23.93: 0 23.93 - 35.89: 0 35.89 - 47.85: 0 47.85 - 59.81: 2 Bond angle restraints: 7366 Sorted by residual: angle pdb=" C38 M1X B 303 " pdb=" C40 M1X B 303 " pdb=" N41 M1X B 303 " ideal model delta sigma weight residual 180.00 120.19 59.81 3.00e+00 1.11e-01 3.98e+02 angle pdb=" C38 M1X A 301 " pdb=" C40 M1X A 301 " pdb=" N41 M1X A 301 " ideal model delta sigma weight residual 180.00 120.19 59.81 3.00e+00 1.11e-01 3.97e+02 angle pdb=" O5' GDP A 302 " pdb=" PA GDP A 302 " pdb=" O3A GDP A 302 " ideal model delta sigma weight residual 102.60 110.73 -8.13 3.00e+00 1.11e-01 7.35e+00 angle pdb=" O1A GDP A 302 " pdb=" PA GDP A 302 " pdb=" O2A GDP A 302 " ideal model delta sigma weight residual 109.50 101.41 8.09 3.00e+00 1.11e-01 7.27e+00 angle pdb=" O1A GDP B 301 " pdb=" PA GDP B 301 " pdb=" O2A GDP B 301 " ideal model delta sigma weight residual 109.50 101.60 7.90 3.00e+00 1.11e-01 6.93e+00 ... (remaining 7361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.44: 2816 18.44 - 36.88: 376 36.88 - 55.32: 114 55.32 - 73.76: 18 73.76 - 92.20: 12 Dihedral angle restraints: 3336 sinusoidal: 1426 harmonic: 1910 Sorted by residual: dihedral pdb=" C4' GDP A 302 " pdb=" O5' GDP A 302 " pdb=" C5' GDP A 302 " pdb=" PA GDP A 302 " ideal model delta sinusoidal sigma weight residual -179.98 -87.78 -92.20 1 2.00e+01 2.50e-03 2.49e+01 dihedral pdb=" O2B GDP A 302 " pdb=" O3A GDP A 302 " pdb=" PB GDP A 302 " pdb=" PA GDP A 302 " ideal model delta sinusoidal sigma weight residual 180.00 121.22 58.78 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" O2B GDP B 301 " pdb=" O3A GDP B 301 " pdb=" PB GDP B 301 " pdb=" PA GDP B 301 " ideal model delta sinusoidal sigma weight residual -180.00 -122.15 -57.85 1 2.00e+01 2.50e-03 1.12e+01 ... (remaining 3333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 470 0.026 - 0.051: 172 0.051 - 0.077: 81 0.077 - 0.103: 47 0.103 - 0.128: 20 Chirality restraints: 790 Sorted by residual: chirality pdb=" CA ASP B 69 " pdb=" N ASP B 69 " pdb=" C ASP B 69 " pdb=" CB ASP B 69 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.11e-01 chirality pdb=" CA ASP A 69 " pdb=" N ASP A 69 " pdb=" C ASP A 69 " pdb=" CB ASP A 69 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA ASP N 105 " pdb=" N ASP N 105 " pdb=" C ASP N 105 " pdb=" CB ASP N 105 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 3.97e-01 ... (remaining 787 not shown) Planarity restraints: 940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 123 " -0.110 9.50e-02 1.11e+02 4.92e-02 1.49e+00 pdb=" NE ARG B 123 " 0.007 2.00e-02 2.50e+03 pdb=" CZ ARG B 123 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B 123 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 123 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 123 " -0.104 9.50e-02 1.11e+02 4.66e-02 1.35e+00 pdb=" NE ARG A 123 " 0.007 2.00e-02 2.50e+03 pdb=" CZ ARG A 123 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 123 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 123 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 139 " 0.019 5.00e-02 4.00e+02 2.86e-02 1.31e+00 pdb=" N PRO A 140 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 140 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 140 " 0.016 5.00e-02 4.00e+02 ... (remaining 937 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.54: 12 2.54 - 3.13: 3806 3.13 - 3.72: 7927 3.72 - 4.31: 9927 4.31 - 4.90: 17072 Nonbonded interactions: 38744 Sorted by model distance: nonbonded pdb=" O1B GDP B 301 " pdb="MG MG B 302 " model vdw 1.945 2.170 nonbonded pdb=" O LYS B 16 " pdb="MG MG B 302 " model vdw 2.025 2.170 nonbonded pdb=" O LYS A 16 " pdb="MG MG A 303 " model vdw 2.026 2.170 nonbonded pdb=" OG SER B 17 " pdb="MG MG B 302 " model vdw 2.086 2.170 nonbonded pdb=" OG SER A 17 " pdb="MG MG A 303 " model vdw 2.182 2.170 ... (remaining 38739 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 204) selection = (chain 'B' and resid 1 through 204) } ncs_group { reference = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.670 Find NCS groups from input model: 0.080 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 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 : 0.013 0.272 5446 Z= 0.643 Angle : 1.236 59.813 7370 Z= 0.468 Chirality : 0.040 0.128 790 Planarity : 0.004 0.049 940 Dihedral : 18.618 92.204 2106 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 6.27 % Allowed : 26.52 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.34), residues: 644 helix: 2.75 (0.36), residues: 200 sheet: 1.42 (0.36), residues: 206 loop : -0.22 (0.43), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 41 TYR 0.008 0.001 TYR N 92 PHE 0.018 0.001 PHE B 141 TRP 0.005 0.001 TRP M 36 HIS 0.001 0.000 HIS B 27 Details of bonding type rmsd covalent geometry : bond 0.01285 ( 5442) covalent geometry : angle 1.23596 ( 7366) SS BOND : bond 0.00381 ( 2) SS BOND : angle 0.38751 ( 4) hydrogen bonds : bond 0.11922 ( 269) hydrogen bonds : angle 5.04568 ( 777) Misc. bond : bond 0.00035 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 125 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.7770 (ttmt) cc_final: 0.7433 (ttmt) REVERT: A 67 MET cc_start: 0.5689 (tmm) cc_final: 0.5448 (tmm) REVERT: A 90 PHE cc_start: 0.7584 (OUTLIER) cc_final: 0.6912 (t80) REVERT: A 125 VAL cc_start: 0.7446 (t) cc_final: 0.7104 (p) REVERT: A 129 GLN cc_start: 0.7467 (mt0) cc_final: 0.7073 (tt0) REVERT: M 57 TYR cc_start: 0.7695 (m-80) cc_final: 0.7401 (m-80) REVERT: M 60 SER cc_start: 0.8725 (m) cc_final: 0.8282 (t) REVERT: B 5 LYS cc_start: 0.7781 (ttmt) cc_final: 0.7179 (ttmt) REVERT: B 22 GLN cc_start: 0.7630 (tm-30) cc_final: 0.7346 (tm-30) REVERT: B 36 ILE cc_start: 0.4995 (OUTLIER) cc_final: 0.4715 (mm) REVERT: B 90 PHE cc_start: 0.7575 (OUTLIER) cc_final: 0.6483 (t80) REVERT: B 96 TYR cc_start: 0.6626 (m-10) cc_final: 0.6282 (m-80) REVERT: B 111 MET cc_start: 0.7370 (tpt) cc_final: 0.7128 (mmm) REVERT: B 125 VAL cc_start: 0.7492 (t) cc_final: 0.7153 (p) outliers start: 35 outliers final: 28 residues processed: 154 average time/residue: 0.0813 time to fit residues: 16.0958 Evaluate side-chains 154 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 90 PHE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain M residue 47 PHE Chi-restraints excluded: chain M residue 73 LYS Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 82 SER Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 47 PHE Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 172 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN B 26 ASN B 43 GLN B 182 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.160934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.136140 restraints weight = 8770.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.140572 restraints weight = 4800.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.143514 restraints weight = 3074.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.145546 restraints weight = 2187.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.146886 restraints weight = 1671.665| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 5446 Z= 0.219 Angle : 0.632 5.888 7370 Z= 0.321 Chirality : 0.043 0.137 790 Planarity : 0.004 0.045 940 Dihedral : 9.083 71.030 901 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 5.73 % Allowed : 25.63 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.34), residues: 644 helix: 2.37 (0.35), residues: 202 sheet: 1.38 (0.37), residues: 202 loop : -0.46 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 41 TYR 0.010 0.002 TYR M 56 PHE 0.026 0.002 PHE B 78 TRP 0.018 0.002 TRP M 36 HIS 0.001 0.000 HIS A 166 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 5442) covalent geometry : angle 0.63210 ( 7366) SS BOND : bond 0.00554 ( 2) SS BOND : angle 0.88489 ( 4) hydrogen bonds : bond 0.08749 ( 269) hydrogen bonds : angle 4.72004 ( 777) Misc. bond : bond 0.00097 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: A 5 LYS cc_start: 0.7953 (ttmt) cc_final: 0.7625 (ttmt) REVERT: A 43 GLN cc_start: 0.7091 (mp-120) cc_final: 0.6840 (mp10) REVERT: A 57 ASP cc_start: 0.7445 (t0) cc_final: 0.7205 (t0) REVERT: A 67 MET cc_start: 0.5744 (tmm) cc_final: 0.5519 (tmm) REVERT: A 125 VAL cc_start: 0.7440 (t) cc_final: 0.7010 (p) REVERT: A 129 GLN cc_start: 0.7812 (mt0) cc_final: 0.7386 (tt0) REVERT: A 167 LYS cc_start: 0.8051 (mmmm) cc_final: 0.7735 (mmmm) REVERT: M 57 TYR cc_start: 0.7742 (m-80) cc_final: 0.7389 (m-80) REVERT: M 60 SER cc_start: 0.8814 (m) cc_final: 0.8345 (t) REVERT: M 101 TYR cc_start: 0.7619 (t80) cc_final: 0.7257 (t80) REVERT: N 98 SER cc_start: 0.8768 (t) cc_final: 0.8528 (m) REVERT: B 5 LYS cc_start: 0.7920 (ttmt) cc_final: 0.7053 (ttmt) REVERT: B 41 ARG cc_start: 0.7500 (ttm110) cc_final: 0.7295 (mtp85) REVERT: B 73 ARG cc_start: 0.7255 (mtm110) cc_final: 0.7012 (mtm110) REVERT: B 96 TYR cc_start: 0.6859 (m-10) cc_final: 0.6355 (m-80) REVERT: B 111 MET cc_start: 0.7643 (tpt) cc_final: 0.7305 (mmm) REVERT: B 125 VAL cc_start: 0.7540 (t) cc_final: 0.7122 (p) REVERT: B 167 LYS cc_start: 0.8108 (mmmm) cc_final: 0.7822 (mmmm) outliers start: 32 outliers final: 24 residues processed: 150 average time/residue: 0.0828 time to fit residues: 15.6085 Evaluate side-chains 148 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 90 PHE Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain M residue 53 SER Chi-restraints excluded: chain M residue 68 SER Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 183 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 30 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 45 optimal weight: 0.0270 chunk 54 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 59 optimal weight: 0.1980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN B 43 GLN B 182 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.162853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.138531 restraints weight = 8726.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.142872 restraints weight = 4756.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.145944 restraints weight = 3065.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.147859 restraints weight = 2152.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.149238 restraints weight = 1646.875| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5446 Z= 0.169 Angle : 0.576 5.901 7370 Z= 0.293 Chirality : 0.041 0.136 790 Planarity : 0.003 0.038 940 Dihedral : 8.054 65.884 872 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 6.09 % Allowed : 27.06 % Favored : 66.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.34), residues: 644 helix: 2.41 (0.35), residues: 202 sheet: 1.29 (0.37), residues: 204 loop : -0.44 (0.43), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 41 TYR 0.009 0.001 TYR M 57 PHE 0.020 0.002 PHE B 141 TRP 0.011 0.001 TRP M 36 HIS 0.001 0.000 HIS B 27 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 5442) covalent geometry : angle 0.57600 ( 7366) SS BOND : bond 0.00477 ( 2) SS BOND : angle 0.61869 ( 4) hydrogen bonds : bond 0.08517 ( 269) hydrogen bonds : angle 4.51034 ( 777) Misc. bond : bond 0.00058 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.7992 (ttmt) cc_final: 0.7662 (ttmt) REVERT: A 43 GLN cc_start: 0.7097 (mp-120) cc_final: 0.6802 (mp10) REVERT: A 67 MET cc_start: 0.5745 (tmm) cc_final: 0.5494 (tmm) REVERT: A 125 VAL cc_start: 0.7489 (t) cc_final: 0.7119 (p) REVERT: A 129 GLN cc_start: 0.7769 (mt0) cc_final: 0.7344 (tt0) REVERT: A 167 LYS cc_start: 0.8007 (mmmm) cc_final: 0.7799 (mmmm) REVERT: M 57 TYR cc_start: 0.7748 (m-80) cc_final: 0.7449 (m-80) REVERT: M 60 SER cc_start: 0.8800 (m) cc_final: 0.8319 (t) REVERT: N 57 TYR cc_start: 0.7761 (m-80) cc_final: 0.7527 (m-80) REVERT: N 98 SER cc_start: 0.8748 (t) cc_final: 0.8514 (m) REVERT: B 5 LYS cc_start: 0.7962 (ttmt) cc_final: 0.7069 (ttmt) REVERT: B 96 TYR cc_start: 0.6797 (m-10) cc_final: 0.6248 (m-80) REVERT: B 111 MET cc_start: 0.7666 (tpt) cc_final: 0.7413 (mmm) REVERT: B 125 VAL cc_start: 0.7562 (t) cc_final: 0.7140 (p) REVERT: B 167 LYS cc_start: 0.8094 (mmmm) cc_final: 0.7814 (mmmm) outliers start: 34 outliers final: 28 residues processed: 152 average time/residue: 0.0808 time to fit residues: 15.5846 Evaluate side-chains 156 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 90 PHE Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain M residue 53 SER Chi-restraints excluded: chain M residue 68 SER Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 183 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 18 optimal weight: 0.1980 chunk 56 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN B 43 GLN B 182 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.159476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.134505 restraints weight = 8541.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.138982 restraints weight = 4611.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.141884 restraints weight = 2931.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.143886 restraints weight = 2086.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.145260 restraints weight = 1596.264| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 5446 Z= 0.218 Angle : 0.627 6.053 7370 Z= 0.323 Chirality : 0.043 0.138 790 Planarity : 0.004 0.035 940 Dihedral : 8.058 59.675 872 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 6.63 % Allowed : 25.99 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.34), residues: 644 helix: 2.31 (0.35), residues: 202 sheet: 1.05 (0.37), residues: 204 loop : -0.63 (0.42), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 41 TYR 0.011 0.002 TYR M 91 PHE 0.018 0.002 PHE B 141 TRP 0.016 0.002 TRP M 36 HIS 0.001 0.000 HIS A 166 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 5442) covalent geometry : angle 0.62711 ( 7366) SS BOND : bond 0.00568 ( 2) SS BOND : angle 0.84701 ( 4) hydrogen bonds : bond 0.09609 ( 269) hydrogen bonds : angle 4.76628 ( 777) Misc. bond : bond 0.00071 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 130 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8040 (ttmt) cc_final: 0.7728 (ttmt) REVERT: A 43 GLN cc_start: 0.7107 (mp-120) cc_final: 0.6899 (mp10) REVERT: A 67 MET cc_start: 0.5861 (tmm) cc_final: 0.5554 (tmm) REVERT: A 125 VAL cc_start: 0.7580 (t) cc_final: 0.6999 (p) REVERT: A 167 LYS cc_start: 0.8072 (mmmm) cc_final: 0.7822 (mmmm) REVERT: M 57 TYR cc_start: 0.7759 (m-80) cc_final: 0.7525 (m-80) REVERT: M 60 SER cc_start: 0.8797 (m) cc_final: 0.8325 (t) REVERT: M 101 TYR cc_start: 0.7713 (t80) cc_final: 0.7029 (t80) REVERT: N 57 TYR cc_start: 0.7792 (m-80) cc_final: 0.7501 (m-80) REVERT: N 98 SER cc_start: 0.8879 (t) cc_final: 0.8646 (m) REVERT: B 5 LYS cc_start: 0.8068 (ttmt) cc_final: 0.7102 (ttmt) REVERT: B 22 GLN cc_start: 0.7505 (tm-30) cc_final: 0.7267 (tp40) REVERT: B 96 TYR cc_start: 0.6820 (m-10) cc_final: 0.6293 (m-80) REVERT: B 111 MET cc_start: 0.7766 (tpt) cc_final: 0.7430 (mmm) REVERT: B 125 VAL cc_start: 0.7636 (t) cc_final: 0.7251 (p) REVERT: B 167 LYS cc_start: 0.8144 (mmmm) cc_final: 0.7793 (mmmm) outliers start: 37 outliers final: 32 residues processed: 156 average time/residue: 0.0903 time to fit residues: 17.4002 Evaluate side-chains 162 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain M residue 53 SER Chi-restraints excluded: chain M residue 68 SER Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 193 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 8 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 0.4980 chunk 61 optimal weight: 0.5980 chunk 39 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: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 GLN A 199 GLN ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN B 182 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.158770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.133709 restraints weight = 8725.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.138178 restraints weight = 4686.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.141147 restraints weight = 2975.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.143052 restraints weight = 2102.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.144447 restraints weight = 1622.937| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 5446 Z= 0.227 Angle : 0.633 6.232 7370 Z= 0.327 Chirality : 0.043 0.140 790 Planarity : 0.004 0.051 940 Dihedral : 7.872 58.713 870 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 6.99 % Allowed : 27.60 % Favored : 65.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.34), residues: 644 helix: 2.31 (0.35), residues: 194 sheet: 1.02 (0.37), residues: 206 loop : -0.81 (0.41), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 123 TYR 0.010 0.002 TYR A 137 PHE 0.016 0.002 PHE B 141 TRP 0.015 0.002 TRP M 36 HIS 0.001 0.000 HIS A 166 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 5442) covalent geometry : angle 0.63254 ( 7366) SS BOND : bond 0.00558 ( 2) SS BOND : angle 0.82282 ( 4) hydrogen bonds : bond 0.09950 ( 269) hydrogen bonds : angle 4.87979 ( 777) Misc. bond : bond 0.00073 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 133 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8079 (ttmt) cc_final: 0.7715 (ttmt) REVERT: A 22 GLN cc_start: 0.7478 (tm-30) cc_final: 0.7105 (tp40) REVERT: A 43 GLN cc_start: 0.7115 (mp-120) cc_final: 0.6897 (mp10) REVERT: A 67 MET cc_start: 0.5822 (tmm) cc_final: 0.5510 (tmm) REVERT: A 123 ARG cc_start: 0.7586 (ttt-90) cc_final: 0.7135 (ttt-90) REVERT: A 125 VAL cc_start: 0.7637 (t) cc_final: 0.6828 (p) REVERT: A 167 LYS cc_start: 0.8090 (mmmm) cc_final: 0.7830 (mmmm) REVERT: A 195 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7713 (tp30) REVERT: M 57 TYR cc_start: 0.7792 (m-80) cc_final: 0.7538 (m-80) REVERT: M 60 SER cc_start: 0.8792 (m) cc_final: 0.8325 (t) REVERT: M 101 TYR cc_start: 0.7776 (t80) cc_final: 0.7032 (t80) REVERT: N 57 TYR cc_start: 0.7806 (m-80) cc_final: 0.7512 (m-80) REVERT: N 98 SER cc_start: 0.8876 (t) cc_final: 0.8674 (m) REVERT: B 5 LYS cc_start: 0.8075 (ttmt) cc_final: 0.7148 (ttmt) REVERT: B 22 GLN cc_start: 0.7565 (tm-30) cc_final: 0.7304 (tp40) REVERT: B 96 TYR cc_start: 0.6804 (m-10) cc_final: 0.6263 (m-80) REVERT: B 167 LYS cc_start: 0.8149 (mmmm) cc_final: 0.7809 (mmmm) outliers start: 39 outliers final: 35 residues processed: 159 average time/residue: 0.0951 time to fit residues: 18.6793 Evaluate side-chains 166 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 131 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain M residue 53 SER Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 193 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 40 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 0.0980 chunk 5 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN B 182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.155391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.130295 restraints weight = 8737.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.134792 restraints weight = 4707.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.137829 restraints weight = 2983.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.139797 restraints weight = 2103.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.141173 restraints weight = 1613.936| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 5446 Z= 0.222 Angle : 0.635 6.318 7370 Z= 0.328 Chirality : 0.043 0.143 790 Planarity : 0.004 0.053 940 Dihedral : 7.907 58.242 870 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 6.09 % Allowed : 29.21 % Favored : 64.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.34), residues: 644 helix: 2.11 (0.35), residues: 202 sheet: 0.99 (0.37), residues: 204 loop : -0.81 (0.42), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 41 TYR 0.012 0.002 TYR A 137 PHE 0.015 0.002 PHE B 141 TRP 0.015 0.002 TRP M 36 HIS 0.001 0.000 HIS B 27 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 5442) covalent geometry : angle 0.63521 ( 7366) SS BOND : bond 0.00534 ( 2) SS BOND : angle 0.83259 ( 4) hydrogen bonds : bond 0.10117 ( 269) hydrogen bonds : angle 4.91204 ( 777) Misc. bond : bond 0.00071 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8048 (ttmt) cc_final: 0.7682 (ttmt) REVERT: A 43 GLN cc_start: 0.7141 (mp-120) cc_final: 0.6911 (mp10) REVERT: A 67 MET cc_start: 0.5742 (tmm) cc_final: 0.5428 (tmm) REVERT: A 125 VAL cc_start: 0.7583 (t) cc_final: 0.7160 (p) REVERT: A 167 LYS cc_start: 0.8097 (mmmm) cc_final: 0.7843 (mmmm) REVERT: M 57 TYR cc_start: 0.7797 (m-80) cc_final: 0.7570 (m-80) REVERT: M 60 SER cc_start: 0.8804 (m) cc_final: 0.8333 (t) REVERT: M 101 TYR cc_start: 0.7725 (t80) cc_final: 0.7061 (t80) REVERT: N 57 TYR cc_start: 0.7837 (m-80) cc_final: 0.7522 (m-80) REVERT: N 98 SER cc_start: 0.8885 (t) cc_final: 0.8653 (m) REVERT: B 5 LYS cc_start: 0.8065 (ttmt) cc_final: 0.7623 (ttmt) REVERT: B 96 TYR cc_start: 0.6801 (m-10) cc_final: 0.6262 (m-80) REVERT: B 167 LYS cc_start: 0.8142 (mmmm) cc_final: 0.7808 (mmmm) outliers start: 34 outliers final: 32 residues processed: 150 average time/residue: 0.0957 time to fit residues: 17.6560 Evaluate side-chains 157 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain M residue 53 SER Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 193 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 23 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 6 optimal weight: 0.2980 chunk 15 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN B 150 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.155859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.130870 restraints weight = 8695.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.135374 restraints weight = 4663.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.138427 restraints weight = 2955.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.140321 restraints weight = 2075.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.141725 restraints weight = 1594.043| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5446 Z= 0.206 Angle : 0.629 6.302 7370 Z= 0.325 Chirality : 0.042 0.143 790 Planarity : 0.004 0.059 940 Dihedral : 7.848 57.553 870 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 6.81 % Allowed : 28.67 % Favored : 64.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.34), residues: 644 helix: 2.13 (0.35), residues: 202 sheet: 1.11 (0.38), residues: 202 loop : -0.86 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 123 TYR 0.010 0.002 TYR A 137 PHE 0.013 0.002 PHE B 141 TRP 0.013 0.002 TRP M 36 HIS 0.001 0.000 HIS B 27 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 5442) covalent geometry : angle 0.62910 ( 7366) SS BOND : bond 0.00514 ( 2) SS BOND : angle 0.74516 ( 4) hydrogen bonds : bond 0.10033 ( 269) hydrogen bonds : angle 4.88278 ( 777) Misc. bond : bond 0.00061 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 132 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8045 (ttmt) cc_final: 0.7639 (ttmt) REVERT: A 43 GLN cc_start: 0.7145 (mp-120) cc_final: 0.6930 (mp10) REVERT: A 67 MET cc_start: 0.5732 (tmm) cc_final: 0.5438 (tmm) REVERT: A 167 LYS cc_start: 0.8090 (mmmm) cc_final: 0.7837 (mmmm) REVERT: M 57 TYR cc_start: 0.7787 (m-80) cc_final: 0.7567 (m-80) REVERT: M 60 SER cc_start: 0.8805 (m) cc_final: 0.8330 (t) REVERT: M 101 TYR cc_start: 0.7719 (t80) cc_final: 0.7080 (t80) REVERT: N 57 TYR cc_start: 0.7846 (m-80) cc_final: 0.7526 (m-80) REVERT: N 98 SER cc_start: 0.8874 (t) cc_final: 0.8645 (m) REVERT: B 5 LYS cc_start: 0.8089 (ttmt) cc_final: 0.7673 (ttmt) REVERT: B 96 TYR cc_start: 0.6735 (m-10) cc_final: 0.6262 (m-80) REVERT: B 167 LYS cc_start: 0.8136 (mmmm) cc_final: 0.7797 (mmmm) outliers start: 38 outliers final: 32 residues processed: 159 average time/residue: 0.0914 time to fit residues: 18.0424 Evaluate side-chains 163 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain M residue 53 SER Chi-restraints excluded: chain M residue 68 SER Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 193 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 14 optimal weight: 0.0980 chunk 19 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 GLN B 43 GLN B 182 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.158396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.133904 restraints weight = 8601.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.138323 restraints weight = 4607.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.141354 restraints weight = 2908.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.143295 restraints weight = 2042.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.144584 restraints weight = 1563.147| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5446 Z= 0.203 Angle : 0.646 6.285 7370 Z= 0.331 Chirality : 0.043 0.141 790 Planarity : 0.004 0.061 940 Dihedral : 7.855 57.155 870 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 6.27 % Allowed : 30.65 % Favored : 63.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.34), residues: 644 helix: 2.14 (0.35), residues: 202 sheet: 1.13 (0.38), residues: 202 loop : -0.93 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 123 TYR 0.046 0.002 TYR M 104 PHE 0.012 0.002 PHE B 141 TRP 0.012 0.002 TRP M 36 HIS 0.001 0.000 HIS B 27 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 5442) covalent geometry : angle 0.64624 ( 7366) SS BOND : bond 0.00480 ( 2) SS BOND : angle 0.69869 ( 4) hydrogen bonds : bond 0.09933 ( 269) hydrogen bonds : angle 4.84839 ( 777) Misc. bond : bond 0.00068 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 130 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.7978 (ttmt) cc_final: 0.7577 (ttmt) REVERT: A 43 GLN cc_start: 0.7125 (mp-120) cc_final: 0.6910 (mp10) REVERT: A 67 MET cc_start: 0.5748 (tmm) cc_final: 0.5445 (tmm) REVERT: A 125 VAL cc_start: 0.7577 (t) cc_final: 0.7162 (p) REVERT: A 167 LYS cc_start: 0.8072 (mmmm) cc_final: 0.7819 (mmmm) REVERT: M 57 TYR cc_start: 0.7750 (m-80) cc_final: 0.7506 (m-80) REVERT: M 60 SER cc_start: 0.8803 (m) cc_final: 0.8331 (t) REVERT: M 101 TYR cc_start: 0.7701 (t80) cc_final: 0.6997 (t80) REVERT: N 57 TYR cc_start: 0.7845 (m-80) cc_final: 0.7520 (m-80) REVERT: N 98 SER cc_start: 0.8872 (t) cc_final: 0.8640 (m) REVERT: B 5 LYS cc_start: 0.8068 (ttmt) cc_final: 0.7660 (ttmt) REVERT: B 96 TYR cc_start: 0.6734 (m-10) cc_final: 0.6273 (m-80) REVERT: B 167 LYS cc_start: 0.8137 (mmmm) cc_final: 0.7800 (mmmm) outliers start: 35 outliers final: 33 residues processed: 154 average time/residue: 0.0906 time to fit residues: 17.3006 Evaluate side-chains 160 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 127 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain M residue 53 SER Chi-restraints excluded: chain M residue 68 SER Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 193 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 26 optimal weight: 0.3980 chunk 56 optimal weight: 0.0870 chunk 1 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 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 = 0.3982 r_free = 0.3982 target = 0.158716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.134280 restraints weight = 8629.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.138761 restraints weight = 4604.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.141786 restraints weight = 2899.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.143655 restraints weight = 2022.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.145009 restraints weight = 1548.913| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5446 Z= 0.195 Angle : 0.658 6.670 7370 Z= 0.339 Chirality : 0.042 0.137 790 Planarity : 0.005 0.064 940 Dihedral : 7.797 56.823 870 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 6.09 % Allowed : 30.47 % Favored : 63.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.34), residues: 644 helix: 2.07 (0.34), residues: 202 sheet: 1.09 (0.37), residues: 202 loop : -0.90 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 41 TYR 0.043 0.002 TYR M 104 PHE 0.012 0.002 PHE B 141 TRP 0.011 0.001 TRP M 36 HIS 0.001 0.000 HIS B 27 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 5442) covalent geometry : angle 0.65793 ( 7366) SS BOND : bond 0.00464 ( 2) SS BOND : angle 0.64624 ( 4) hydrogen bonds : bond 0.09864 ( 269) hydrogen bonds : angle 4.76027 ( 777) Misc. bond : bond 0.00050 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.7972 (ttmt) cc_final: 0.7562 (ttmt) REVERT: A 43 GLN cc_start: 0.7122 (mp-120) cc_final: 0.6904 (mp10) REVERT: A 67 MET cc_start: 0.5731 (tmm) cc_final: 0.5438 (tmm) REVERT: A 125 VAL cc_start: 0.7513 (t) cc_final: 0.7091 (p) REVERT: A 167 LYS cc_start: 0.8061 (mmmm) cc_final: 0.7808 (mmmm) REVERT: M 60 SER cc_start: 0.8814 (m) cc_final: 0.8337 (t) REVERT: N 57 TYR cc_start: 0.7856 (m-80) cc_final: 0.7522 (m-80) REVERT: N 98 SER cc_start: 0.8864 (t) cc_final: 0.8609 (m) REVERT: B 5 LYS cc_start: 0.8023 (ttmt) cc_final: 0.7441 (ttmt) REVERT: B 96 TYR cc_start: 0.6703 (m-10) cc_final: 0.6217 (m-80) REVERT: B 167 LYS cc_start: 0.8130 (mmmm) cc_final: 0.7794 (mmmm) outliers start: 34 outliers final: 33 residues processed: 152 average time/residue: 0.0931 time to fit residues: 17.5426 Evaluate side-chains 161 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain M residue 53 SER Chi-restraints excluded: chain M residue 68 SER Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 193 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 31 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 6 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN ** B 182 GLN ** 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 = 0.3949 r_free = 0.3949 target = 0.155440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.130751 restraints weight = 8712.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.135157 restraints weight = 4706.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.138101 restraints weight = 2993.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.140034 restraints weight = 2117.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.141328 restraints weight = 1624.727| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5446 Z= 0.215 Angle : 0.670 6.745 7370 Z= 0.345 Chirality : 0.043 0.156 790 Planarity : 0.005 0.068 940 Dihedral : 7.800 56.554 870 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 6.09 % Allowed : 30.47 % Favored : 63.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.34), residues: 644 helix: 2.02 (0.34), residues: 202 sheet: 1.05 (0.37), residues: 202 loop : -0.94 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 41 TYR 0.039 0.002 TYR M 104 PHE 0.012 0.002 PHE B 141 TRP 0.013 0.002 TRP M 36 HIS 0.001 0.000 HIS B 166 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 5442) covalent geometry : angle 0.66951 ( 7366) SS BOND : bond 0.00542 ( 2) SS BOND : angle 0.75514 ( 4) hydrogen bonds : bond 0.10018 ( 269) hydrogen bonds : angle 4.82628 ( 777) Misc. bond : bond 0.00070 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 133 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.7991 (ttmt) cc_final: 0.7577 (ttmt) REVERT: A 43 GLN cc_start: 0.7126 (mp-120) cc_final: 0.6900 (mp10) REVERT: A 67 MET cc_start: 0.5680 (tmm) cc_final: 0.5404 (tmm) REVERT: A 123 ARG cc_start: 0.7790 (ttt-90) cc_final: 0.7553 (ttt-90) REVERT: A 125 VAL cc_start: 0.7530 (t) cc_final: 0.6896 (p) REVERT: A 167 LYS cc_start: 0.8080 (mmmm) cc_final: 0.7831 (mmmm) REVERT: M 60 SER cc_start: 0.8805 (m) cc_final: 0.8326 (t) REVERT: N 57 TYR cc_start: 0.7872 (m-80) cc_final: 0.7538 (m-80) REVERT: N 98 SER cc_start: 0.8876 (t) cc_final: 0.8655 (m) REVERT: B 5 LYS cc_start: 0.8043 (ttmt) cc_final: 0.7188 (ttmt) REVERT: B 73 ARG cc_start: 0.7486 (mtm-85) cc_final: 0.7254 (mtm110) REVERT: B 96 TYR cc_start: 0.6697 (m-10) cc_final: 0.6229 (m-80) REVERT: B 167 LYS cc_start: 0.8147 (mmmm) cc_final: 0.7806 (mmmm) outliers start: 34 outliers final: 33 residues processed: 157 average time/residue: 0.0925 time to fit residues: 17.8369 Evaluate side-chains 166 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 133 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain M residue 53 SER Chi-restraints excluded: chain M residue 68 SER Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 193 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 25 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 0.0370 chunk 57 optimal weight: 0.1980 chunk 55 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.4980 chunk 39 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.160289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.136033 restraints weight = 8646.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.140469 restraints weight = 4585.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.143488 restraints weight = 2885.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.145425 restraints weight = 2006.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.146779 restraints weight = 1524.618| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5446 Z= 0.178 Angle : 0.653 6.588 7370 Z= 0.334 Chirality : 0.042 0.142 790 Planarity : 0.005 0.064 940 Dihedral : 7.813 56.560 870 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 5.91 % Allowed : 30.47 % Favored : 63.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.34), residues: 644 helix: 2.15 (0.34), residues: 202 sheet: 1.07 (0.37), residues: 202 loop : -0.88 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 41 TYR 0.037 0.002 TYR M 104 PHE 0.012 0.002 PHE B 141 TRP 0.010 0.001 TRP M 36 HIS 0.002 0.000 HIS B 27 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 5442) covalent geometry : angle 0.65275 ( 7366) SS BOND : bond 0.00452 ( 2) SS BOND : angle 0.53072 ( 4) hydrogen bonds : bond 0.09576 ( 269) hydrogen bonds : angle 4.68518 ( 777) Misc. bond : bond 0.00064 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1094.68 seconds wall clock time: 19 minutes 41.54 seconds (1181.54 seconds total)