Starting phenix.real_space_refine on Fri Jul 3 16:29:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pf3_13366/07_2026/7pf3_13366.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pf3_13366/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7pf3_13366/07_2026/7pf3_13366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pf3_13366/07_2026/7pf3_13366.map" model { file = "/net/cci-nas-00/data/ceres_data/7pf3_13366/07_2026/7pf3_13366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pf3_13366/07_2026/7pf3_13366.cif" } 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-6108/lib/python3.11/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: 2.99, per 1000 atoms: 0.22 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: 0.88 Conformation dependent library (CDL) restraints added in 364.8 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: 1.44 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: 2.62 Time building geometry restraints manager: 1.24 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=" C3' DA J 100 " pdb=" O3' DA J 100 " ideal model delta sigma weight residual 1.435 1.388 0.047 1.30e-02 5.92e+03 1.32e+01 bond pdb=" C3' DC I 659 " pdb=" O3' DC I 659 " ideal model delta sigma weight residual 1.435 1.388 0.047 1.30e-02 5.92e+03 1.31e+01 bond pdb=" C3' DG I 709 " pdb=" O3' DG I 709 " ideal model delta sigma weight residual 1.435 1.481 -0.046 1.30e-02 5.92e+03 1.23e+01 bond pdb=" C3' DT J 163 " pdb=" O3' DT J 163 " ideal model delta sigma weight residual 1.435 1.391 0.044 1.30e-02 5.92e+03 1.16e+01 bond pdb=" C3' DC I 692 " pdb=" O3' DC I 692 " ideal model delta sigma weight residual 1.435 1.391 0.044 1.30e-02 5.92e+03 1.16e+01 ... (remaining 14381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 20317 2.70 - 5.40: 477 5.40 - 8.10: 46 8.10 - 10.80: 10 10.80 - 13.50: 3 Bond angle restraints: 20853 Sorted by residual: angle pdb=" O4' DT J 108 " pdb=" C4' DT J 108 " pdb=" C3' DT J 108 " ideal model delta sigma weight residual 106.00 102.82 3.18 6.00e-01 2.78e+00 2.81e+01 angle pdb=" O4' DT J 77 " pdb=" C4' DT J 77 " pdb=" C3' DT J 77 " ideal model delta sigma weight residual 106.00 102.84 3.16 6.00e-01 2.78e+00 2.78e+01 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=" O4' DT J 35 " pdb=" C4' DT J 35 " pdb=" C3' DT J 35 " ideal model delta sigma weight residual 106.00 102.96 3.04 6.00e-01 2.78e+00 2.58e+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 ... (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: 1583 0.050 - 0.100: 599 0.100 - 0.150: 168 0.150 - 0.200: 22 0.200 - 0.250: 4 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=" C3' DG I 709 " pdb=" C4' DG I 709 " pdb=" O3' DG I 709 " pdb=" C2' DG I 709 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.21 2.00e-01 2.50e+01 1.10e+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: 2.060 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 12.730 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 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 : 0.008 0.063 14386 Z= 0.684 Angle : 1.063 13.497 20853 Z= 0.809 Chirality : 0.056 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/Z covalent geometry : bond 0.00823 / 0.68 (14386) covalent geometry : angle 1.06263 / 0.81 (20853) hydrogen bonds : bond 0.10173 / 6.75 ( 849) hydrogen bonds : angle 4.80558 / 3.43 ( 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 : 0.277 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: 0.1123 time to fit residues: 29.1516 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 : 0.249 ------------------------------------------------------------------------------- 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: 20.0000 chunk 53 optimal weight: 8.9990 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: 20.0000 chunk 106 optimal weight: 5.9990 overall best weight: 1.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 73 ASN ** 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** ** q 84 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 = 0.2928 r_free = 0.2928 target = 0.030337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.022544 restraints weight = 130182.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.023366 restraints weight = 63971.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.023914 restraints weight = 40791.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.024259 restraints weight = 30339.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.024503 restraints weight = 25047.592| |-----------------------------------------------------------------------------| r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14386 Z= 0.173 Angle : 0.723 9.883 20853 Z= 0.416 Chirality : 0.046 0.271 2376 Planarity : 0.005 0.054 1478 Dihedral : 32.773 176.293 4581 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.44 % Allowed : 9.96 % Favored : 88.60 % 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: 0.60 (0.27), residues: 825 helix: 1.02 (0.20), residues: 586 sheet: -2.59 (1.43), residues: 10 loop : -0.95 (0.34), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG r 33 TYR 0.019 0.002 TYR p 88 PHE 0.019 0.001 PHE r 65 HIS 0.006 0.001 HIS p 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.17 (14386) covalent geometry : angle 0.72329 / 0.42 (20853) hydrogen bonds : bond 0.04620 / 3.07 ( 849) hydrogen bonds : angle 3.66554 / 2.64 ( 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 183 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 173 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 50 GLU cc_start: 0.9388 (mt-10) cc_final: 0.8971 (mt-10) REVERT: k 120 MET cc_start: 0.8580 (mtm) cc_final: 0.8078 (mtt) REVERT: l 25 ASN cc_start: 0.8657 (OUTLIER) cc_final: 0.7825 (t0) REVERT: l 59 LYS cc_start: 0.9609 (tttp) cc_final: 0.9042 (ttpp) REVERT: l 63 GLU cc_start: 0.9285 (pt0) cc_final: 0.9001 (pt0) REVERT: l 84 MET cc_start: 0.8558 (tpp) cc_final: 0.8233 (tpp) REVERT: m 94 ASN cc_start: 0.9280 (t0) cc_final: 0.8947 (t0) REVERT: m 95 LYS cc_start: 0.9043 (mmmt) cc_final: 0.8675 (mmmt) REVERT: n 51 ASP cc_start: 0.8927 (p0) cc_final: 0.8539 (p0) REVERT: n 68 ASP cc_start: 0.9551 (t70) cc_final: 0.9331 (t70) REVERT: n 113 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8945 (mm-30) REVERT: n 116 LYS cc_start: 0.9514 (mtmm) cc_final: 0.8908 (ptpp) REVERT: n 120 LYS cc_start: 0.9566 (mttt) cc_final: 0.9293 (mttt) REVERT: o 54 TYR cc_start: 0.9412 (m-80) cc_final: 0.8844 (m-80) REVERT: o 90 MET cc_start: 0.9408 (mmp) cc_final: 0.9004 (mmm) REVERT: o 93 GLN cc_start: 0.9313 (tt0) cc_final: 0.7829 (tp40) REVERT: o 97 GLU cc_start: 0.9014 (mp0) cc_final: 0.8225 (mp0) REVERT: o 105 GLU cc_start: 0.9029 (tp30) cc_final: 0.8772 (tp30) REVERT: p 59 LYS cc_start: 0.9481 (tppt) cc_final: 0.9100 (tppt) REVERT: p 63 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8624 (pm20) REVERT: p 93 GLN cc_start: 0.9034 (tm-30) cc_final: 0.8681 (tm-30) REVERT: q 64 GLU cc_start: 0.9264 (tm-30) cc_final: 0.9045 (pp20) REVERT: q 90 ASP cc_start: 0.8982 (t70) cc_final: 0.8603 (t70) REVERT: q 94 ASN cc_start: 0.9233 (t0) cc_final: 0.8998 (m-40) REVERT: q 104 GLN cc_start: 0.8889 (mm-40) cc_final: 0.8609 (mm-40) REVERT: r 95 GLN cc_start: 0.9645 (tt0) cc_final: 0.9304 (tt0) REVERT: s 107 ASN cc_start: 0.8250 (t0) cc_final: 0.7975 (t0) outliers start: 10 outliers final: 3 residues processed: 177 average time/residue: 0.0985 time to fit residues: 25.1503 Evaluate side-chains 145 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 140 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain p residue 63 GLU Chi-restraints excluded: chain p residue 97 LEU Chi-restraints excluded: chain r residue 82 HIS 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: 5.9990 chunk 58 optimal weight: 3.9990 chunk 17 optimal weight: 20.0000 chunk 54 optimal weight: 7.9990 chunk 98 optimal weight: 20.0000 chunk 64 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 24 optimal weight: 0.4980 chunk 8 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... k 108 ASN k 113 HIS l 25 ASN ** l 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 49 HIS ** 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 = 0.2917 r_free = 0.2917 target = 0.030031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2506 r_free = 0.2506 target = 0.022287 restraints weight = 132820.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.023121 restraints weight = 65452.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.023654 restraints weight = 41516.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.024024 restraints weight = 30889.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.024289 restraints weight = 25253.818| |-----------------------------------------------------------------------------| r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14386 Z= 0.173 Angle : 0.699 9.765 20853 Z= 0.400 Chirality : 0.044 0.263 2376 Planarity : 0.005 0.051 1478 Dihedral : 32.541 179.504 4581 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.73 % Allowed : 13.56 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.28), residues: 825 helix: 1.44 (0.21), residues: 586 sheet: -2.24 (1.57), residues: 10 loop : -0.96 (0.34), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG o 131 TYR 0.021 0.002 TYR q 57 PHE 0.015 0.001 PHE k 104 HIS 0.008 0.001 HIS p 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.17 (14386) covalent geometry : angle 0.69949 / 0.40 (20853) hydrogen bonds : bond 0.05006 / 3.35 ( 849) hydrogen bonds : angle 3.45936 / 2.50 ( 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 162 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 50 GLU cc_start: 0.9399 (mt-10) cc_final: 0.8981 (mt-10) REVERT: k 104 PHE cc_start: 0.9344 (m-80) cc_final: 0.9108 (m-80) REVERT: k 120 MET cc_start: 0.8676 (mtm) cc_final: 0.8181 (mtt) REVERT: l 25 ASN cc_start: 0.8789 (OUTLIER) cc_final: 0.7587 (t0) REVERT: l 59 LYS cc_start: 0.9612 (tttp) cc_final: 0.9070 (ttpp) REVERT: l 63 GLU cc_start: 0.9212 (pt0) cc_final: 0.8994 (pt0) REVERT: l 84 MET cc_start: 0.8614 (tpp) cc_final: 0.8194 (tpp) REVERT: m 95 LYS cc_start: 0.9009 (mmmt) cc_final: 0.8779 (mmmt) REVERT: n 51 ASP cc_start: 0.8992 (p0) cc_final: 0.8615 (p0) REVERT: n 82 HIS cc_start: 0.9187 (t70) cc_final: 0.8986 (t70) REVERT: n 113 GLU cc_start: 0.9191 (mm-30) cc_final: 0.8982 (mm-30) REVERT: n 116 LYS cc_start: 0.9489 (mtmm) cc_final: 0.9026 (ptpp) REVERT: n 120 LYS cc_start: 0.9556 (mttt) cc_final: 0.9311 (mttm) REVERT: o 90 MET cc_start: 0.9405 (mmp) cc_final: 0.9028 (mmm) REVERT: o 93 GLN cc_start: 0.9307 (tt0) cc_final: 0.8551 (tp40) REVERT: o 105 GLU cc_start: 0.9053 (tp30) cc_final: 0.8796 (tp30) REVERT: p 59 LYS cc_start: 0.9461 (tppt) cc_final: 0.8632 (tppt) REVERT: p 63 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8384 (mp0) REVERT: p 84 MET cc_start: 0.9085 (tpp) cc_final: 0.8873 (tpp) REVERT: p 93 GLN cc_start: 0.9089 (tm-30) cc_final: 0.8731 (tm-30) REVERT: q 90 ASP cc_start: 0.8885 (t70) cc_final: 0.8538 (t70) REVERT: q 94 ASN cc_start: 0.9247 (t0) cc_final: 0.8899 (m-40) REVERT: q 104 GLN cc_start: 0.8995 (mm-40) cc_final: 0.8484 (mm-40) REVERT: r 85 LYS cc_start: 0.9749 (mmmm) cc_final: 0.9480 (mmmm) outliers start: 12 outliers final: 7 residues processed: 154 average time/residue: 0.1126 time to fit residues: 24.9804 Evaluate side-chains 147 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 138 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain k residue 100 LEU Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain m residue 114 VAL Chi-restraints excluded: chain n residue 44 VAL Chi-restraints excluded: chain o residue 97 GLU Chi-restraints excluded: chain p residue 63 GLU Chi-restraints excluded: chain r residue 82 HIS Chi-restraints excluded: chain r residue 106 LEU Chi-restraints excluded: chain s residue 44 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 109 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 87 optimal weight: 30.0000 chunk 49 optimal weight: 0.8980 chunk 95 optimal weight: 20.0000 chunk 61 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... k 108 ASN l 25 ASN l 75 HIS ** 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.029480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.021971 restraints weight = 132045.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.022805 restraints weight = 64057.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.023365 restraints weight = 40281.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.023744 restraints weight = 29371.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.023974 restraints weight = 23891.026| |-----------------------------------------------------------------------------| r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14386 Z= 0.207 Angle : 0.693 9.523 20853 Z= 0.395 Chirality : 0.043 0.260 2376 Planarity : 0.005 0.053 1478 Dihedral : 32.434 179.882 4581 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.45 % Allowed : 15.87 % Favored : 81.67 % 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: 1.46 (0.28), residues: 825 helix: 1.79 (0.21), residues: 584 sheet: -2.12 (1.68), residues: 10 loop : -1.04 (0.35), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG k 69 TYR 0.021 0.002 TYR q 57 PHE 0.006 0.001 PHE q 25 HIS 0.007 0.001 HIS p 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.21 (14386) covalent geometry : angle 0.69305 / 0.40 (20853) hydrogen bonds : bond 0.05493 / 3.70 ( 849) hydrogen bonds : angle 3.41048 / 2.47 ( 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 158 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 50 GLU cc_start: 0.9401 (mt-10) cc_final: 0.8978 (mt-10) REVERT: k 120 MET cc_start: 0.8715 (mtm) cc_final: 0.8198 (mtt) REVERT: l 25 ASN cc_start: 0.9101 (OUTLIER) cc_final: 0.7733 (t0) REVERT: l 59 LYS cc_start: 0.9625 (tttp) cc_final: 0.9105 (ttpp) REVERT: l 63 GLU cc_start: 0.9234 (pt0) cc_final: 0.9017 (pt0) REVERT: l 84 MET cc_start: 0.8691 (tpp) cc_final: 0.8201 (tpp) REVERT: m 64 GLU cc_start: 0.9296 (tm-30) cc_final: 0.9093 (pp20) REVERT: m 95 LYS cc_start: 0.9000 (mmmt) cc_final: 0.8718 (mmmt) REVERT: n 51 ASP cc_start: 0.9060 (p0) cc_final: 0.8702 (p0) REVERT: o 51 ILE cc_start: 0.9347 (OUTLIER) cc_final: 0.9142 (mm) REVERT: o 60 LEU cc_start: 0.9060 (mt) cc_final: 0.8641 (mt) REVERT: o 90 MET cc_start: 0.9418 (mmp) cc_final: 0.9065 (mmm) REVERT: o 93 GLN cc_start: 0.9256 (tt0) cc_final: 0.8897 (tt0) REVERT: o 105 GLU cc_start: 0.9066 (tp30) cc_final: 0.8846 (tp30) REVERT: p 59 LYS cc_start: 0.9447 (tppt) cc_final: 0.8609 (tppp) REVERT: p 63 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8406 (mp0) REVERT: p 84 MET cc_start: 0.9197 (tpp) cc_final: 0.8994 (tpp) REVERT: p 93 GLN cc_start: 0.9153 (tm-30) cc_final: 0.8782 (tm-30) REVERT: q 36 LYS cc_start: 0.9151 (mmtt) cc_final: 0.8870 (mmtt) REVERT: q 90 ASP cc_start: 0.8860 (t70) cc_final: 0.8535 (t70) REVERT: q 94 ASN cc_start: 0.9263 (t0) cc_final: 0.8929 (m-40) REVERT: q 104 GLN cc_start: 0.9014 (mm-40) cc_final: 0.8796 (mm-40) REVERT: s 107 ASN cc_start: 0.8249 (t0) cc_final: 0.7887 (t0) outliers start: 17 outliers final: 9 residues processed: 148 average time/residue: 0.1040 time to fit residues: 22.5029 Evaluate side-chains 140 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain k residue 100 LEU Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain m residue 114 VAL Chi-restraints excluded: chain o residue 51 ILE Chi-restraints excluded: chain o residue 82 LEU Chi-restraints excluded: chain o residue 97 GLU Chi-restraints excluded: chain p residue 62 LEU Chi-restraints excluded: chain p residue 63 GLU Chi-restraints excluded: chain p residue 97 LEU Chi-restraints excluded: chain r residue 82 HIS Chi-restraints excluded: chain r residue 106 LEU Chi-restraints excluded: chain s residue 92 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 80 optimal weight: 20.0000 chunk 16 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... k 108 ASN 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.030103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.022539 restraints weight = 130877.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.023402 restraints weight = 62932.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.023964 restraints weight = 39388.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.024356 restraints weight = 28925.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.024562 restraints weight = 23394.725| |-----------------------------------------------------------------------------| r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14386 Z= 0.150 Angle : 0.669 10.535 20853 Z= 0.383 Chirality : 0.043 0.264 2376 Planarity : 0.004 0.051 1478 Dihedral : 32.236 179.701 4581 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.03 % Allowed : 17.03 % Favored : 79.94 % 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: 1.55 (0.28), residues: 825 helix: 1.84 (0.21), residues: 586 sheet: -2.01 (1.70), residues: 10 loop : -0.97 (0.36), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG r 33 TYR 0.024 0.001 TYR q 57 PHE 0.005 0.001 PHE m 25 HIS 0.004 0.001 HIS n 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.15 (14386) covalent geometry : angle 0.66855 / 0.38 (20853) hydrogen bonds : bond 0.03999 / 2.69 ( 849) hydrogen bonds : angle 3.27693 / 2.37 ( 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 172 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 50 GLU cc_start: 0.9405 (mt-10) cc_final: 0.8972 (mt-10) REVERT: k 120 MET cc_start: 0.8684 (mtm) cc_final: 0.8227 (mtt) REVERT: l 25 ASN cc_start: 0.9160 (OUTLIER) cc_final: 0.7821 (t0) REVERT: l 59 LYS cc_start: 0.9610 (tttp) cc_final: 0.9086 (ttpp) REVERT: l 63 GLU cc_start: 0.9200 (pt0) cc_final: 0.8988 (pt0) REVERT: l 84 MET cc_start: 0.8717 (tpp) cc_final: 0.8213 (tpp) REVERT: m 56 GLU cc_start: 0.9300 (tt0) cc_final: 0.9015 (tt0) REVERT: m 68 ASN cc_start: 0.9100 (m-40) cc_final: 0.8688 (m110) REVERT: n 34 LYS cc_start: 0.8898 (mmtt) cc_final: 0.8670 (mmtt) REVERT: n 51 ASP cc_start: 0.8970 (p0) cc_final: 0.8609 (p0) REVERT: n 76 GLU cc_start: 0.9214 (mm-30) cc_final: 0.8817 (tp30) REVERT: n 93 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8620 (mt-10) REVERT: n 116 LYS cc_start: 0.9569 (mtmm) cc_final: 0.9219 (ptpp) REVERT: o 90 MET cc_start: 0.9405 (mmp) cc_final: 0.9047 (mmm) REVERT: o 93 GLN cc_start: 0.9236 (tt0) cc_final: 0.8465 (tp40) REVERT: o 105 GLU cc_start: 0.9075 (tp30) cc_final: 0.8830 (tp30) REVERT: o 126 LEU cc_start: 0.9445 (tp) cc_final: 0.9103 (tp) REVERT: p 59 LYS cc_start: 0.9420 (tppt) cc_final: 0.9026 (tppp) REVERT: p 63 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8582 (pm20) REVERT: p 74 GLU cc_start: 0.9260 (mt-10) cc_final: 0.9016 (mm-30) REVERT: p 84 MET cc_start: 0.9164 (tpp) cc_final: 0.8949 (tpp) REVERT: p 93 GLN cc_start: 0.9176 (tm-30) cc_final: 0.8818 (tm-30) REVERT: q 64 GLU cc_start: 0.9341 (tm-30) cc_final: 0.9121 (pp20) REVERT: q 90 ASP cc_start: 0.8835 (t70) cc_final: 0.8536 (t70) REVERT: q 94 ASN cc_start: 0.9200 (t0) cc_final: 0.8859 (m-40) REVERT: q 104 GLN cc_start: 0.8767 (mm-40) cc_final: 0.8288 (mm-40) REVERT: s 107 ASN cc_start: 0.8150 (t0) cc_final: 0.7660 (t0) outliers start: 21 outliers final: 8 residues processed: 162 average time/residue: 0.0947 time to fit residues: 22.6513 Evaluate side-chains 149 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 139 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain k residue 100 LEU Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 26 ILE Chi-restraints excluded: chain l residue 62 LEU 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 r residue 82 HIS Chi-restraints excluded: chain r residue 106 LEU Chi-restraints excluded: chain s residue 86 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 8.9990 chunk 24 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 95 optimal weight: 20.0000 chunk 85 optimal weight: 20.0000 chunk 41 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** l 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 108 ASN q 89 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.030239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2517 r_free = 0.2517 target = 0.022433 restraints weight = 131402.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.023262 restraints weight = 64496.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.023807 restraints weight = 41272.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.024188 restraints weight = 30722.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.024388 restraints weight = 25178.654| |-----------------------------------------------------------------------------| r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 14386 Z= 0.144 Angle : 0.672 11.252 20853 Z= 0.383 Chirality : 0.042 0.264 2376 Planarity : 0.004 0.050 1478 Dihedral : 32.113 179.968 4581 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.60 % Allowed : 17.89 % 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: 1.57 (0.28), residues: 825 helix: 1.86 (0.21), residues: 584 sheet: -2.14 (1.67), residues: 10 loop : -0.96 (0.36), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG p 39 TYR 0.027 0.002 TYR q 57 PHE 0.005 0.001 PHE r 65 HIS 0.004 0.001 HIS p 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.14 (14386) covalent geometry : angle 0.67174 / 0.38 (20853) hydrogen bonds : bond 0.03885 / 2.61 ( 849) hydrogen bonds : angle 3.24231 / 2.35 ( 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 162 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.283 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: 0.9394 (mt-10) cc_final: 0.8979 (mt-10) REVERT: k 73 GLU cc_start: 0.9419 (tt0) cc_final: 0.9082 (pt0) REVERT: k 90 MET cc_start: 0.9182 (mmm) cc_final: 0.8783 (mmm) REVERT: k 120 MET cc_start: 0.8613 (mtm) cc_final: 0.8171 (mtt) REVERT: l 53 GLU cc_start: 0.8846 (pm20) cc_final: 0.8283 (pm20) REVERT: l 59 LYS cc_start: 0.9616 (tttp) cc_final: 0.9058 (ttpp) REVERT: l 84 MET cc_start: 0.8736 (tpp) cc_final: 0.8220 (tpp) REVERT: m 56 GLU cc_start: 0.9327 (tt0) cc_final: 0.8998 (tt0) REVERT: m 64 GLU cc_start: 0.9317 (tm-30) cc_final: 0.9053 (pp20) REVERT: n 34 LYS cc_start: 0.8860 (mmtt) cc_final: 0.8656 (mmtt) REVERT: n 51 ASP cc_start: 0.8960 (p0) cc_final: 0.8571 (p0) REVERT: n 76 GLU cc_start: 0.9215 (mm-30) cc_final: 0.8810 (tp30) REVERT: n 93 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8559 (mt-10) REVERT: n 116 LYS cc_start: 0.9569 (mtmm) cc_final: 0.9219 (ptpp) REVERT: o 50 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8801 (pp20) REVERT: o 60 LEU cc_start: 0.8983 (mt) cc_final: 0.8585 (mt) REVERT: o 90 MET cc_start: 0.9364 (mmp) cc_final: 0.9002 (mmm) REVERT: o 93 GLN cc_start: 0.9217 (tt0) cc_final: 0.8875 (tt0) REVERT: o 105 GLU cc_start: 0.9088 (tp30) cc_final: 0.8839 (tp30) REVERT: p 59 LYS cc_start: 0.9430 (tppt) cc_final: 0.9007 (tppp) REVERT: p 63 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8559 (pm20) REVERT: p 74 GLU cc_start: 0.9256 (mt-10) cc_final: 0.9003 (mm-30) REVERT: p 93 GLN cc_start: 0.9170 (tm-30) cc_final: 0.8793 (tm-30) REVERT: q 64 GLU cc_start: 0.9345 (tm-30) cc_final: 0.9123 (pp20) REVERT: q 90 ASP cc_start: 0.8822 (t70) cc_final: 0.8526 (t70) REVERT: q 94 ASN cc_start: 0.9169 (t0) cc_final: 0.8839 (m-40) outliers start: 18 outliers final: 11 residues processed: 152 average time/residue: 0.1035 time to fit residues: 22.9910 Evaluate side-chains 149 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain k residue 92 LEU Chi-restraints excluded: chain k residue 100 LEU Chi-restraints excluded: chain l residue 26 ILE Chi-restraints excluded: chain l residue 62 LEU Chi-restraints excluded: chain m residue 114 VAL Chi-restraints excluded: chain o residue 50 GLU Chi-restraints excluded: chain o residue 97 GLU Chi-restraints excluded: chain p residue 62 LEU Chi-restraints excluded: chain p residue 63 GLU Chi-restraints excluded: chain p residue 97 LEU Chi-restraints excluded: chain r residue 82 HIS Chi-restraints excluded: chain r residue 106 LEU 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: 0.0980 chunk 96 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 22 optimal weight: 0.9980 chunk 103 optimal weight: 20.0000 chunk 50 optimal weight: 0.8980 chunk 73 optimal weight: 20.0000 chunk 57 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 90 optimal weight: 20.0000 chunk 106 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** l 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 49 HIS ** o 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.030508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.022857 restraints weight = 131212.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.023704 restraints weight = 64239.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.024254 restraints weight = 40604.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.024646 restraints weight = 29966.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.024882 restraints weight = 24412.419| |-----------------------------------------------------------------------------| r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 14386 Z= 0.140 Angle : 0.674 11.530 20853 Z= 0.383 Chirality : 0.042 0.265 2376 Planarity : 0.004 0.049 1478 Dihedral : 31.979 179.775 4581 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.74 % Allowed : 18.90 % Favored : 78.35 % 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: 1.49 (0.28), residues: 825 helix: 1.78 (0.21), residues: 584 sheet: -2.25 (1.62), residues: 10 loop : -0.90 (0.36), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG p 39 TYR 0.029 0.001 TYR q 57 PHE 0.011 0.001 PHE l 61 HIS 0.002 0.001 HIS p 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.14 (14386) covalent geometry : angle 0.67407 / 0.38 (20853) hydrogen bonds : bond 0.03721 / 2.52 ( 849) hydrogen bonds : angle 3.23892 / 2.33 ( 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 168 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.346 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: 0.9388 (mt-10) cc_final: 0.8973 (mt-10) REVERT: k 73 GLU cc_start: 0.9398 (tt0) cc_final: 0.9093 (pt0) REVERT: k 104 PHE cc_start: 0.9261 (m-80) cc_final: 0.8988 (m-80) REVERT: k 120 MET cc_start: 0.8613 (mtm) cc_final: 0.8210 (mtt) REVERT: l 52 GLU cc_start: 0.8700 (pm20) cc_final: 0.7944 (pm20) REVERT: l 53 GLU cc_start: 0.8751 (pm20) cc_final: 0.8174 (pm20) REVERT: l 59 LYS cc_start: 0.9501 (tttp) cc_final: 0.8638 (tptm) REVERT: l 63 GLU cc_start: 0.9211 (pt0) cc_final: 0.8659 (mp0) REVERT: l 84 MET cc_start: 0.8757 (tpp) cc_final: 0.8244 (tpp) REVERT: m 56 GLU cc_start: 0.9340 (tt0) cc_final: 0.9002 (tt0) REVERT: m 64 GLU cc_start: 0.9321 (tm-30) cc_final: 0.9068 (pp20) REVERT: n 34 LYS cc_start: 0.8896 (mmtt) cc_final: 0.8653 (mmtt) REVERT: n 51 ASP cc_start: 0.8889 (p0) cc_final: 0.8480 (p0) REVERT: n 71 GLU cc_start: 0.9055 (tp30) cc_final: 0.8832 (tp30) REVERT: n 76 GLU cc_start: 0.9246 (mm-30) cc_final: 0.8887 (tp30) REVERT: n 93 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8633 (mt-10) REVERT: n 116 LYS cc_start: 0.9562 (mtmm) cc_final: 0.9183 (ptpp) REVERT: o 50 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8770 (pp20) REVERT: o 60 LEU cc_start: 0.8947 (mt) cc_final: 0.8655 (mt) REVERT: o 90 MET cc_start: 0.9347 (mmp) cc_final: 0.9038 (mmm) REVERT: o 93 GLN cc_start: 0.9208 (tt0) cc_final: 0.8847 (tt0) REVERT: o 105 GLU cc_start: 0.9092 (tp30) cc_final: 0.8803 (tp30) REVERT: p 59 LYS cc_start: 0.9409 (tppt) cc_final: 0.8966 (tppp) REVERT: p 63 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8538 (pm20) REVERT: p 74 GLU cc_start: 0.9242 (mt-10) cc_final: 0.9009 (mm-30) REVERT: p 93 GLN cc_start: 0.9128 (tm-30) cc_final: 0.8732 (tm-30) REVERT: q 36 LYS cc_start: 0.9108 (mmtt) cc_final: 0.8850 (mmtt) REVERT: q 90 ASP cc_start: 0.8800 (t70) cc_final: 0.8539 (t70) REVERT: q 94 ASN cc_start: 0.9145 (t0) cc_final: 0.8837 (m-40) REVERT: r 57 LYS cc_start: 0.9500 (mtpt) cc_final: 0.9203 (ttmm) REVERT: r 93 GLU cc_start: 0.9125 (mp0) cc_final: 0.8782 (mm-30) outliers start: 19 outliers final: 12 residues processed: 158 average time/residue: 0.1051 time to fit residues: 24.1940 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 : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain k residue 92 LEU Chi-restraints excluded: chain k residue 100 LEU Chi-restraints excluded: chain k residue 103 LEU 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 46 VAL Chi-restraints excluded: chain o residue 50 GLU Chi-restraints excluded: chain o residue 97 GLU Chi-restraints excluded: chain p residue 62 LEU Chi-restraints excluded: chain p residue 63 GLU Chi-restraints excluded: chain p residue 97 LEU Chi-restraints excluded: chain r residue 82 HIS Chi-restraints excluded: chain s residue 86 LEU 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: 20.0000 chunk 96 optimal weight: 20.0000 chunk 20 optimal weight: 1.9990 chunk 78 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 chunk 24 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 92 optimal weight: 20.0000 chunk 107 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** l 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.029303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.021766 restraints weight = 133931.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2535 r_free = 0.2535 target = 0.022602 restraints weight = 65612.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.023163 restraints weight = 41663.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.023519 restraints weight = 30494.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.023782 restraints weight = 24984.507| |-----------------------------------------------------------------------------| r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 14386 Z= 0.226 Angle : 0.713 11.913 20853 Z= 0.401 Chirality : 0.043 0.257 2376 Planarity : 0.005 0.050 1478 Dihedral : 32.099 179.875 4581 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.60 % Allowed : 20.06 % Favored : 77.34 % 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: 1.53 (0.29), residues: 825 helix: 1.83 (0.21), residues: 584 sheet: -2.19 (1.69), residues: 10 loop : -0.94 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG p 39 TYR 0.023 0.002 TYR q 57 PHE 0.010 0.001 PHE q 25 HIS 0.007 0.002 HIS p 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.23 (14386) covalent geometry : angle 0.71311 / 0.40 (20853) hydrogen bonds : bond 0.06232 / 4.20 ( 849) hydrogen bonds : angle 3.39740 / 2.46 ( 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: 18 poor density : 134 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 50 GLU cc_start: 0.9399 (mt-10) cc_final: 0.9001 (mt-10) REVERT: k 73 GLU cc_start: 0.9426 (tt0) cc_final: 0.9113 (pt0) REVERT: k 90 MET cc_start: 0.9325 (mmm) cc_final: 0.8919 (mmm) REVERT: k 120 MET cc_start: 0.8674 (mtm) cc_final: 0.8153 (mtt) REVERT: l 59 LYS cc_start: 0.9488 (tttp) cc_final: 0.9238 (ttpp) REVERT: l 84 MET cc_start: 0.8764 (tpp) cc_final: 0.8290 (tpp) REVERT: m 56 GLU cc_start: 0.9353 (tt0) cc_final: 0.8940 (tt0) REVERT: n 34 LYS cc_start: 0.8984 (mmtt) cc_final: 0.8732 (mmtt) REVERT: n 51 ASP cc_start: 0.9014 (p0) cc_final: 0.8663 (p0) REVERT: n 76 GLU cc_start: 0.9293 (mm-30) cc_final: 0.8923 (tp30) REVERT: n 93 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8650 (mt-10) REVERT: n 116 LYS cc_start: 0.9512 (mtmm) cc_final: 0.9124 (ptpp) REVERT: o 90 MET cc_start: 0.9384 (mmp) cc_final: 0.9077 (mmm) REVERT: o 93 GLN cc_start: 0.9168 (tt0) cc_final: 0.8798 (tt0) REVERT: o 105 GLU cc_start: 0.9100 (tp30) cc_final: 0.8838 (tp30) REVERT: p 59 LYS cc_start: 0.9413 (tppt) cc_final: 0.8974 (tppp) REVERT: p 63 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8653 (pm20) REVERT: p 74 GLU cc_start: 0.9288 (mt-10) cc_final: 0.9047 (mm-30) REVERT: p 93 GLN cc_start: 0.9171 (tm-30) cc_final: 0.8746 (tm-30) REVERT: q 90 ASP cc_start: 0.8854 (t70) cc_final: 0.8532 (t70) REVERT: q 94 ASN cc_start: 0.9209 (t0) cc_final: 0.8822 (m-40) REVERT: s 107 ASN cc_start: 0.8404 (t0) cc_final: 0.8139 (t0) outliers start: 18 outliers final: 8 residues processed: 143 average time/residue: 0.1021 time to fit residues: 21.1843 Evaluate side-chains 139 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain k residue 100 LEU 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 p residue 62 LEU Chi-restraints excluded: chain p residue 63 GLU Chi-restraints excluded: chain p residue 97 LEU Chi-restraints excluded: chain r residue 82 HIS Chi-restraints excluded: chain s residue 86 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 45 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 105 optimal weight: 0.0970 chunk 74 optimal weight: 30.0000 chunk 75 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 84 optimal weight: 20.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** l 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.030059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2518 r_free = 0.2518 target = 0.022448 restraints weight = 131127.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.023295 restraints weight = 63211.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.023843 restraints weight = 39819.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.024226 restraints weight = 29391.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.024453 restraints weight = 23981.752| |-----------------------------------------------------------------------------| r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14386 Z= 0.145 Angle : 0.694 14.851 20853 Z= 0.389 Chirality : 0.043 0.272 2376 Planarity : 0.004 0.048 1478 Dihedral : 32.031 179.891 4581 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.16 % Allowed : 20.49 % Favored : 77.34 % 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: 1.67 (0.29), residues: 825 helix: 1.89 (0.21), residues: 584 sheet: -2.14 (1.70), residues: 10 loop : -0.76 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG p 39 TYR 0.020 0.002 TYR q 57 PHE 0.007 0.001 PHE o 67 HIS 0.003 0.001 HIS n 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 (14386) covalent geometry : angle 0.69386 / 0.39 (20853) hydrogen bonds : bond 0.03738 / 2.50 ( 849) hydrogen bonds : angle 3.27087 / 2.36 ( 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 156 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.339 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: 0.9399 (mt-10) cc_final: 0.8976 (mt-10) REVERT: k 73 GLU cc_start: 0.9407 (tt0) cc_final: 0.9079 (pt0) REVERT: k 90 MET cc_start: 0.9282 (mmm) cc_final: 0.8886 (mmm) REVERT: k 120 MET cc_start: 0.8620 (mtm) cc_final: 0.8192 (mtt) REVERT: l 59 LYS cc_start: 0.9463 (tttp) cc_final: 0.8770 (ttpp) REVERT: l 63 GLU cc_start: 0.9159 (pt0) cc_final: 0.8588 (mp0) REVERT: l 84 MET cc_start: 0.8795 (tpp) cc_final: 0.8276 (tpp) REVERT: m 56 GLU cc_start: 0.9324 (tt0) cc_final: 0.8978 (tt0) REVERT: m 61 GLU cc_start: 0.9098 (tm-30) cc_final: 0.8884 (tm-30) REVERT: m 64 GLU cc_start: 0.9299 (tm-30) cc_final: 0.9092 (pp20) REVERT: n 34 LYS cc_start: 0.8954 (mmtt) cc_final: 0.8722 (mmtt) REVERT: n 51 ASP cc_start: 0.8964 (p0) cc_final: 0.8624 (p0) REVERT: n 76 GLU cc_start: 0.9262 (mm-30) cc_final: 0.8915 (tp30) REVERT: n 93 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8618 (mt-10) REVERT: n 116 LYS cc_start: 0.9557 (mtmm) cc_final: 0.9170 (ptpp) REVERT: o 50 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8838 (pp20) REVERT: o 90 MET cc_start: 0.9357 (mmp) cc_final: 0.8991 (mmm) REVERT: o 93 GLN cc_start: 0.9116 (tt0) cc_final: 0.8527 (tp40) REVERT: p 59 LYS cc_start: 0.9396 (tppt) cc_final: 0.8956 (tppp) REVERT: p 63 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8611 (pm20) REVERT: p 74 GLU cc_start: 0.9236 (mt-10) cc_final: 0.9015 (mm-30) REVERT: p 93 GLN cc_start: 0.9143 (tm-30) cc_final: 0.8696 (tm-30) REVERT: q 38 ASN cc_start: 0.8395 (m110) cc_final: 0.7768 (p0) REVERT: q 90 ASP cc_start: 0.8799 (t70) cc_final: 0.8548 (t70) REVERT: q 94 ASN cc_start: 0.9165 (t0) cc_final: 0.8772 (m-40) REVERT: q 95 LYS cc_start: 0.9302 (mmtt) cc_final: 0.8981 (tmtt) REVERT: r 93 GLU cc_start: 0.9108 (mp0) cc_final: 0.8651 (mm-30) outliers start: 15 outliers final: 8 residues processed: 149 average time/residue: 0.1216 time to fit residues: 26.0031 Evaluate side-chains 146 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain k residue 100 LEU 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 p residue 63 GLU Chi-restraints excluded: chain p residue 97 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 52 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 75 optimal weight: 20.0000 chunk 6 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 88 optimal weight: 30.0000 chunk 93 optimal weight: 20.0000 chunk 100 optimal weight: 20.0000 chunk 108 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** o 108 ASN ** q 84 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 = 0.2895 r_free = 0.2895 target = 0.029378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.021831 restraints weight = 133445.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.022659 restraints weight = 65088.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.023200 restraints weight = 41325.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.023567 restraints weight = 30698.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.023802 restraints weight = 25052.248| |-----------------------------------------------------------------------------| r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14386 Z= 0.191 Angle : 0.722 16.046 20853 Z= 0.401 Chirality : 0.042 0.261 2376 Planarity : 0.004 0.049 1478 Dihedral : 32.042 179.399 4581 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.88 % Allowed : 21.07 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.29), residues: 825 helix: 1.91 (0.21), residues: 584 sheet: -2.12 (1.79), residues: 10 loop : -0.80 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG p 39 TYR 0.042 0.002 TYR q 57 PHE 0.009 0.001 PHE q 25 HIS 0.006 0.001 HIS p 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.19 (14386) covalent geometry : angle 0.72222 / 0.40 (20853) hydrogen bonds : bond 0.05138 / 3.45 ( 849) hydrogen bonds : angle 3.35657 / 2.43 ( 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 144 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 50 GLU cc_start: 0.9405 (mt-10) cc_final: 0.8995 (mt-10) REVERT: k 73 GLU cc_start: 0.9406 (tt0) cc_final: 0.9095 (pt0) REVERT: k 90 MET cc_start: 0.9310 (mmm) cc_final: 0.8913 (mmm) REVERT: k 120 MET cc_start: 0.8641 (mtm) cc_final: 0.8151 (mtt) REVERT: l 59 LYS cc_start: 0.9492 (tttp) cc_final: 0.8798 (ttpp) REVERT: l 63 GLU cc_start: 0.9171 (pt0) cc_final: 0.8616 (mp0) REVERT: l 84 MET cc_start: 0.8788 (tpp) cc_final: 0.8280 (tpp) REVERT: m 41 GLU cc_start: 0.8875 (pm20) cc_final: 0.8593 (pm20) REVERT: m 56 GLU cc_start: 0.9349 (tt0) cc_final: 0.8934 (tt0) REVERT: m 61 GLU cc_start: 0.9124 (tm-30) cc_final: 0.8904 (tm-30) REVERT: n 34 LYS cc_start: 0.8987 (mmtt) cc_final: 0.8745 (mmtt) REVERT: n 51 ASP cc_start: 0.9015 (p0) cc_final: 0.8736 (p0) REVERT: n 76 GLU cc_start: 0.9309 (mm-30) cc_final: 0.8966 (tp30) REVERT: n 116 LYS cc_start: 0.9522 (mtmm) cc_final: 0.9146 (ptpp) REVERT: o 50 GLU cc_start: 0.9094 (OUTLIER) cc_final: 0.8885 (pp20) REVERT: o 90 MET cc_start: 0.9344 (mmp) cc_final: 0.9036 (mmm) REVERT: o 93 GLN cc_start: 0.9145 (tt0) cc_final: 0.8506 (tp40) REVERT: p 59 LYS cc_start: 0.9399 (tppt) cc_final: 0.8952 (tppp) REVERT: p 63 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8656 (pm20) REVERT: p 74 GLU cc_start: 0.9265 (mt-10) cc_final: 0.9038 (mm-30) REVERT: p 93 GLN cc_start: 0.9165 (tm-30) cc_final: 0.8719 (tm-30) REVERT: q 90 ASP cc_start: 0.8885 (t70) cc_final: 0.8528 (t70) REVERT: q 94 ASN cc_start: 0.9186 (t0) cc_final: 0.8800 (m-40) REVERT: q 95 LYS cc_start: 0.9305 (mmtt) cc_final: 0.9017 (tmtt) REVERT: r 93 GLU cc_start: 0.9135 (mp0) cc_final: 0.8683 (mm-30) outliers start: 13 outliers final: 8 residues processed: 138 average time/residue: 0.1175 time to fit residues: 23.4156 Evaluate side-chains 139 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain k residue 100 LEU 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 p residue 63 GLU Chi-restraints excluded: chain p residue 97 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 98 optimal weight: 20.0000 chunk 57 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 74 optimal weight: 30.0000 chunk 27 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 73 optimal weight: 20.0000 chunk 1 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** l 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 49 HIS ** 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 = 0.030021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2517 r_free = 0.2517 target = 0.022389 restraints weight = 132784.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.023215 restraints weight = 64207.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.023771 restraints weight = 40591.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.024110 restraints weight = 30084.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.024357 restraints weight = 24950.724| |-----------------------------------------------------------------------------| r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14386 Z= 0.148 Angle : 0.697 14.340 20853 Z= 0.391 Chirality : 0.042 0.273 2376 Planarity : 0.004 0.048 1478 Dihedral : 31.963 179.055 4581 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.73 % Allowed : 21.07 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.29), residues: 825 helix: 1.95 (0.21), residues: 584 sheet: -1.94 (1.76), residues: 10 loop : -0.76 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG r 33 TYR 0.023 0.002 TYR r 83 PHE 0.006 0.001 PHE o 104 HIS 0.007 0.001 HIS n 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.15 (14386) covalent geometry : angle 0.69714 / 0.39 (20853) hydrogen bonds : bond 0.03798 / 2.54 ( 849) hydrogen bonds : angle 3.28966 / 2.37 ( 2113) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1685.12 seconds wall clock time: 29 minutes 54.15 seconds (1794.15 seconds total)