Starting phenix.real_space_refine on Wed Mar 4 17:04:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pf3_13366/03_2026/7pf3_13366.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pf3_13366/03_2026/7pf3_13366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7pf3_13366/03_2026/7pf3_13366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pf3_13366/03_2026/7pf3_13366.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pf3_13366/03_2026/7pf3_13366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pf3_13366/03_2026/7pf3_13366.map" } resolution = 4.0 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2230 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 334 5.49 5 S 10 5.16 5 C 7420 2.51 5 N 2528 2.21 5 O 3178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13470 Number of models: 1 Model: "" Number of chains: 11 Chain: "k" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 798 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "l" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "m" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "n" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "o" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 798 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "p" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "q" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "r" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "J" Number of atoms: 3442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 3442 Classifications: {'DNA': 167} Link IDs: {'rna3p': 166} Chain: "I" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 3405 Classifications: {'DNA': 167} Link IDs: {'rna3p': 166} Chain: "s" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 535 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Time building chain proxies: 2.54, per 1000 atoms: 0.19 Number of scatterers: 13470 At special positions: 0 Unit cell: (139.65, 133.35, 74.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 334 15.00 O 3178 8.00 N 2528 7.00 C 7420 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 362.4 milliseconds 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1566 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 11 sheets defined 70.5% alpha, 3.1% beta 161 base pairs and 296 stacking pairs defined. Time for finding SS restraints: 2.28 Creating SS restraints... Processing helix chain 'k' and resid 44 through 57 Processing helix chain 'k' and resid 63 through 79 removed outlier: 3.519A pdb=" N PHE k 67 " --> pdb=" O ARG k 63 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP k 77 " --> pdb=" O GLU k 73 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE k 78 " --> pdb=" O ILE k 74 " (cutoff:3.500A) Processing helix chain 'k' and resid 85 through 114 Processing helix chain 'k' and resid 120 through 132 removed outlier: 3.735A pdb=" N ILE k 124 " --> pdb=" O MET k 120 " (cutoff:3.500A) Processing helix chain 'l' and resid 24 through 29 removed outlier: 3.500A pdb=" N GLN l 27 " --> pdb=" O ASP l 24 " (cutoff:3.500A) Processing helix chain 'l' and resid 30 through 41 Processing helix chain 'l' and resid 49 through 76 removed outlier: 4.344A pdb=" N GLU l 53 " --> pdb=" O LEU l 49 " (cutoff:3.500A) Processing helix chain 'l' and resid 82 through 93 removed outlier: 3.599A pdb=" N VAL l 86 " --> pdb=" O THR l 82 " (cutoff:3.500A) Processing helix chain 'm' and resid 16 through 21 Processing helix chain 'm' and resid 26 through 37 Processing helix chain 'm' and resid 45 through 73 removed outlier: 4.228A pdb=" N VAL m 49 " --> pdb=" O ALA m 45 " (cutoff:3.500A) Processing helix chain 'm' and resid 79 through 89 Processing helix chain 'm' and resid 90 through 97 Processing helix chain 'n' and resid 37 through 49 removed outlier: 3.595A pdb=" N VAL n 41 " --> pdb=" O TYR n 37 " (cutoff:3.500A) Processing helix chain 'n' and resid 55 through 84 Processing helix chain 'n' and resid 90 through 102 Processing helix chain 'n' and resid 103 through 123 Processing helix chain 'o' and resid 44 through 57 Processing helix chain 'o' and resid 63 through 76 Processing helix chain 'o' and resid 85 through 114 Processing helix chain 'o' and resid 120 through 132 Processing helix chain 'p' and resid 25 through 29 Processing helix chain 'p' and resid 30 through 41 Processing helix chain 'p' and resid 49 through 76 removed outlier: 4.063A pdb=" N GLU p 53 " --> pdb=" O LEU p 49 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASP p 68 " --> pdb=" O ASN p 64 " (cutoff:3.500A) Processing helix chain 'p' and resid 82 through 94 Processing helix chain 'q' and resid 16 through 21 Processing helix chain 'q' and resid 26 through 37 Processing helix chain 'q' and resid 45 through 73 removed outlier: 4.270A pdb=" N VAL q 49 " --> pdb=" O ALA q 45 " (cutoff:3.500A) Processing helix chain 'q' and resid 79 through 89 Processing helix chain 'q' and resid 90 through 97 Processing helix chain 'q' and resid 112 through 116 Processing helix chain 'r' and resid 37 through 49 removed outlier: 3.620A pdb=" N VAL r 41 " --> pdb=" O TYR r 37 " (cutoff:3.500A) Processing helix chain 'r' and resid 55 through 84 removed outlier: 3.939A pdb=" N ASN r 84 " --> pdb=" O LEU r 80 " (cutoff:3.500A) Processing helix chain 'r' and resid 90 through 102 Processing helix chain 'r' and resid 104 through 124 Processing helix chain 's' and resid 38 through 49 removed outlier: 3.926A pdb=" N LEU s 42 " --> pdb=" O PRO s 38 " (cutoff:3.500A) Processing helix chain 's' and resid 58 through 69 Processing helix chain 's' and resid 72 through 74 No H-bonds generated for 'chain 's' and resid 72 through 74' Processing helix chain 's' and resid 75 through 89 Processing sheet with id=AA1, first strand: chain 'k' and resid 83 through 84 removed outlier: 6.632A pdb=" N ARG k 83 " --> pdb=" O VAL l 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'k' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'l' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'm' and resid 42 through 43 removed outlier: 7.565A pdb=" N ARG m 42 " --> pdb=" O ILE n 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'm' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'm' and resid 101 through 102 removed outlier: 6.422A pdb=" N THR m 101 " --> pdb=" O TYR p 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'o' and resid 83 through 84 removed outlier: 6.707A pdb=" N ARG o 83 " --> pdb=" O VAL p 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'o' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'q' and resid 42 through 43 removed outlier: 7.124A pdb=" N ARG q 42 " --> pdb=" O ILE r 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'q' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 's' and resid 56 through 57 436 hydrogen bonds defined for protein. 1287 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 413 hydrogen bonds 826 hydrogen bond angles 0 basepair planarities 161 basepair parallelities 296 stacking parallelities Total time for adding SS restraints: 2.52 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2465 1.33 - 1.45: 4950 1.45 - 1.57: 6285 1.57 - 1.69: 666 1.69 - 1.81: 20 Bond restraints: 14386 Sorted by residual: bond pdb=" CG GLU l 53 " pdb=" CD GLU l 53 " ideal model delta sigma weight residual 1.516 1.462 0.054 2.50e-02 1.60e+03 4.59e+00 bond pdb=" CD GLU q 61 " pdb=" OE1 GLU q 61 " ideal model delta sigma weight residual 1.249 1.210 0.039 1.90e-02 2.77e+03 4.31e+00 bond pdb=" CB ASP k 81 " pdb=" CG ASP k 81 " ideal model delta sigma weight residual 1.516 1.567 -0.051 2.50e-02 1.60e+03 4.22e+00 bond pdb=" CB GLU l 53 " pdb=" CG GLU l 53 " ideal model delta sigma weight residual 1.520 1.461 0.059 3.00e-02 1.11e+03 3.86e+00 bond pdb=" C3' DG I 709 " pdb=" O3' DG I 709 " ideal model delta sigma weight residual 1.422 1.481 -0.059 3.00e-02 1.11e+03 3.82e+00 ... (remaining 14381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 20464 2.70 - 5.40: 334 5.40 - 8.10: 42 8.10 - 10.80: 10 10.80 - 13.50: 3 Bond angle restraints: 20853 Sorted by residual: angle pdb=" CB ARG r 79 " pdb=" CG ARG r 79 " pdb=" CD ARG r 79 " ideal model delta sigma weight residual 111.30 123.37 -12.07 2.30e+00 1.89e-01 2.76e+01 angle pdb=" N GLU q 61 " pdb=" CA GLU q 61 " pdb=" CB GLU q 61 " ideal model delta sigma weight residual 110.28 118.14 -7.86 1.55e+00 4.16e-01 2.57e+01 angle pdb=" N GLU p 63 " pdb=" CA GLU p 63 " pdb=" CB GLU p 63 " ideal model delta sigma weight residual 110.28 117.74 -7.46 1.55e+00 4.16e-01 2.32e+01 angle pdb=" CB MET n 62 " pdb=" CG MET n 62 " pdb=" SD MET n 62 " ideal model delta sigma weight residual 112.70 126.20 -13.50 3.00e+00 1.11e-01 2.02e+01 angle pdb=" CA LYS m 36 " pdb=" CB LYS m 36 " pdb=" CG LYS m 36 " ideal model delta sigma weight residual 114.10 122.23 -8.13 2.00e+00 2.50e-01 1.65e+01 ... (remaining 20848 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 6098 35.99 - 71.98: 1671 71.98 - 107.96: 26 107.96 - 143.95: 2 143.95 - 179.94: 2 Dihedral angle restraints: 7799 sinusoidal: 5368 harmonic: 2431 Sorted by residual: dihedral pdb=" CA GLU o 50 " pdb=" C GLU o 50 " pdb=" N ILE o 51 " pdb=" CA ILE o 51 " ideal model delta harmonic sigma weight residual 180.00 153.59 26.41 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA ILE l 50 " pdb=" C ILE l 50 " pdb=" N TYR l 51 " pdb=" CA TYR l 51 " ideal model delta harmonic sigma weight residual 180.00 -157.18 -22.82 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA HIS r 82 " pdb=" C HIS r 82 " pdb=" N TYR r 83 " pdb=" CA TYR r 83 " ideal model delta harmonic sigma weight residual -180.00 -158.35 -21.65 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 7796 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1773 0.050 - 0.100: 476 0.100 - 0.150: 107 0.150 - 0.200: 17 0.200 - 0.250: 3 Chirality restraints: 2376 Sorted by residual: chirality pdb=" CA GLU o 50 " pdb=" N GLU o 50 " pdb=" C GLU o 50 " pdb=" CB GLU o 50 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA ILE q 79 " pdb=" N ILE q 79 " pdb=" C ILE q 79 " pdb=" CB ILE q 79 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB THR l 54 " pdb=" CA THR l 54 " pdb=" OG1 THR l 54 " pdb=" CG2 THR l 54 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 2373 not shown) Planarity restraints: 1478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP k 81 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.80e+00 pdb=" C ASP k 81 " -0.054 2.00e-02 2.50e+03 pdb=" O ASP k 81 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU k 82 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR p 88 " 0.015 2.00e-02 2.50e+03 2.11e-02 8.90e+00 pdb=" CG TYR p 88 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR p 88 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR p 88 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR p 88 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR p 88 " 0.019 2.00e-02 2.50e+03 pdb=" CZ TYR p 88 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR p 88 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG r 33 " -0.203 9.50e-02 1.11e+02 9.25e-02 8.74e+00 pdb=" NE ARG r 33 " 0.001 2.00e-02 2.50e+03 pdb=" CZ ARG r 33 " 0.036 2.00e-02 2.50e+03 pdb=" NH1 ARG r 33 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG r 33 " -0.018 2.00e-02 2.50e+03 ... (remaining 1475 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2974 2.79 - 3.32: 12723 3.32 - 3.85: 29001 3.85 - 4.37: 32233 4.37 - 4.90: 44479 Nonbonded interactions: 121410 Sorted by model distance: nonbonded pdb=" OG SER m 40 " pdb=" O ARG m 42 " model vdw 2.266 3.040 nonbonded pdb=" OH TYR m 39 " pdb=" OE1 GLU n 71 " model vdw 2.271 3.040 nonbonded pdb=" NH1 ARG p 35 " pdb=" OP2 DC I 663 " model vdw 2.273 3.120 nonbonded pdb=" OD2 ASP p 68 " pdb=" NH2 ARG p 92 " model vdw 2.308 3.120 nonbonded pdb=" NH1 ARG m 42 " pdb=" OG1 THR n 88 " model vdw 2.320 3.120 ... (remaining 121405 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'k' selection = chain 'o' } ncs_group { reference = chain 'l' selection = chain 'p' } ncs_group { reference = chain 'm' selection = chain 'q' } ncs_group { reference = chain 'n' selection = chain 'r' } 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: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.950 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 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 : 0.007 0.063 14386 Z= 0.331 Angle : 0.944 13.497 20853 Z= 0.529 Chirality : 0.049 0.250 2376 Planarity : 0.008 0.115 1478 Dihedral : 29.233 179.937 6233 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.14 % Allowed : 0.43 % Favored : 99.42 % 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: -0.63 (0.26), residues: 825 helix: 0.01 (0.20), residues: 578 sheet: -2.57 (1.26), residues: 10 loop : -1.10 (0.33), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.001 ARG r 33 TYR 0.041 0.004 TYR p 88 PHE 0.037 0.003 PHE r 70 HIS 0.009 0.002 HIS p 75 Details of bonding type rmsd covalent geometry : bond 0.00748 (14386) covalent geometry : angle 0.94421 (20853) hydrogen bonds : bond 0.10173 ( 849) hydrogen bonds : angle 4.80558 ( 2113) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 185 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 50 GLU cc_start: 0.9413 (mt-10) cc_final: 0.8893 (mt-10) REVERT: k 120 MET cc_start: 0.8777 (mtm) cc_final: 0.8134 (mtt) REVERT: l 31 LYS cc_start: 0.9221 (ttmm) cc_final: 0.8954 (ttmm) REVERT: l 49 LEU cc_start: 0.9607 (tp) cc_final: 0.8614 (tp) REVERT: l 59 LYS cc_start: 0.9510 (tttp) cc_final: 0.9057 (ttpp) REVERT: l 63 GLU cc_start: 0.9320 (pt0) cc_final: 0.9078 (pt0) REVERT: n 51 ASP cc_start: 0.9015 (p0) cc_final: 0.8718 (p0) REVERT: n 68 ASP cc_start: 0.9573 (t70) cc_final: 0.9285 (t0) REVERT: n 108 LYS cc_start: 0.9711 (ptpt) cc_final: 0.9505 (ptpp) REVERT: n 113 GLU cc_start: 0.9317 (mm-30) cc_final: 0.8991 (mm-30) REVERT: n 116 LYS cc_start: 0.9525 (mtmm) cc_final: 0.9106 (ptpp) REVERT: o 54 TYR cc_start: 0.9479 (m-80) cc_final: 0.8860 (m-80) REVERT: o 90 MET cc_start: 0.9418 (mmp) cc_final: 0.8987 (mmm) REVERT: o 93 GLN cc_start: 0.9262 (tt0) cc_final: 0.8518 (tp40) REVERT: o 97 GLU cc_start: 0.9192 (mp0) cc_final: 0.8499 (mp0) REVERT: p 59 LYS cc_start: 0.9606 (tppt) cc_final: 0.9256 (tppt) REVERT: p 63 GLU cc_start: 0.9228 (pm20) cc_final: 0.8880 (pm20) REVERT: p 93 GLN cc_start: 0.9099 (tm-30) cc_final: 0.8642 (tm-30) REVERT: q 36 LYS cc_start: 0.9244 (mmtt) cc_final: 0.8927 (mmtm) REVERT: q 62 ILE cc_start: 0.9846 (pt) cc_final: 0.9248 (pt) REVERT: q 72 ASP cc_start: 0.9399 (m-30) cc_final: 0.9158 (m-30) REVERT: q 92 GLU cc_start: 0.9072 (mt-10) cc_final: 0.8418 (tt0) REVERT: q 104 GLN cc_start: 0.8809 (mm-40) cc_final: 0.8445 (mm-40) REVERT: q 118 LYS cc_start: 0.8094 (mttt) cc_final: 0.7886 (mmmt) REVERT: r 83 TYR cc_start: 0.7545 (m-80) cc_final: 0.6734 (m-80) REVERT: r 84 ASN cc_start: 0.9195 (m-40) cc_final: 0.8784 (m-40) REVERT: r 95 GLN cc_start: 0.9692 (tt0) cc_final: 0.9446 (tt0) REVERT: s 72 VAL cc_start: 0.9120 (p) cc_final: 0.8627 (p) REVERT: s 107 ASN cc_start: 0.8073 (t0) cc_final: 0.7858 (t0) outliers start: 1 outliers final: 0 residues processed: 185 average time/residue: 0.1241 time to fit residues: 32.2693 Evaluate side-chains 142 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 0.0070 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: k 108 ASN ** k 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 25 ASN ** m 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 49 HIS n 84 ASN ** o 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.030506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.022660 restraints weight = 129851.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.023499 restraints weight = 63886.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.024046 restraints weight = 40807.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.024342 restraints weight = 30564.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.024625 restraints weight = 25948.349| |-----------------------------------------------------------------------------| r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14386 Z= 0.184 Angle : 0.643 11.481 20853 Z= 0.375 Chirality : 0.036 0.171 2376 Planarity : 0.005 0.059 1478 Dihedral : 32.040 176.418 4581 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.15 % Allowed : 10.10 % Favored : 88.74 % 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: 0.95 (0.27), residues: 825 helix: 1.30 (0.21), residues: 586 sheet: -2.49 (1.52), residues: 10 loop : -0.87 (0.34), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG n 99 TYR 0.016 0.002 TYR p 88 PHE 0.025 0.001 PHE r 65 HIS 0.003 0.001 HIS p 75 Details of bonding type rmsd covalent geometry : bond 0.00394 (14386) covalent geometry : angle 0.64276 (20853) hydrogen bonds : bond 0.03983 ( 849) hydrogen bonds : angle 3.38900 ( 2113) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 174 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 50 GLU cc_start: 0.9427 (mt-10) cc_final: 0.9009 (mt-10) REVERT: k 90 MET cc_start: 0.9070 (mmm) cc_final: 0.8857 (mmm) REVERT: k 108 ASN cc_start: 0.9663 (OUTLIER) cc_final: 0.9286 (t0) REVERT: k 120 MET cc_start: 0.8579 (mtm) cc_final: 0.8006 (mtt) REVERT: l 25 ASN cc_start: 0.8656 (OUTLIER) cc_final: 0.8112 (t0) REVERT: l 59 LYS cc_start: 0.9595 (tttp) cc_final: 0.9019 (ttpp) REVERT: l 63 GLU cc_start: 0.9242 (pt0) cc_final: 0.8949 (pt0) REVERT: l 84 MET cc_start: 0.8557 (tpp) cc_final: 0.8118 (tpp) REVERT: m 102 ILE cc_start: 0.9345 (mm) cc_final: 0.9029 (mt) REVERT: n 51 ASP cc_start: 0.8971 (p0) cc_final: 0.8598 (p0) REVERT: n 68 ASP cc_start: 0.9544 (t70) cc_final: 0.9311 (t0) REVERT: n 108 LYS cc_start: 0.9607 (ptpt) cc_final: 0.9406 (ptpp) REVERT: n 113 GLU cc_start: 0.9232 (mm-30) cc_final: 0.8976 (mm-30) REVERT: n 116 LYS cc_start: 0.9501 (mtmm) cc_final: 0.8995 (ptpp) REVERT: n 120 LYS cc_start: 0.9569 (mttt) cc_final: 0.9325 (mttm) REVERT: o 90 MET cc_start: 0.9426 (mmp) cc_final: 0.9027 (mmm) REVERT: o 93 GLN cc_start: 0.9157 (tt0) cc_final: 0.8389 (tp40) REVERT: o 105 GLU cc_start: 0.9078 (tp30) cc_final: 0.8810 (tp30) REVERT: o 126 LEU cc_start: 0.9468 (tp) cc_final: 0.9140 (tt) REVERT: p 59 LYS cc_start: 0.9462 (tppt) cc_final: 0.9097 (tppp) REVERT: p 63 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8570 (pm20) REVERT: p 93 GLN cc_start: 0.9044 (tm-30) cc_final: 0.8680 (tm-30) REVERT: q 36 LYS cc_start: 0.9223 (mmtt) cc_final: 0.9011 (mmtt) REVERT: q 90 ASP cc_start: 0.9011 (t70) cc_final: 0.8691 (t70) REVERT: q 94 ASN cc_start: 0.9220 (t0) cc_final: 0.8932 (m-40) REVERT: q 104 GLN cc_start: 0.8933 (mm-40) cc_final: 0.8678 (mm-40) REVERT: r 83 TYR cc_start: 0.7405 (m-80) cc_final: 0.6466 (m-10) REVERT: r 106 LEU cc_start: 0.9720 (OUTLIER) cc_final: 0.9512 (mp) REVERT: s 107 ASN cc_start: 0.8267 (t0) cc_final: 0.8045 (t0) outliers start: 8 outliers final: 2 residues processed: 177 average time/residue: 0.1157 time to fit residues: 29.4554 Evaluate side-chains 144 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 138 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain k residue 80 THR Chi-restraints excluded: chain k residue 108 ASN Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain n residue 44 VAL Chi-restraints excluded: chain p residue 63 GLU Chi-restraints excluded: chain r residue 106 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 109 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 17 optimal weight: 20.0000 chunk 54 optimal weight: 7.9990 chunk 98 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: k 108 ASN ** k 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 25 ASN l 75 HIS ** o 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.030711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.022994 restraints weight = 132835.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.023837 restraints weight = 65283.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.024373 restraints weight = 41515.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.024762 restraints weight = 30869.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.025006 restraints weight = 25333.809| |-----------------------------------------------------------------------------| r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14386 Z= 0.170 Angle : 0.627 10.448 20853 Z= 0.363 Chirality : 0.035 0.191 2376 Planarity : 0.004 0.054 1478 Dihedral : 31.635 178.382 4581 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.88 % Allowed : 12.84 % Favored : 85.28 % 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: 1.47 (0.28), residues: 825 helix: 1.75 (0.21), residues: 586 sheet: -2.21 (1.62), residues: 10 loop : -0.89 (0.35), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG m 42 TYR 0.016 0.001 TYR q 57 PHE 0.024 0.001 PHE n 65 HIS 0.004 0.001 HIS p 75 Details of bonding type rmsd covalent geometry : bond 0.00370 (14386) covalent geometry : angle 0.62739 (20853) hydrogen bonds : bond 0.03587 ( 849) hydrogen bonds : angle 3.25325 ( 2113) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 50 GLU cc_start: 0.9397 (mt-10) cc_final: 0.8969 (mt-10) REVERT: k 90 MET cc_start: 0.9125 (mmm) cc_final: 0.8864 (mmm) REVERT: k 97 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8547 (mt-10) REVERT: k 105 GLU cc_start: 0.8754 (pp20) cc_final: 0.8537 (pp20) REVERT: k 120 MET cc_start: 0.8631 (mtm) cc_final: 0.8165 (mtt) REVERT: l 59 LYS cc_start: 0.9614 (tttp) cc_final: 0.9032 (ttpp) REVERT: l 63 GLU cc_start: 0.9222 (pt0) cc_final: 0.8927 (pt0) REVERT: l 84 MET cc_start: 0.8652 (tpp) cc_final: 0.8230 (tpp) REVERT: n 51 ASP cc_start: 0.8879 (p0) cc_final: 0.8460 (p0) REVERT: n 113 GLU cc_start: 0.9186 (mm-30) cc_final: 0.8947 (mm-30) REVERT: n 116 LYS cc_start: 0.9518 (mtmm) cc_final: 0.8963 (ptpp) REVERT: n 120 LYS cc_start: 0.9564 (mttt) cc_final: 0.9301 (mttm) REVERT: o 51 ILE cc_start: 0.9377 (OUTLIER) cc_final: 0.9157 (mm) REVERT: o 90 MET cc_start: 0.9380 (mmp) cc_final: 0.9022 (mmm) REVERT: o 93 GLN cc_start: 0.9137 (tt0) cc_final: 0.8392 (tp40) REVERT: o 105 GLU cc_start: 0.9060 (tp30) cc_final: 0.8786 (tp30) REVERT: p 59 LYS cc_start: 0.9451 (tppt) cc_final: 0.9073 (tppp) REVERT: p 63 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8500 (pm20) REVERT: p 93 GLN cc_start: 0.9095 (tm-30) cc_final: 0.8715 (tm-30) REVERT: q 36 LYS cc_start: 0.9239 (mmtt) cc_final: 0.8989 (mmtt) REVERT: q 90 ASP cc_start: 0.8890 (t70) cc_final: 0.8590 (t70) REVERT: q 94 ASN cc_start: 0.9182 (t0) cc_final: 0.8901 (m-40) REVERT: q 104 GLN cc_start: 0.8833 (mm-40) cc_final: 0.8564 (mm-40) outliers start: 13 outliers final: 4 residues processed: 173 average time/residue: 0.1085 time to fit residues: 27.3057 Evaluate side-chains 147 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 141 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain k residue 100 LEU Chi-restraints excluded: chain m residue 114 VAL Chi-restraints excluded: chain n residue 44 VAL Chi-restraints excluded: chain o residue 51 ILE Chi-restraints excluded: chain o residue 97 GLU Chi-restraints excluded: chain p residue 63 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 109 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: k 108 ASN k 113 HIS l 25 ASN ** m 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 49 HIS ** o 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 108 ASN ** q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 82 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.029023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2475 r_free = 0.2475 target = 0.021367 restraints weight = 135778.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2518 r_free = 0.2518 target = 0.022156 restraints weight = 67203.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.022661 restraints weight = 43165.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.023016 restraints weight = 32488.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.023223 restraints weight = 26853.900| |-----------------------------------------------------------------------------| r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 14386 Z= 0.283 Angle : 0.658 9.823 20853 Z= 0.384 Chirality : 0.037 0.185 2376 Planarity : 0.005 0.078 1478 Dihedral : 31.586 179.748 4581 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.88 % Allowed : 16.02 % Favored : 82.11 % 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: 1.62 (0.28), residues: 825 helix: 1.88 (0.21), residues: 586 sheet: -1.90 (1.71), residues: 10 loop : -0.92 (0.36), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG r 79 TYR 0.016 0.002 TYR l 98 PHE 0.010 0.002 PHE l 100 HIS 0.010 0.002 HIS r 82 Details of bonding type rmsd covalent geometry : bond 0.00620 (14386) covalent geometry : angle 0.65769 (20853) hydrogen bonds : bond 0.06349 ( 849) hydrogen bonds : angle 3.44997 ( 2113) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 50 GLU cc_start: 0.9380 (mt-10) cc_final: 0.8992 (mt-10) REVERT: k 97 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8618 (mt-10) REVERT: k 105 GLU cc_start: 0.8848 (pp20) cc_final: 0.8261 (pp20) REVERT: k 106 ASP cc_start: 0.9033 (m-30) cc_final: 0.8692 (m-30) REVERT: k 120 MET cc_start: 0.8748 (mtm) cc_final: 0.8195 (mtt) REVERT: l 23 ARG cc_start: 0.8415 (ptp90) cc_final: 0.7824 (pmt-80) REVERT: l 24 ASP cc_start: 0.8359 (t0) cc_final: 0.8146 (t0) REVERT: l 49 LEU cc_start: 0.9433 (tp) cc_final: 0.8943 (tp) REVERT: l 52 GLU cc_start: 0.8712 (pm20) cc_final: 0.7952 (pm20) REVERT: l 53 GLU cc_start: 0.8758 (pm20) cc_final: 0.8171 (pm20) REVERT: l 59 LYS cc_start: 0.9624 (tttp) cc_final: 0.9061 (ttpp) REVERT: l 63 GLU cc_start: 0.9200 (pt0) cc_final: 0.8972 (pt0) REVERT: l 84 MET cc_start: 0.8745 (tpp) cc_final: 0.8329 (tpp) REVERT: m 56 GLU cc_start: 0.9312 (tt0) cc_final: 0.9073 (tt0) REVERT: n 51 ASP cc_start: 0.8984 (p0) cc_final: 0.8669 (p0) REVERT: o 90 MET cc_start: 0.9341 (mmp) cc_final: 0.9030 (mmm) REVERT: o 93 GLN cc_start: 0.9038 (tt0) cc_final: 0.8177 (tp40) REVERT: o 105 GLU cc_start: 0.9020 (tp30) cc_final: 0.8741 (tp30) REVERT: o 120 MET cc_start: 0.8343 (mtt) cc_final: 0.8082 (mtt) REVERT: p 59 LYS cc_start: 0.9464 (tppt) cc_final: 0.9159 (tppp) REVERT: p 93 GLN cc_start: 0.9194 (tm-30) cc_final: 0.8810 (tm-30) REVERT: q 90 ASP cc_start: 0.8935 (t70) cc_final: 0.8529 (t0) REVERT: q 94 ASN cc_start: 0.9294 (t0) cc_final: 0.8936 (m-40) REVERT: q 104 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8486 (mm-40) REVERT: r 76 GLU cc_start: 0.9452 (tp30) cc_final: 0.9034 (mm-30) outliers start: 13 outliers final: 5 residues processed: 157 average time/residue: 0.1207 time to fit residues: 27.2943 Evaluate side-chains 139 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 134 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain m residue 114 VAL Chi-restraints excluded: chain o residue 97 GLU Chi-restraints excluded: chain p residue 63 GLU Chi-restraints excluded: chain s residue 93 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 47 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 107 optimal weight: 20.0000 chunk 28 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 25 ASN ** o 68 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 = 0.2920 r_free = 0.2920 target = 0.030086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2520 r_free = 0.2520 target = 0.022469 restraints weight = 132744.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.023304 restraints weight = 64277.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.023875 restraints weight = 40676.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.024243 restraints weight = 29916.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.024454 restraints weight = 24564.096| |-----------------------------------------------------------------------------| r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14386 Z= 0.169 Angle : 0.634 10.566 20853 Z= 0.364 Chirality : 0.034 0.167 2376 Planarity : 0.004 0.051 1478 Dihedral : 31.530 179.650 4581 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.30 % Allowed : 18.04 % Favored : 80.66 % 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: 1.76 (0.28), residues: 825 helix: 1.98 (0.21), residues: 586 sheet: -1.82 (1.72), residues: 10 loop : -0.86 (0.37), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG p 39 TYR 0.023 0.001 TYR q 57 PHE 0.008 0.001 PHE k 67 HIS 0.004 0.001 HIS p 75 Details of bonding type rmsd covalent geometry : bond 0.00370 (14386) covalent geometry : angle 0.63438 (20853) hydrogen bonds : bond 0.03408 ( 849) hydrogen bonds : angle 3.24008 ( 2113) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 152 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 50 GLU cc_start: 0.9402 (mt-10) cc_final: 0.9058 (mt-10) REVERT: k 73 GLU cc_start: 0.9371 (tt0) cc_final: 0.8965 (pt0) REVERT: k 93 GLN cc_start: 0.9346 (tt0) cc_final: 0.9121 (tp40) REVERT: k 105 GLU cc_start: 0.8937 (pp20) cc_final: 0.8294 (pp20) REVERT: k 106 ASP cc_start: 0.9047 (m-30) cc_final: 0.8681 (m-30) REVERT: k 120 MET cc_start: 0.8703 (mtm) cc_final: 0.8221 (mtt) REVERT: l 23 ARG cc_start: 0.8349 (ptp90) cc_final: 0.7844 (pmt-80) REVERT: l 25 ASN cc_start: 0.9246 (OUTLIER) cc_final: 0.7937 (m-40) REVERT: l 49 LEU cc_start: 0.9511 (tp) cc_final: 0.8992 (tp) REVERT: l 52 GLU cc_start: 0.8609 (pm20) cc_final: 0.7777 (pm20) REVERT: l 53 GLU cc_start: 0.8663 (pm20) cc_final: 0.7987 (pm20) REVERT: l 59 LYS cc_start: 0.9618 (tttp) cc_final: 0.9009 (ttpp) REVERT: l 63 GLU cc_start: 0.9142 (pt0) cc_final: 0.8911 (pt0) REVERT: l 84 MET cc_start: 0.8816 (tpp) cc_final: 0.8337 (tpp) REVERT: m 56 GLU cc_start: 0.9323 (tt0) cc_final: 0.8990 (tt0) REVERT: n 51 ASP cc_start: 0.8904 (p0) cc_final: 0.8514 (p0) REVERT: n 116 LYS cc_start: 0.9570 (mtmm) cc_final: 0.9236 (ptpp) REVERT: o 90 MET cc_start: 0.9320 (mmp) cc_final: 0.9027 (mmm) REVERT: o 93 GLN cc_start: 0.9079 (tt0) cc_final: 0.8285 (tp40) REVERT: o 105 GLU cc_start: 0.9094 (tp30) cc_final: 0.8833 (tp30) REVERT: p 59 LYS cc_start: 0.9428 (tppt) cc_final: 0.9113 (tppp) REVERT: p 84 MET cc_start: 0.9203 (tpp) cc_final: 0.8150 (tpp) REVERT: p 88 TYR cc_start: 0.8544 (m-80) cc_final: 0.7615 (m-10) REVERT: p 93 GLN cc_start: 0.9180 (tm-30) cc_final: 0.8793 (tm-30) REVERT: q 38 ASN cc_start: 0.8372 (m110) cc_final: 0.7779 (p0) REVERT: q 90 ASP cc_start: 0.8776 (t70) cc_final: 0.8515 (t70) REVERT: q 94 ASN cc_start: 0.9201 (t0) cc_final: 0.8848 (m-40) REVERT: r 83 TYR cc_start: 0.8545 (t80) cc_final: 0.7872 (t80) REVERT: r 93 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8746 (mm-30) outliers start: 9 outliers final: 5 residues processed: 156 average time/residue: 0.1163 time to fit residues: 26.0820 Evaluate side-chains 145 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 139 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 22 LEU Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain m residue 114 VAL Chi-restraints excluded: chain o residue 97 GLU Chi-restraints excluded: chain p residue 63 GLU Chi-restraints excluded: chain s residue 92 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 39 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 48 optimal weight: 8.9990 chunk 16 optimal weight: 0.6980 chunk 95 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 41 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 68 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 = 0.2933 r_free = 0.2933 target = 0.030300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.022751 restraints weight = 130129.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.023592 restraints weight = 62964.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.024145 restraints weight = 39638.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.024503 restraints weight = 29272.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.024748 restraints weight = 24089.661| |-----------------------------------------------------------------------------| r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14386 Z= 0.165 Angle : 0.627 10.925 20853 Z= 0.360 Chirality : 0.034 0.190 2376 Planarity : 0.004 0.052 1478 Dihedral : 31.313 179.030 4581 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.59 % Allowed : 18.90 % Favored : 79.51 % 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: 1.87 (0.29), residues: 825 helix: 2.04 (0.21), residues: 584 sheet: -1.96 (1.71), residues: 10 loop : -0.71 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG p 39 TYR 0.024 0.001 TYR q 57 PHE 0.012 0.001 PHE r 65 HIS 0.006 0.001 HIS l 75 Details of bonding type rmsd covalent geometry : bond 0.00362 (14386) covalent geometry : angle 0.62715 (20853) hydrogen bonds : bond 0.03521 ( 849) hydrogen bonds : angle 3.14293 ( 2113) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 154 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 50 GLU cc_start: 0.9408 (mt-10) cc_final: 0.9058 (mt-10) REVERT: k 93 GLN cc_start: 0.9318 (tt0) cc_final: 0.9023 (tp40) REVERT: k 104 PHE cc_start: 0.9340 (m-80) cc_final: 0.9075 (m-80) REVERT: k 105 GLU cc_start: 0.8958 (pp20) cc_final: 0.8345 (pp20) REVERT: k 106 ASP cc_start: 0.9088 (m-30) cc_final: 0.8645 (m-30) REVERT: k 120 MET cc_start: 0.8665 (mtm) cc_final: 0.8216 (mtt) REVERT: l 23 ARG cc_start: 0.8287 (ptp90) cc_final: 0.7689 (pmt-80) REVERT: l 49 LEU cc_start: 0.9479 (tp) cc_final: 0.8933 (tp) REVERT: l 52 GLU cc_start: 0.8523 (pm20) cc_final: 0.7643 (pm20) REVERT: l 53 GLU cc_start: 0.8584 (pm20) cc_final: 0.7940 (pm20) REVERT: l 59 LYS cc_start: 0.9594 (tttp) cc_final: 0.9050 (ttpp) REVERT: l 79 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8804 (pttm) REVERT: l 84 MET cc_start: 0.8836 (tpp) cc_final: 0.8338 (tpp) REVERT: m 56 GLU cc_start: 0.9328 (tt0) cc_final: 0.9010 (tt0) REVERT: n 51 ASP cc_start: 0.8871 (p0) cc_final: 0.8489 (p0) REVERT: n 116 LYS cc_start: 0.9517 (mtmm) cc_final: 0.9136 (ptpp) REVERT: o 81 ASP cc_start: 0.8813 (p0) cc_final: 0.8552 (p0) REVERT: o 90 MET cc_start: 0.9285 (mmp) cc_final: 0.9017 (mmm) REVERT: o 93 GLN cc_start: 0.9030 (tt0) cc_final: 0.8176 (tp40) REVERT: p 59 LYS cc_start: 0.9411 (tppt) cc_final: 0.9092 (tppp) REVERT: p 84 MET cc_start: 0.9209 (tpp) cc_final: 0.8330 (tpp) REVERT: p 88 TYR cc_start: 0.8647 (m-80) cc_final: 0.7694 (m-80) REVERT: p 93 GLN cc_start: 0.9146 (tm-30) cc_final: 0.8672 (tm-30) REVERT: q 38 ASN cc_start: 0.8346 (m110) cc_final: 0.7851 (p0) REVERT: q 90 ASP cc_start: 0.8754 (t70) cc_final: 0.8501 (t70) REVERT: q 94 ASN cc_start: 0.9186 (t0) cc_final: 0.8836 (m-40) REVERT: r 57 LYS cc_start: 0.9546 (mtpt) cc_final: 0.9290 (ttmm) REVERT: r 83 TYR cc_start: 0.8607 (t80) cc_final: 0.8141 (t80) REVERT: r 93 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8771 (mm-30) outliers start: 11 outliers final: 6 residues processed: 160 average time/residue: 0.1127 time to fit residues: 26.0932 Evaluate side-chains 149 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 142 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain k residue 100 LEU Chi-restraints excluded: chain l residue 22 LEU Chi-restraints excluded: chain l residue 79 LYS Chi-restraints excluded: chain m residue 16 THR Chi-restraints excluded: chain m residue 114 VAL Chi-restraints excluded: chain p residue 63 GLU Chi-restraints excluded: chain s residue 86 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 51 optimal weight: 0.6980 chunk 96 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.030351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2544 r_free = 0.2544 target = 0.022776 restraints weight = 130375.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.023621 restraints weight = 63451.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.024182 restraints weight = 40145.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.024534 restraints weight = 29797.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.024779 restraints weight = 24488.145| |-----------------------------------------------------------------------------| r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 14386 Z= 0.166 Angle : 0.645 10.927 20853 Z= 0.367 Chirality : 0.035 0.207 2376 Planarity : 0.004 0.052 1478 Dihedral : 31.248 179.499 4581 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.02 % Allowed : 18.90 % Favored : 79.08 % 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: 1.76 (0.29), residues: 825 helix: 1.97 (0.21), residues: 586 sheet: -1.97 (1.74), residues: 10 loop : -0.79 (0.38), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG p 39 TYR 0.021 0.001 TYR q 57 PHE 0.010 0.001 PHE r 65 HIS 0.007 0.001 HIS l 75 Details of bonding type rmsd covalent geometry : bond 0.00368 (14386) covalent geometry : angle 0.64479 (20853) hydrogen bonds : bond 0.03521 ( 849) hydrogen bonds : angle 3.15626 ( 2113) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 50 GLU cc_start: 0.9416 (mt-10) cc_final: 0.9082 (mt-10) REVERT: k 73 GLU cc_start: 0.9364 (tt0) cc_final: 0.8948 (pt0) REVERT: k 104 PHE cc_start: 0.9352 (m-80) cc_final: 0.9140 (m-80) REVERT: k 105 GLU cc_start: 0.8943 (pp20) cc_final: 0.8303 (pp20) REVERT: k 106 ASP cc_start: 0.9069 (m-30) cc_final: 0.8630 (m-30) REVERT: k 120 MET cc_start: 0.8633 (mtm) cc_final: 0.8147 (mtt) REVERT: l 23 ARG cc_start: 0.8256 (ptp90) cc_final: 0.7689 (pmt-80) REVERT: l 24 ASP cc_start: 0.8319 (t0) cc_final: 0.8048 (t0) REVERT: l 49 LEU cc_start: 0.9451 (tp) cc_final: 0.8850 (tp) REVERT: l 52 GLU cc_start: 0.8474 (pm20) cc_final: 0.7637 (pm20) REVERT: l 53 GLU cc_start: 0.8456 (pm20) cc_final: 0.7825 (pm20) REVERT: l 59 LYS cc_start: 0.9482 (tttp) cc_final: 0.9208 (ttpp) REVERT: l 79 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8832 (pttm) REVERT: l 84 MET cc_start: 0.8863 (tpp) cc_final: 0.8374 (tpp) REVERT: m 56 GLU cc_start: 0.9359 (tt0) cc_final: 0.9035 (tt0) REVERT: m 68 ASN cc_start: 0.9348 (m-40) cc_final: 0.9013 (m110) REVERT: n 51 ASP cc_start: 0.8883 (p0) cc_final: 0.8494 (p0) REVERT: n 116 LYS cc_start: 0.9532 (mtmm) cc_final: 0.9151 (ptpp) REVERT: o 50 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8777 (pp20) REVERT: o 90 MET cc_start: 0.9280 (mmp) cc_final: 0.8985 (mmm) REVERT: o 93 GLN cc_start: 0.9154 (tt0) cc_final: 0.8407 (tp40) REVERT: p 59 LYS cc_start: 0.9408 (tppt) cc_final: 0.9084 (tppp) REVERT: p 84 MET cc_start: 0.9222 (tpp) cc_final: 0.8811 (tpp) REVERT: p 93 GLN cc_start: 0.9135 (tm-30) cc_final: 0.8665 (tm-30) REVERT: q 36 LYS cc_start: 0.9127 (mmtt) cc_final: 0.8908 (mmtt) REVERT: q 38 ASN cc_start: 0.8338 (m110) cc_final: 0.7840 (p0) REVERT: q 90 ASP cc_start: 0.8672 (t70) cc_final: 0.8425 (t70) REVERT: q 94 ASN cc_start: 0.9167 (t0) cc_final: 0.8792 (m-40) REVERT: r 57 LYS cc_start: 0.9546 (mtpt) cc_final: 0.9271 (ttmm) REVERT: r 76 GLU cc_start: 0.9330 (mm-30) cc_final: 0.9110 (tp30) REVERT: r 93 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8773 (mm-30) outliers start: 14 outliers final: 7 residues processed: 161 average time/residue: 0.1198 time to fit residues: 27.7320 Evaluate side-chains 154 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 145 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 62 LEU Chi-restraints excluded: chain l residue 79 LYS Chi-restraints excluded: chain m residue 16 THR Chi-restraints excluded: chain m residue 114 VAL Chi-restraints excluded: chain o residue 50 GLU Chi-restraints excluded: chain p residue 63 GLU Chi-restraints excluded: chain r residue 82 HIS Chi-restraints excluded: chain s residue 86 LEU Chi-restraints excluded: chain s residue 93 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 27 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.028168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2441 r_free = 0.2441 target = 0.020581 restraints weight = 141571.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2485 r_free = 0.2485 target = 0.021358 restraints weight = 70956.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.021874 restraints weight = 45929.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.022188 restraints weight = 34533.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2544 r_free = 0.2544 target = 0.022411 restraints weight = 28828.333| |-----------------------------------------------------------------------------| r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 14386 Z= 0.335 Angle : 0.708 10.899 20853 Z= 0.408 Chirality : 0.039 0.193 2376 Planarity : 0.005 0.053 1478 Dihedral : 31.625 175.304 4581 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.02 % Allowed : 19.19 % Favored : 78.79 % 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: 1.68 (0.29), residues: 825 helix: 1.90 (0.21), residues: 584 sheet: -1.83 (1.82), residues: 10 loop : -0.78 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG r 33 TYR 0.023 0.002 TYR q 57 PHE 0.011 0.002 PHE l 100 HIS 0.008 0.002 HIS l 75 Details of bonding type rmsd covalent geometry : bond 0.00741 (14386) covalent geometry : angle 0.70801 (20853) hydrogen bonds : bond 0.06948 ( 849) hydrogen bonds : angle 3.57969 ( 2113) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 50 GLU cc_start: 0.9398 (mt-10) cc_final: 0.9015 (mt-10) REVERT: k 105 GLU cc_start: 0.8896 (pp20) cc_final: 0.8206 (pp20) REVERT: k 106 ASP cc_start: 0.8984 (m-30) cc_final: 0.8570 (m-30) REVERT: k 120 MET cc_start: 0.8656 (mtm) cc_final: 0.8003 (mtt) REVERT: l 23 ARG cc_start: 0.8271 (ptp90) cc_final: 0.7642 (pmt-80) REVERT: l 49 LEU cc_start: 0.9472 (tp) cc_final: 0.9130 (tp) REVERT: l 52 GLU cc_start: 0.8467 (pm20) cc_final: 0.8098 (pm20) REVERT: l 53 GLU cc_start: 0.8490 (pm20) cc_final: 0.8116 (pm20) REVERT: l 59 LYS cc_start: 0.9513 (tttp) cc_final: 0.9306 (ttpp) REVERT: l 84 MET cc_start: 0.8834 (tpp) cc_final: 0.8387 (tpp) REVERT: m 56 GLU cc_start: 0.9396 (tt0) cc_final: 0.9043 (tt0) REVERT: n 34 LYS cc_start: 0.8971 (mmtt) cc_final: 0.8705 (mmtt) REVERT: n 51 ASP cc_start: 0.9055 (p0) cc_final: 0.8845 (p0) REVERT: n 113 GLU cc_start: 0.9172 (mm-30) cc_final: 0.8900 (mm-30) REVERT: n 116 LYS cc_start: 0.9505 (mtmm) cc_final: 0.9152 (ptpp) REVERT: o 50 GLU cc_start: 0.9110 (OUTLIER) cc_final: 0.8834 (pp20) REVERT: o 93 GLN cc_start: 0.9232 (tt0) cc_final: 0.8635 (tp40) REVERT: p 59 LYS cc_start: 0.9419 (tppt) cc_final: 0.9104 (tppp) REVERT: p 84 MET cc_start: 0.9240 (tpp) cc_final: 0.8738 (tpp) REVERT: p 93 GLN cc_start: 0.9146 (tm-30) cc_final: 0.8738 (tm-30) REVERT: q 90 ASP cc_start: 0.8874 (t70) cc_final: 0.8570 (t70) REVERT: q 94 ASN cc_start: 0.9271 (t0) cc_final: 0.8863 (m-40) REVERT: r 93 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8747 (mm-30) outliers start: 14 outliers final: 9 residues processed: 146 average time/residue: 0.1182 time to fit residues: 24.8285 Evaluate side-chains 143 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 62 LEU Chi-restraints excluded: chain m residue 16 THR Chi-restraints excluded: chain m residue 114 VAL Chi-restraints excluded: chain o residue 50 GLU Chi-restraints excluded: chain o residue 80 THR Chi-restraints excluded: chain o residue 130 ILE Chi-restraints excluded: chain p residue 63 GLU Chi-restraints excluded: chain r residue 82 HIS Chi-restraints excluded: chain s residue 86 LEU Chi-restraints excluded: chain s residue 93 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 45 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 105 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: k 93 GLN ** l 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.029678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.022137 restraints weight = 134599.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.022965 restraints weight = 65178.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.023505 restraints weight = 41368.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.023870 restraints weight = 30758.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.024090 restraints weight = 25324.318| |-----------------------------------------------------------------------------| r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 14386 Z= 0.176 Angle : 0.671 11.296 20853 Z= 0.378 Chirality : 0.035 0.182 2376 Planarity : 0.004 0.051 1478 Dihedral : 31.477 178.636 4581 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.44 % Allowed : 19.62 % Favored : 78.93 % 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: 1.81 (0.29), residues: 825 helix: 2.01 (0.21), residues: 584 sheet: -1.95 (1.68), residues: 10 loop : -0.76 (0.39), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG q 29 TYR 0.017 0.002 TYR q 57 PHE 0.008 0.001 PHE k 67 HIS 0.006 0.001 HIS p 75 Details of bonding type rmsd covalent geometry : bond 0.00394 (14386) covalent geometry : angle 0.67074 (20853) hydrogen bonds : bond 0.03536 ( 849) hydrogen bonds : angle 3.27746 ( 2113) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 50 GLU cc_start: 0.9414 (mt-10) cc_final: 0.9016 (mt-10) REVERT: k 73 GLU cc_start: 0.9321 (tt0) cc_final: 0.8911 (pt0) REVERT: k 93 GLN cc_start: 0.9287 (tt0) cc_final: 0.9051 (tp40) REVERT: k 105 GLU cc_start: 0.8982 (pp20) cc_final: 0.8329 (pp20) REVERT: k 106 ASP cc_start: 0.9018 (m-30) cc_final: 0.8625 (m-30) REVERT: k 120 MET cc_start: 0.8580 (mtm) cc_final: 0.8046 (mtt) REVERT: l 23 ARG cc_start: 0.8256 (ptp90) cc_final: 0.7588 (pmt-80) REVERT: l 24 ASP cc_start: 0.8372 (t0) cc_final: 0.8090 (t0) REVERT: l 49 LEU cc_start: 0.9441 (tp) cc_final: 0.8819 (tp) REVERT: l 52 GLU cc_start: 0.8418 (pm20) cc_final: 0.7566 (pm20) REVERT: l 53 GLU cc_start: 0.8553 (pm20) cc_final: 0.7985 (pm20) REVERT: l 59 LYS cc_start: 0.9473 (tttp) cc_final: 0.8775 (ttpp) REVERT: l 63 GLU cc_start: 0.9220 (pt0) cc_final: 0.8636 (mp0) REVERT: l 84 MET cc_start: 0.8904 (tpp) cc_final: 0.8403 (tpp) REVERT: m 56 GLU cc_start: 0.9366 (tt0) cc_final: 0.8999 (tt0) REVERT: n 51 ASP cc_start: 0.8958 (p0) cc_final: 0.8675 (p0) REVERT: n 116 LYS cc_start: 0.9533 (mtmm) cc_final: 0.9201 (ptpp) REVERT: o 50 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8800 (pp20) REVERT: o 93 GLN cc_start: 0.9040 (tt0) cc_final: 0.8408 (tp40) REVERT: p 59 LYS cc_start: 0.9401 (tppt) cc_final: 0.9098 (tppp) REVERT: p 84 MET cc_start: 0.9193 (tpp) cc_final: 0.8771 (tpp) REVERT: p 93 GLN cc_start: 0.9112 (tm-30) cc_final: 0.8682 (tm-30) REVERT: q 90 ASP cc_start: 0.8757 (t70) cc_final: 0.8458 (t70) REVERT: q 94 ASN cc_start: 0.9203 (t0) cc_final: 0.8807 (m-40) REVERT: r 57 LYS cc_start: 0.9521 (mtpt) cc_final: 0.9248 (ttmm) REVERT: r 76 GLU cc_start: 0.9337 (mm-30) cc_final: 0.9135 (tp30) outliers start: 10 outliers final: 6 residues processed: 152 average time/residue: 0.1204 time to fit residues: 26.1500 Evaluate side-chains 147 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 140 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 16 THR Chi-restraints excluded: chain m residue 114 VAL Chi-restraints excluded: chain o residue 50 GLU Chi-restraints excluded: chain o residue 80 THR Chi-restraints excluded: chain o residue 130 ILE Chi-restraints excluded: chain p residue 63 GLU Chi-restraints excluded: chain s residue 86 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 52 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 37 optimal weight: 0.0470 chunk 3 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 overall best weight: 1.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** l 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 84 ASN s 107 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.029595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2509 r_free = 0.2509 target = 0.022015 restraints weight = 134521.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.022845 restraints weight = 66244.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.023383 restraints weight = 42210.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.023756 restraints weight = 31566.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.023982 restraints weight = 25893.905| |-----------------------------------------------------------------------------| r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 14386 Z= 0.190 Angle : 0.676 11.297 20853 Z= 0.381 Chirality : 0.035 0.186 2376 Planarity : 0.005 0.061 1478 Dihedral : 31.378 179.520 4581 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.30 % Allowed : 20.78 % Favored : 77.92 % 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: 1.77 (0.29), residues: 825 helix: 1.95 (0.21), residues: 586 sheet: -1.88 (1.69), residues: 10 loop : -0.71 (0.40), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG r 33 TYR 0.017 0.001 TYR q 57 PHE 0.008 0.001 PHE l 100 HIS 0.006 0.001 HIS l 75 Details of bonding type rmsd covalent geometry : bond 0.00425 (14386) covalent geometry : angle 0.67557 (20853) hydrogen bonds : bond 0.04108 ( 849) hydrogen bonds : angle 3.34086 ( 2113) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 144 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 50 GLU cc_start: 0.9413 (mt-10) cc_final: 0.9071 (mt-10) REVERT: k 73 GLU cc_start: 0.9327 (tt0) cc_final: 0.8916 (pt0) REVERT: k 104 PHE cc_start: 0.9378 (m-80) cc_final: 0.9113 (m-80) REVERT: k 105 GLU cc_start: 0.8954 (pp20) cc_final: 0.8720 (pp20) REVERT: k 120 MET cc_start: 0.8608 (mtm) cc_final: 0.8072 (mtt) REVERT: l 23 ARG cc_start: 0.8236 (ptp90) cc_final: 0.7420 (pmt-80) REVERT: l 24 ASP cc_start: 0.8324 (t0) cc_final: 0.8018 (t0) REVERT: l 49 LEU cc_start: 0.9492 (tp) cc_final: 0.8978 (tp) REVERT: l 52 GLU cc_start: 0.8409 (pm20) cc_final: 0.7589 (pm20) REVERT: l 53 GLU cc_start: 0.8532 (pm20) cc_final: 0.7939 (pm20) REVERT: l 59 LYS cc_start: 0.9465 (tttp) cc_final: 0.8760 (ttpp) REVERT: l 63 GLU cc_start: 0.9210 (pt0) cc_final: 0.8597 (mp0) REVERT: l 74 GLU cc_start: 0.9177 (pt0) cc_final: 0.8847 (mt-10) REVERT: l 79 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8835 (pttp) REVERT: l 84 MET cc_start: 0.8883 (tpp) cc_final: 0.8383 (tpp) REVERT: m 56 GLU cc_start: 0.9374 (tt0) cc_final: 0.9007 (tt0) REVERT: n 51 ASP cc_start: 0.8976 (p0) cc_final: 0.8707 (p0) REVERT: n 71 GLU cc_start: 0.9016 (tp30) cc_final: 0.8806 (tp30) REVERT: n 113 GLU cc_start: 0.9195 (mm-30) cc_final: 0.8873 (mm-30) REVERT: n 116 LYS cc_start: 0.9516 (mtmm) cc_final: 0.9190 (ptpp) REVERT: o 50 GLU cc_start: 0.9085 (OUTLIER) cc_final: 0.8810 (pp20) REVERT: o 93 GLN cc_start: 0.9020 (tt0) cc_final: 0.8397 (tp40) REVERT: p 59 LYS cc_start: 0.9407 (tppt) cc_final: 0.9082 (tppp) REVERT: p 84 MET cc_start: 0.9165 (tpp) cc_final: 0.8683 (tpp) REVERT: p 93 GLN cc_start: 0.9098 (tm-30) cc_final: 0.8670 (tm-30) REVERT: q 90 ASP cc_start: 0.8623 (t70) cc_final: 0.8345 (t70) REVERT: q 94 ASN cc_start: 0.9188 (t0) cc_final: 0.8812 (m-40) REVERT: r 57 LYS cc_start: 0.9525 (mtpt) cc_final: 0.9230 (ttmm) REVERT: r 83 TYR cc_start: 0.8206 (t80) cc_final: 0.7967 (t80) REVERT: r 93 GLU cc_start: 0.9131 (mp0) cc_final: 0.8710 (mm-30) outliers start: 9 outliers final: 6 residues processed: 150 average time/residue: 0.1239 time to fit residues: 26.4807 Evaluate side-chains 147 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 79 LYS Chi-restraints excluded: chain m residue 16 THR Chi-restraints excluded: chain m residue 114 VAL Chi-restraints excluded: chain o residue 50 GLU Chi-restraints excluded: chain o residue 130 ILE Chi-restraints excluded: chain p residue 63 GLU Chi-restraints excluded: chain q residue 92 GLU Chi-restraints excluded: chain s residue 86 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 98 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 50 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 84 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 = 0.2897 r_free = 0.2897 target = 0.029315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2495 r_free = 0.2495 target = 0.021699 restraints weight = 137189.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.022506 restraints weight = 67791.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.023042 restraints weight = 43435.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.023407 restraints weight = 32537.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.023642 restraints weight = 26778.130| |-----------------------------------------------------------------------------| r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 14386 Z= 0.221 Angle : 0.683 11.111 20853 Z= 0.387 Chirality : 0.036 0.182 2376 Planarity : 0.005 0.055 1478 Dihedral : 31.439 179.999 4581 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.44 % Allowed : 20.63 % Favored : 77.92 % 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: 1.73 (0.29), residues: 825 helix: 1.92 (0.21), residues: 586 sheet: -1.65 (1.70), residues: 10 loop : -0.74 (0.40), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG n 99 TYR 0.017 0.002 TYR q 57 PHE 0.009 0.001 PHE l 100 HIS 0.007 0.001 HIS l 75 Details of bonding type rmsd covalent geometry : bond 0.00491 (14386) covalent geometry : angle 0.68338 (20853) hydrogen bonds : bond 0.04649 ( 849) hydrogen bonds : angle 3.42141 ( 2113) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1800.85 seconds wall clock time: 31 minutes 50.63 seconds (1910.63 seconds total)