Starting phenix.real_space_refine on Sat Sep 12 09:37:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pf3_13366/09_2026/7pf3_13366.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pf3_13366/09_2026/7pf3_13366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7pf3_13366/09_2026/7pf3_13366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pf3_13366/09_2026/7pf3_13366.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pf3_13366/09_2026/7pf3_13366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pf3_13366/09_2026/7pf3_13366.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2230 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 334 5.49 5 S 10 5.16 5 C 7420 2.51 5 N 2528 2.21 5 O 3178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/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: 2.56, per 1000 atoms: 0.19 Number of scatterers: 13470 At special positions: 0 Unit cell: (139.65, 133.35, 74.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 334 15.00 O 3178 8.00 N 2528 7.00 C 7420 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 417.3 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: 1.71 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: 2.70 Time building geometry restraints manager: 1.14 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: 20312 2.70 - 5.40: 481 5.40 - 8.10: 47 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: 2.320 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.210 Find NCS groups from input model: 0.090 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: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.940 ------------------------------------------------------------------------------- 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= 0.685 Angle : 1.070 13.497 20853 Z= 0.816 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 1.06989 / 0.82 (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 : 0.347 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: 0.8892 (mt-10) REVERT: k 120 MET cc_start: 0.8777 (mtm) cc_final: 0.8039 (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: 0.8613 (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: 0.8717 (p0) REVERT: n 68 ASP cc_start: 0.9573 (t70) cc_final: 0.9286 (t0) REVERT: n 108 LYS cc_start: 0.9711 (ptpt) cc_final: 0.9504 (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: 0.8517 (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: 0.8643 (tm-30) REVERT: q 36 LYS cc_start: 0.9244 (mmtt) cc_final: 0.8926 (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 34 LYS cc_start: 0.8743 (mppt) cc_final: 0.8493 (mmtm) 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: 0.8783 (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: 0.7859 (t0) outliers start: 1 outliers final: 0 residues processed: 185 average time/residue: 0.1265 time to fit residues: 32.9662 Evaluate side-chains 141 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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: 0.8980 chunk 100 optimal weight: 20.0000 chunk 106 optimal weight: 5.9990 overall best weight: 1.3804 ------------------------------------------------------------------------------- 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 = 0.2929 r_free = 0.2929 target = 0.030353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.022561 restraints weight = 130073.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.023382 restraints weight = 63766.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.023923 restraints weight = 40721.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.024275 restraints weight = 30370.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.024527 restraints weight = 25054.966| |-----------------------------------------------------------------------------| r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14386 Z= 0.165 Angle : 0.740 9.911 20853 Z= 0.419 Chirality : 0.047 0.294 2376 Planarity : 0.005 0.054 1478 Dihedral : 32.683 177.478 4581 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.44 % Allowed : 9.67 % Favored : 88.89 % 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: 0.59 (0.27), residues: 825 helix: 1.01 (0.21), residues: 586 sheet: -2.58 (1.44), 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 0.007 0.001 HIS p 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.16 (14386) covalent geometry : angle 0.74031 / 0.42 (20853) hydrogen bonds : bond 0.04652 / 3.11 ( 849) hydrogen bonds : angle 3.67024 / 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 185 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 175 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 50 GLU cc_start: 0.9379 (mt-10) cc_final: 0.8949 (mt-10) REVERT: k 120 MET cc_start: 0.8580 (mtm) cc_final: 0.8074 (mtt) REVERT: l 25 ASN cc_start: 0.8654 (OUTLIER) cc_final: 0.7903 (t0) REVERT: l 59 LYS cc_start: 0.9607 (tttp) cc_final: 0.9034 (ttpp) REVERT: l 63 GLU cc_start: 0.9284 (pt0) cc_final: 0.8997 (pt0) REVERT: l 84 MET cc_start: 0.8562 (tpp) cc_final: 0.8221 (tpp) REVERT: m 94 ASN cc_start: 0.9283 (t0) cc_final: 0.8955 (t0) REVERT: m 95 LYS cc_start: 0.9046 (mmmt) cc_final: 0.8693 (mmmt) REVERT: n 51 ASP cc_start: 0.8932 (p0) cc_final: 0.8535 (p0) REVERT: n 68 ASP cc_start: 0.9552 (t70) cc_final: 0.9330 (t70) REVERT: n 108 LYS cc_start: 0.9635 (ptpt) cc_final: 0.9419 (ptpp) REVERT: n 113 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8947 (mm-30) REVERT: n 116 LYS cc_start: 0.9513 (mtmm) cc_final: 0.8907 (ptpp) REVERT: n 120 LYS cc_start: 0.9567 (mttt) cc_final: 0.9295 (mttt) REVERT: o 54 TYR cc_start: 0.9412 (m-80) cc_final: 0.8845 (m-80) REVERT: o 90 MET cc_start: 0.9411 (mmp) cc_final: 0.9004 (mmm) REVERT: o 93 GLN cc_start: 0.9317 (tt0) cc_final: 0.7833 (tp40) REVERT: o 97 GLU cc_start: 0.9019 (mp0) cc_final: 0.8230 (mp0) REVERT: o 126 LEU cc_start: 0.9438 (tp) cc_final: 0.9110 (tt) REVERT: p 59 LYS cc_start: 0.9481 (tppt) cc_final: 0.9103 (tppt) REVERT: p 63 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8623 (pm20) REVERT: p 93 GLN cc_start: 0.9027 (tm-30) cc_final: 0.8669 (tm-30) REVERT: q 64 GLU cc_start: 0.9270 (tm-30) cc_final: 0.9051 (pp20) REVERT: q 90 ASP cc_start: 0.8980 (t70) cc_final: 0.8600 (t70) REVERT: q 94 ASN cc_start: 0.9243 (t0) cc_final: 0.8924 (m-40) REVERT: q 104 GLN cc_start: 0.8888 (mm-40) cc_final: 0.8615 (mm-40) REVERT: r 95 GLN cc_start: 0.9644 (tt0) cc_final: 0.9303 (tt0) REVERT: s 107 ASN cc_start: 0.8258 (t0) cc_final: 0.7980 (t0) outliers start: 10 outliers final: 4 residues processed: 179 average time/residue: 0.1156 time to fit residues: 29.9365 Evaluate side-chains 146 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 140 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain k residue 124 ILE 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: 2.9990 chunk 58 optimal weight: 3.9990 chunk 17 optimal weight: 20.0000 chunk 54 optimal weight: 8.9990 chunk 98 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 11 optimal weight: 0.3980 chunk 24 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... k 108 ASN k 113 HIS l 25 ASN ** m 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 49 HIS ** o 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.030429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2518 r_free = 0.2518 target = 0.022593 restraints weight = 131964.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.023423 restraints weight = 65046.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.023968 restraints weight = 41362.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.024343 restraints weight = 30849.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.024567 restraints weight = 25261.014| |-----------------------------------------------------------------------------| r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14386 Z= 0.153 Angle : 0.709 10.060 20853 Z= 0.400 Chirality : 0.045 0.287 2376 Planarity : 0.005 0.050 1478 Dihedral : 32.428 179.956 4581 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.88 % Allowed : 12.84 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.28), residues: 825 helix: 1.37 (0.21), residues: 586 sheet: -2.31 (1.55), residues: 10 loop : -0.94 (0.34), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG o 83 TYR 0.021 0.001 TYR q 57 PHE 0.018 0.001 PHE k 104 HIS 0.007 0.001 HIS p 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.15 (14386) covalent geometry : angle 0.70897 / 0.40 (20853) hydrogen bonds : bond 0.04328 / 2.89 ( 849) hydrogen bonds : angle 3.44045 / 2.49 ( 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 169 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 0.212 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 48 LEU cc_start: 0.9891 (mm) cc_final: 0.9662 (mp) REVERT: k 50 GLU cc_start: 0.9394 (mt-10) cc_final: 0.8967 (mt-10) REVERT: k 104 PHE cc_start: 0.9344 (m-80) cc_final: 0.9109 (m-80) REVERT: k 120 MET cc_start: 0.8662 (mtm) cc_final: 0.8146 (mtt) REVERT: l 25 ASN cc_start: 0.8822 (OUTLIER) cc_final: 0.8099 (t0) REVERT: l 59 LYS cc_start: 0.9592 (tttp) cc_final: 0.9028 (ttpp) REVERT: l 63 GLU cc_start: 0.9235 (pt0) cc_final: 0.8985 (pt0) REVERT: l 84 MET cc_start: 0.8595 (tpp) cc_final: 0.8171 (tpp) REVERT: m 68 ASN cc_start: 0.9087 (m-40) cc_final: 0.8517 (m110) REVERT: m 94 ASN cc_start: 0.9278 (t0) cc_final: 0.8937 (t0) REVERT: m 95 LYS cc_start: 0.8995 (mmmt) cc_final: 0.8541 (mmmt) REVERT: n 51 ASP cc_start: 0.8971 (p0) cc_final: 0.8565 (p0) REVERT: n 68 ASP cc_start: 0.9533 (t70) cc_final: 0.9321 (t0) REVERT: n 108 LYS cc_start: 0.9626 (ptpt) cc_final: 0.9407 (ptpp) REVERT: n 120 LYS cc_start: 0.9558 (mttt) cc_final: 0.9270 (mttt) REVERT: o 60 LEU cc_start: 0.9151 (mt) cc_final: 0.8714 (mt) REVERT: o 90 MET cc_start: 0.9395 (mmp) cc_final: 0.9040 (mmm) REVERT: o 93 GLN cc_start: 0.9313 (tt0) cc_final: 0.8993 (tt0) REVERT: o 105 GLU cc_start: 0.9019 (tp30) cc_final: 0.8772 (tp30) REVERT: p 59 LYS cc_start: 0.9456 (tppt) cc_final: 0.9140 (tppp) REVERT: p 93 GLN cc_start: 0.9064 (tm-30) cc_final: 0.8721 (tm-30) REVERT: q 36 LYS cc_start: 0.9170 (mmtt) cc_final: 0.8826 (mmtm) REVERT: q 90 ASP cc_start: 0.8846 (t70) cc_final: 0.8511 (t70) REVERT: q 94 ASN cc_start: 0.9217 (t0) cc_final: 0.8957 (m-40) REVERT: q 104 GLN cc_start: 0.8977 (mm-40) cc_final: 0.8449 (mm-40) REVERT: r 85 LYS cc_start: 0.9734 (mmmm) cc_final: 0.9477 (mmmm) outliers start: 13 outliers final: 9 residues processed: 160 average time/residue: 0.1080 time to fit residues: 24.9697 Evaluate side-chains 151 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 62 LEU 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: 6.9990 chunk 43 optimal weight: 2.9990 chunk 87 optimal weight: 20.0000 chunk 49 optimal weight: 2.9990 chunk 95 optimal weight: 20.0000 chunk 61 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 68 optimal weight: 9.9990 chunk 108 optimal weight: 8.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.030108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2519 r_free = 0.2519 target = 0.022538 restraints weight = 130079.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.023375 restraints weight = 62799.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.023959 restraints weight = 39540.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.024317 restraints weight = 28784.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.024574 restraints weight = 23536.889| |-----------------------------------------------------------------------------| r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14386 Z= 0.166 Angle : 0.691 9.928 20853 Z= 0.390 Chirality : 0.043 0.283 2376 Planarity : 0.004 0.051 1478 Dihedral : 32.247 179.932 4581 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.31 % Allowed : 14.57 % Favored : 83.12 % 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: 1.41 (0.28), residues: 825 helix: 1.74 (0.21), residues: 584 sheet: -2.09 (1.68), residues: 10 loop : -0.99 (0.35), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG k 69 TYR 0.011 0.001 TYR q 57 PHE 0.007 0.001 PHE k 67 HIS 0.006 0.001 HIS p 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.17 (14386) covalent geometry : angle 0.69098 / 0.39 (20853) hydrogen bonds : bond 0.04509 / 3.03 ( 849) hydrogen bonds : angle 3.32741 / 2.41 ( 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 166 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.242 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: 0.9409 (mt-10) cc_final: 0.8976 (mt-10) REVERT: k 73 GLU cc_start: 0.9388 (tt0) cc_final: 0.9094 (pt0) REVERT: k 105 GLU cc_start: 0.8967 (pp20) cc_final: 0.8480 (pp20) REVERT: k 120 MET cc_start: 0.8700 (mtm) cc_final: 0.8214 (mtt) REVERT: l 25 ASN cc_start: 0.9185 (OUTLIER) cc_final: 0.7194 (t0) REVERT: l 59 LYS cc_start: 0.9617 (tttp) cc_final: 0.9049 (ttpp) REVERT: l 63 GLU cc_start: 0.9247 (pt0) cc_final: 0.8991 (pt0) REVERT: l 84 MET cc_start: 0.8684 (tpp) cc_final: 0.8193 (tpp) REVERT: m 64 GLU cc_start: 0.9272 (tm-30) cc_final: 0.9059 (pp20) REVERT: n 51 ASP cc_start: 0.9008 (p0) cc_final: 0.8634 (p0) REVERT: n 120 LYS cc_start: 0.9570 (mttt) cc_final: 0.9319 (mttt) REVERT: o 51 ILE cc_start: 0.9337 (OUTLIER) cc_final: 0.9132 (mm) REVERT: o 82 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.9013 (mm) REVERT: o 90 MET cc_start: 0.9437 (mmp) cc_final: 0.9030 (mmm) REVERT: o 93 GLN cc_start: 0.9273 (tt0) cc_final: 0.8496 (tp40) REVERT: o 105 GLU cc_start: 0.9030 (tp30) cc_final: 0.8826 (tp30) REVERT: p 59 LYS cc_start: 0.9442 (tppt) cc_final: 0.9114 (tppt) REVERT: p 93 GLN cc_start: 0.9103 (tm-30) cc_final: 0.8764 (tm-30) REVERT: q 90 ASP cc_start: 0.8814 (t70) cc_final: 0.8507 (t70) REVERT: q 94 ASN cc_start: 0.9228 (t0) cc_final: 0.8917 (m-40) REVERT: q 104 GLN cc_start: 0.9016 (mm-40) cc_final: 0.8767 (mm-40) REVERT: r 85 LYS cc_start: 0.9751 (mmmm) cc_final: 0.9497 (mmmm) REVERT: s 107 ASN cc_start: 0.8168 (t0) cc_final: 0.7852 (t0) outliers start: 16 outliers final: 7 residues processed: 157 average time/residue: 0.1056 time to fit residues: 24.0345 Evaluate side-chains 143 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain m residue 114 VAL Chi-restraints excluded: chain o residue 51 ILE Chi-restraints excluded: chain o residue 82 LEU Chi-restraints excluded: chain o residue 97 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 r residue 106 LEU Chi-restraints excluded: chain s residue 44 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 47 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 80 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.2916 r_free = 0.2916 target = 0.030109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2525 r_free = 0.2525 target = 0.022640 restraints weight = 130717.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.023490 restraints weight = 62967.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.024079 restraints weight = 39337.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.024461 restraints weight = 28439.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.024717 restraints weight = 23009.341| |-----------------------------------------------------------------------------| r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2245 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= 0.166 Angle : 0.691 10.408 20853 Z= 0.389 Chirality : 0.043 0.283 2376 Planarity : 0.004 0.051 1478 Dihedral : 32.113 179.653 4581 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.60 % Allowed : 16.16 % Favored : 81.24 % 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: 1.60 (0.28), residues: 825 helix: 1.88 (0.21), residues: 584 sheet: -2.04 (1.73), residues: 10 loop : -0.94 (0.36), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG q 29 TYR 0.019 0.001 TYR q 57 PHE 0.006 0.001 PHE k 67 HIS 0.005 0.001 HIS p 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.17 (14386) covalent geometry : angle 0.69056 / 0.39 (20853) hydrogen bonds : bond 0.04432 / 2.99 ( 849) hydrogen bonds : angle 3.32461 / 2.41 ( 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 163 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 0.347 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: 0.9404 (mt-10) cc_final: 0.8976 (mt-10) REVERT: k 93 GLN cc_start: 0.9368 (tt0) cc_final: 0.9101 (tp40) REVERT: k 105 GLU cc_start: 0.9086 (pp20) cc_final: 0.8879 (pp20) REVERT: k 106 ASP cc_start: 0.9120 (m-30) cc_final: 0.8880 (m-30) REVERT: k 120 MET cc_start: 0.8671 (mtm) cc_final: 0.8201 (mtt) REVERT: l 25 ASN cc_start: 0.9272 (OUTLIER) cc_final: 0.8081 (t0) REVERT: l 59 LYS cc_start: 0.9606 (tttp) cc_final: 0.9074 (ttpp) REVERT: l 63 GLU cc_start: 0.9220 (pt0) cc_final: 0.8986 (pt0) REVERT: l 84 MET cc_start: 0.8720 (tpp) cc_final: 0.8222 (tpp) REVERT: m 56 GLU cc_start: 0.9303 (tt0) cc_final: 0.8985 (tt0) REVERT: m 64 GLU cc_start: 0.9332 (tm-30) cc_final: 0.9127 (tm-30) REVERT: n 34 LYS cc_start: 0.8874 (mmtt) cc_final: 0.8673 (mmtt) REVERT: n 51 ASP cc_start: 0.8971 (p0) cc_final: 0.8591 (p0) REVERT: n 116 LYS cc_start: 0.9532 (mtmm) cc_final: 0.9030 (ptpp) REVERT: n 120 LYS cc_start: 0.9562 (mttt) cc_final: 0.9291 (mttt) REVERT: o 82 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8942 (mm) REVERT: o 90 MET cc_start: 0.9407 (mmp) cc_final: 0.9053 (mmm) REVERT: o 93 GLN cc_start: 0.9255 (tt0) cc_final: 0.8456 (tp40) REVERT: o 105 GLU cc_start: 0.9048 (tp30) cc_final: 0.8837 (tp30) REVERT: p 59 LYS cc_start: 0.9444 (tppt) cc_final: 0.9050 (tppp) REVERT: p 63 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8592 (pm20) REVERT: p 93 GLN cc_start: 0.9158 (tm-30) cc_final: 0.8842 (tm-30) REVERT: q 90 ASP cc_start: 0.8834 (t70) cc_final: 0.8544 (t70) REVERT: q 94 ASN cc_start: 0.9220 (t0) cc_final: 0.8920 (m-40) REVERT: q 104 GLN cc_start: 0.8858 (mm-40) cc_final: 0.8366 (mm-40) REVERT: s 107 ASN cc_start: 0.8188 (t0) cc_final: 0.7761 (t0) outliers start: 18 outliers final: 6 residues processed: 155 average time/residue: 0.1058 time to fit residues: 23.9277 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 : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 26 ILE Chi-restraints excluded: chain m residue 114 VAL Chi-restraints excluded: chain o residue 82 LEU Chi-restraints excluded: chain o residue 97 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 92 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: 5.9990 chunk 24 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 95 optimal weight: 20.0000 chunk 85 optimal weight: 20.0000 chunk 41 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 108 ASN l 25 ASN ** n 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 108 ASN q 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.030316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.022788 restraints weight = 129558.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.023646 restraints weight = 62201.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.024223 restraints weight = 38827.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.024592 restraints weight = 28318.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.024869 restraints weight = 23092.701| |-----------------------------------------------------------------------------| r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14386 Z= 0.150 Angle : 0.686 11.260 20853 Z= 0.386 Chirality : 0.042 0.285 2376 Planarity : 0.004 0.051 1478 Dihedral : 32.009 179.246 4581 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.16 % Allowed : 16.88 % Favored : 80.95 % 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: 1.60 (0.28), residues: 825 helix: 1.88 (0.21), residues: 584 sheet: -2.14 (1.69), residues: 10 loop : -0.92 (0.36), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG p 39 TYR 0.027 0.002 TYR q 57 PHE 0.010 0.001 PHE k 104 HIS 0.005 0.001 HIS p 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.15 (14386) covalent geometry : angle 0.68589 / 0.39 (20853) hydrogen bonds : bond 0.04011 / 2.70 ( 849) hydrogen bonds : angle 3.30209 / 2.39 ( 2113) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 50 GLU cc_start: 0.9403 (mt-10) cc_final: 0.8996 (mt-10) REVERT: k 93 GLN cc_start: 0.9347 (tt0) cc_final: 0.9085 (tp40) REVERT: k 105 GLU cc_start: 0.9111 (pp20) cc_final: 0.8821 (pp20) REVERT: k 106 ASP cc_start: 0.9081 (m-30) cc_final: 0.8714 (m-30) REVERT: k 120 MET cc_start: 0.8661 (mtm) cc_final: 0.8166 (mtt) REVERT: l 25 ASN cc_start: 0.9385 (OUTLIER) cc_final: 0.8175 (t0) REVERT: l 52 GLU cc_start: 0.8785 (pm20) cc_final: 0.8068 (pm20) REVERT: l 53 GLU cc_start: 0.8856 (pm20) cc_final: 0.8272 (pm20) REVERT: l 59 LYS cc_start: 0.9597 (tttp) cc_final: 0.9074 (ttpp) REVERT: l 63 GLU cc_start: 0.9224 (pt0) cc_final: 0.8983 (pt0) REVERT: l 84 MET cc_start: 0.8758 (tpp) cc_final: 0.8299 (tpp) REVERT: m 56 GLU cc_start: 0.9313 (tt0) cc_final: 0.9014 (tt0) REVERT: n 51 ASP cc_start: 0.8963 (p0) cc_final: 0.8588 (p0) REVERT: n 116 LYS cc_start: 0.9531 (mtmm) cc_final: 0.9060 (mtmm) REVERT: n 120 LYS cc_start: 0.9563 (mttt) cc_final: 0.9294 (mttt) REVERT: o 50 GLU cc_start: 0.9093 (OUTLIER) cc_final: 0.8891 (pp20) REVERT: o 82 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8898 (mm) REVERT: o 90 MET cc_start: 0.9413 (mmp) cc_final: 0.9036 (mmm) REVERT: o 93 GLN cc_start: 0.9231 (tt0) cc_final: 0.8429 (tp40) REVERT: o 105 GLU cc_start: 0.9065 (tp30) cc_final: 0.8835 (tp30) REVERT: p 59 LYS cc_start: 0.9439 (tppt) cc_final: 0.9040 (tppp) REVERT: p 63 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8586 (pm20) REVERT: p 93 GLN cc_start: 0.9165 (tm-30) cc_final: 0.8797 (tm-30) REVERT: q 64 GLU cc_start: 0.9365 (tm-30) cc_final: 0.9129 (pp20) REVERT: q 90 ASP cc_start: 0.8788 (t70) cc_final: 0.8486 (t70) REVERT: q 94 ASN cc_start: 0.9174 (t0) cc_final: 0.8871 (m-40) outliers start: 15 outliers final: 6 residues processed: 158 average time/residue: 0.1088 time to fit residues: 24.8431 Evaluate side-chains 150 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 26 ILE Chi-restraints excluded: chain m residue 114 VAL Chi-restraints excluded: chain o residue 50 GLU Chi-restraints excluded: chain o residue 82 LEU Chi-restraints excluded: chain o residue 97 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 51 optimal weight: 0.9980 chunk 96 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 22 optimal weight: 0.8980 chunk 103 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 chunk 73 optimal weight: 20.0000 chunk 57 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 90 optimal weight: 20.0000 chunk 106 optimal weight: 5.9990 overall best weight: 1.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 108 ASN l 25 ASN ** 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.030107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2526 r_free = 0.2526 target = 0.022616 restraints weight = 130107.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.023485 restraints weight = 63000.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.024039 restraints weight = 39297.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.024442 restraints weight = 28738.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.024667 restraints weight = 23149.701| |-----------------------------------------------------------------------------| r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14386 Z= 0.164 Angle : 0.694 11.843 20853 Z= 0.389 Chirality : 0.042 0.282 2376 Planarity : 0.004 0.051 1478 Dihedral : 31.958 179.253 4581 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.16 % Allowed : 18.76 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.28), residues: 825 helix: 1.89 (0.21), residues: 584 sheet: -2.20 (1.68), residues: 10 loop : -0.97 (0.36), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG p 39 TYR 0.029 0.002 TYR q 57 PHE 0.007 0.001 PHE l 100 HIS 0.005 0.001 HIS p 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.16 (14386) covalent geometry : angle 0.69406 / 0.39 (20853) hydrogen bonds : bond 0.04362 / 2.93 ( 849) hydrogen bonds : angle 3.32393 / 2.39 ( 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 158 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 50 GLU cc_start: 0.9386 (mt-10) cc_final: 0.8988 (mt-10) REVERT: k 90 MET cc_start: 0.9291 (mmm) cc_final: 0.8847 (mmm) REVERT: k 93 GLN cc_start: 0.9348 (tt0) cc_final: 0.8976 (tp40) REVERT: k 105 GLU cc_start: 0.9084 (pp20) cc_final: 0.8684 (pp20) REVERT: k 106 ASP cc_start: 0.9086 (m-30) cc_final: 0.8656 (m-30) REVERT: k 120 MET cc_start: 0.8637 (mtm) cc_final: 0.8168 (mtt) REVERT: l 25 ASN cc_start: 0.9426 (OUTLIER) cc_final: 0.8243 (t0) REVERT: l 52 GLU cc_start: 0.8656 (pm20) cc_final: 0.7896 (pm20) REVERT: l 53 GLU cc_start: 0.8764 (pm20) cc_final: 0.8138 (pm20) REVERT: l 59 LYS cc_start: 0.9609 (tttp) cc_final: 0.9061 (ttpp) REVERT: l 63 GLU cc_start: 0.9223 (pt0) cc_final: 0.8992 (pt0) REVERT: l 84 MET cc_start: 0.8804 (tpp) cc_final: 0.8337 (tpp) REVERT: m 56 GLU cc_start: 0.9332 (tt0) cc_final: 0.9047 (tt0) REVERT: n 51 ASP cc_start: 0.8937 (p0) cc_final: 0.8537 (p0) REVERT: n 93 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8583 (mt-10) REVERT: n 116 LYS cc_start: 0.9525 (mtmm) cc_final: 0.9152 (mtmm) REVERT: o 50 GLU cc_start: 0.9084 (OUTLIER) cc_final: 0.8863 (pp20) REVERT: o 82 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8887 (mm) REVERT: o 90 MET cc_start: 0.9391 (mmp) cc_final: 0.8990 (mmm) REVERT: o 93 GLN cc_start: 0.9205 (tt0) cc_final: 0.8365 (tp40) REVERT: o 105 GLU cc_start: 0.9041 (tp30) cc_final: 0.8783 (tp30) REVERT: p 59 LYS cc_start: 0.9437 (tppt) cc_final: 0.9030 (tppp) REVERT: p 63 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8591 (pm20) REVERT: p 93 GLN cc_start: 0.9152 (tm-30) cc_final: 0.8771 (tm-30) REVERT: q 64 GLU cc_start: 0.9348 (tm-30) cc_final: 0.9128 (pp20) REVERT: q 90 ASP cc_start: 0.8747 (t70) cc_final: 0.8475 (t70) REVERT: q 94 ASN cc_start: 0.9182 (t0) cc_final: 0.8889 (m-40) REVERT: q 95 LYS cc_start: 0.9308 (mmtt) cc_final: 0.8799 (mtpp) REVERT: r 93 GLU cc_start: 0.9147 (mp0) cc_final: 0.8722 (mm-30) REVERT: s 107 ASN cc_start: 0.8141 (t0) cc_final: 0.7870 (t0) outliers start: 15 outliers final: 8 residues processed: 150 average time/residue: 0.1189 time to fit residues: 25.9020 Evaluate side-chains 152 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 26 ILE 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 82 LEU Chi-restraints excluded: chain o residue 97 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 27 optimal weight: 20.0000 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: 0.9990 chunk 39 optimal weight: 0.9990 chunk 92 optimal weight: 20.0000 chunk 107 optimal weight: 0.0870 chunk 45 optimal weight: 2.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 25 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.030306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.022547 restraints weight = 130422.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.023391 restraints weight = 64176.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.023927 restraints weight = 41014.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.024312 restraints weight = 30580.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.024545 restraints weight = 25111.201| |-----------------------------------------------------------------------------| r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14386 Z= 0.149 Angle : 0.694 13.555 20853 Z= 0.387 Chirality : 0.042 0.285 2376 Planarity : 0.004 0.050 1478 Dihedral : 31.907 179.368 4581 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.16 % Allowed : 19.34 % Favored : 78.50 % 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: 1.65 (0.29), residues: 825 helix: 1.93 (0.21), residues: 584 sheet: -2.27 (1.65), residues: 10 loop : -0.94 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG p 39 TYR 0.023 0.002 TYR q 57 PHE 0.011 0.001 PHE k 104 HIS 0.005 0.001 HIS p 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.15 (14386) covalent geometry : angle 0.69393 / 0.39 (20853) hydrogen bonds : bond 0.03974 / 2.68 ( 849) hydrogen bonds : angle 3.27178 / 2.35 ( 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 164 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 0.347 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: 0.9396 (mt-10) cc_final: 0.8988 (mt-10) REVERT: k 90 MET cc_start: 0.9291 (mmm) cc_final: 0.8895 (mmm) REVERT: k 105 GLU cc_start: 0.9091 (pp20) cc_final: 0.8643 (pp20) REVERT: k 106 ASP cc_start: 0.9104 (m-30) cc_final: 0.8680 (m-30) REVERT: k 120 MET cc_start: 0.8656 (mtm) cc_final: 0.8170 (mtt) REVERT: l 25 ASN cc_start: 0.9425 (OUTLIER) cc_final: 0.8354 (t0) REVERT: l 52 GLU cc_start: 0.8633 (pm20) cc_final: 0.7885 (pm20) REVERT: l 53 GLU cc_start: 0.8751 (pm20) cc_final: 0.8112 (pm20) REVERT: l 59 LYS cc_start: 0.9608 (tttp) cc_final: 0.9017 (ttpp) REVERT: l 63 GLU cc_start: 0.9210 (pt0) cc_final: 0.8979 (pt0) REVERT: l 84 MET cc_start: 0.8817 (tpp) cc_final: 0.8336 (tpp) REVERT: m 56 GLU cc_start: 0.9329 (tt0) cc_final: 0.9052 (tt0) REVERT: n 51 ASP cc_start: 0.8958 (p0) cc_final: 0.8573 (p0) REVERT: n 93 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8567 (mt-10) REVERT: n 116 LYS cc_start: 0.9518 (mtmm) cc_final: 0.9153 (mtmm) REVERT: o 50 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8853 (pp20) REVERT: o 90 MET cc_start: 0.9359 (mmp) cc_final: 0.9023 (mmm) REVERT: o 93 GLN cc_start: 0.9078 (tt0) cc_final: 0.8325 (tp40) REVERT: o 105 GLU cc_start: 0.9061 (tp30) cc_final: 0.8781 (tp30) REVERT: p 59 LYS cc_start: 0.9423 (tppt) cc_final: 0.9094 (tppp) REVERT: p 93 GLN cc_start: 0.9147 (tm-30) cc_final: 0.8696 (tm-30) REVERT: q 36 LYS cc_start: 0.9133 (mmtt) cc_final: 0.8907 (mmtm) REVERT: q 38 ASN cc_start: 0.8401 (m110) cc_final: 0.7781 (p0) REVERT: q 64 GLU cc_start: 0.9357 (tm-30) cc_final: 0.9122 (pp20) REVERT: q 90 ASP cc_start: 0.8739 (t70) cc_final: 0.8451 (t70) REVERT: q 94 ASN cc_start: 0.9164 (t0) cc_final: 0.8878 (m-40) REVERT: r 93 GLU cc_start: 0.9123 (mp0) cc_final: 0.8700 (mm-30) outliers start: 15 outliers final: 8 residues processed: 156 average time/residue: 0.1179 time to fit residues: 27.2447 Evaluate side-chains 147 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 26 ILE 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 45 optimal weight: 0.0070 chunk 15 optimal weight: 0.0370 chunk 47 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 74 optimal weight: 30.0000 chunk 75 optimal weight: 20.0000 chunk 87 optimal weight: 30.0000 chunk 84 optimal weight: 20.0000 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 25 ASN ** n 49 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.030585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.022827 restraints weight = 131319.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.023662 restraints weight = 64735.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.024198 restraints weight = 41177.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.024569 restraints weight = 30672.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.024781 restraints weight = 25298.882| |-----------------------------------------------------------------------------| r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 14386 Z= 0.140 Angle : 0.706 14.687 20853 Z= 0.391 Chirality : 0.042 0.288 2376 Planarity : 0.004 0.050 1478 Dihedral : 31.826 179.993 4581 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.88 % Allowed : 19.48 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.29), residues: 825 helix: 1.86 (0.21), residues: 584 sheet: -2.28 (1.65), residues: 10 loop : -0.91 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG p 39 TYR 0.022 0.002 TYR r 83 PHE 0.007 0.001 PHE k 67 HIS 0.004 0.001 HIS p 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.14 (14386) covalent geometry : angle 0.70562 / 0.39 (20853) hydrogen bonds : bond 0.03663 / 2.47 ( 849) hydrogen bonds : angle 3.26633 / 2.33 ( 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 163 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.271 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: 0.9401 (mt-10) cc_final: 0.9051 (mt-10) REVERT: k 90 MET cc_start: 0.9220 (mmm) cc_final: 0.8863 (mmm) REVERT: k 93 GLN cc_start: 0.9263 (tt0) cc_final: 0.8984 (tp40) REVERT: k 105 GLU cc_start: 0.9056 (pp20) cc_final: 0.8561 (pp20) REVERT: k 106 ASP cc_start: 0.9101 (m-30) cc_final: 0.8661 (m-30) REVERT: k 120 MET cc_start: 0.8650 (mtm) cc_final: 0.8223 (mtt) REVERT: l 25 ASN cc_start: 0.9385 (OUTLIER) cc_final: 0.9075 (m110) REVERT: l 52 GLU cc_start: 0.8582 (pm20) cc_final: 0.7825 (pm20) REVERT: l 53 GLU cc_start: 0.8778 (pm20) cc_final: 0.8163 (pm20) REVERT: l 59 LYS cc_start: 0.9622 (tttp) cc_final: 0.9017 (ttpp) REVERT: l 63 GLU cc_start: 0.9194 (pt0) cc_final: 0.8978 (pt0) REVERT: l 84 MET cc_start: 0.8801 (tpp) cc_final: 0.8309 (tpp) REVERT: m 56 GLU cc_start: 0.9310 (tt0) cc_final: 0.9021 (tt0) REVERT: n 51 ASP cc_start: 0.8882 (p0) cc_final: 0.8470 (p0) REVERT: n 71 GLU cc_start: 0.9043 (tp30) cc_final: 0.8813 (tp30) REVERT: n 93 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8568 (mt-10) REVERT: n 116 LYS cc_start: 0.9518 (mtmm) cc_final: 0.9148 (mtmm) REVERT: o 50 GLU cc_start: 0.9058 (OUTLIER) cc_final: 0.8832 (pp20) REVERT: o 90 MET cc_start: 0.9372 (mmp) cc_final: 0.8988 (mmm) REVERT: o 93 GLN cc_start: 0.9061 (tt0) cc_final: 0.8343 (tp40) REVERT: o 105 GLU cc_start: 0.9038 (tp30) cc_final: 0.8709 (tp30) REVERT: p 59 LYS cc_start: 0.9421 (tppt) cc_final: 0.8997 (tppp) REVERT: p 63 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8553 (pm20) REVERT: p 93 GLN cc_start: 0.9110 (tm-30) cc_final: 0.8663 (tm-30) REVERT: q 36 LYS cc_start: 0.9153 (mmtt) cc_final: 0.8908 (mmtm) REVERT: q 38 ASN cc_start: 0.8359 (m110) cc_final: 0.7748 (p0) REVERT: q 64 GLU cc_start: 0.9336 (tm-30) cc_final: 0.9104 (pp20) REVERT: q 90 ASP cc_start: 0.8766 (t70) cc_final: 0.8494 (t70) REVERT: q 94 ASN cc_start: 0.9121 (t0) cc_final: 0.8908 (m-40) REVERT: r 93 GLU cc_start: 0.9101 (mp0) cc_final: 0.8673 (mm-30) outliers start: 13 outliers final: 8 residues processed: 154 average time/residue: 0.1182 time to fit residues: 26.2905 Evaluate side-chains 154 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 26 ILE 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 o residue 108 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 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: 0.9980 chunk 69 optimal weight: 4.9990 chunk 75 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 88 optimal weight: 40.0000 chunk 93 optimal weight: 20.0000 chunk 100 optimal weight: 30.0000 chunk 108 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 25 ASN ** 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.030219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.022553 restraints weight = 132010.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.023380 restraints weight = 64289.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.023911 restraints weight = 40929.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.024291 restraints weight = 30460.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.024492 restraints weight = 24939.444| |-----------------------------------------------------------------------------| r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 14386 Z= 0.167 Angle : 0.721 15.216 20853 Z= 0.397 Chirality : 0.042 0.281 2376 Planarity : 0.004 0.051 1478 Dihedral : 31.815 179.996 4581 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.88 % Allowed : 20.06 % Favored : 78.07 % 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: 1.66 (0.29), residues: 825 helix: 1.91 (0.21), residues: 584 sheet: -2.21 (1.65), residues: 10 loop : -0.85 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG p 39 TYR 0.025 0.002 TYR r 83 PHE 0.018 0.001 PHE k 104 HIS 0.006 0.001 HIS p 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.17 (14386) covalent geometry : angle 0.72129 / 0.40 (20853) hydrogen bonds : bond 0.04306 / 2.90 ( 849) hydrogen bonds : angle 3.32772 / 2.39 ( 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 155 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 50 GLU cc_start: 0.9386 (mt-10) cc_final: 0.9053 (mt-10) REVERT: k 73 GLU cc_start: 0.9385 (tt0) cc_final: 0.8921 (pt0) REVERT: k 90 MET cc_start: 0.9277 (mmm) cc_final: 0.8865 (mmm) REVERT: k 93 GLN cc_start: 0.9166 (tt0) cc_final: 0.8880 (tp40) REVERT: k 105 GLU cc_start: 0.9025 (pp20) cc_final: 0.8506 (pp20) REVERT: k 106 ASP cc_start: 0.9088 (m-30) cc_final: 0.8647 (m-30) REVERT: k 120 MET cc_start: 0.8664 (mtm) cc_final: 0.8177 (mtt) REVERT: l 25 ASN cc_start: 0.9272 (t0) cc_final: 0.8952 (m110) REVERT: l 59 LYS cc_start: 0.9619 (tttp) cc_final: 0.8992 (ttpp) REVERT: l 63 GLU cc_start: 0.9210 (pt0) cc_final: 0.8990 (pt0) REVERT: l 84 MET cc_start: 0.8817 (tpp) cc_final: 0.8343 (tpp) REVERT: m 41 GLU cc_start: 0.8793 (pm20) cc_final: 0.8365 (pm20) REVERT: m 56 GLU cc_start: 0.9335 (tt0) cc_final: 0.9045 (tt0) REVERT: n 51 ASP cc_start: 0.8916 (p0) cc_final: 0.8513 (p0) REVERT: n 93 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8564 (mt-10) REVERT: n 113 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8864 (mm-30) REVERT: n 116 LYS cc_start: 0.9514 (mtmm) cc_final: 0.9120 (ptpp) REVERT: o 50 GLU cc_start: 0.9055 (OUTLIER) cc_final: 0.8831 (pp20) REVERT: o 82 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8917 (mm) REVERT: o 90 MET cc_start: 0.9366 (mmp) cc_final: 0.9013 (mmm) REVERT: o 93 GLN cc_start: 0.9070 (tt0) cc_final: 0.8357 (tp40) REVERT: p 59 LYS cc_start: 0.9416 (tppt) cc_final: 0.9081 (tppp) REVERT: p 93 GLN cc_start: 0.9139 (tm-30) cc_final: 0.8675 (tm-30) REVERT: q 38 ASN cc_start: 0.8327 (m110) cc_final: 0.7803 (p0) REVERT: q 64 GLU cc_start: 0.9344 (tm-30) cc_final: 0.9130 (pp20) REVERT: q 90 ASP cc_start: 0.8753 (t70) cc_final: 0.8464 (t70) REVERT: q 94 ASN cc_start: 0.9162 (t0) cc_final: 0.8894 (m-40) REVERT: r 93 GLU cc_start: 0.9126 (mp0) cc_final: 0.8689 (mm-30) outliers start: 13 outliers final: 8 residues processed: 147 average time/residue: 0.1166 time to fit residues: 24.5487 Evaluate side-chains 151 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 26 ILE Chi-restraints excluded: chain m residue 114 VAL Chi-restraints excluded: chain o residue 50 GLU Chi-restraints excluded: chain o residue 82 LEU Chi-restraints excluded: chain o residue 108 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 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: 2.9990 chunk 50 optimal weight: 2.9990 chunk 74 optimal weight: 30.0000 chunk 27 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 73 optimal weight: 20.0000 chunk 1 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.030275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2527 r_free = 0.2527 target = 0.022694 restraints weight = 133419.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.023530 restraints weight = 64676.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.024061 restraints weight = 40909.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.024453 restraints weight = 30265.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.024684 restraints weight = 24673.079| |-----------------------------------------------------------------------------| r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 14386 Z= 0.185 Angle : 0.893 59.194 20853 Z= 0.519 Chirality : 0.042 0.281 2376 Planarity : 0.004 0.051 1478 Dihedral : 31.816 179.993 4581 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.59 % Allowed : 20.35 % Favored : 78.07 % Cbeta Deviations : 0.13 % 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: 1.64 (0.29), residues: 825 helix: 1.89 (0.21), residues: 584 sheet: -2.20 (1.65), residues: 10 loop : -0.85 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG o 116 TYR 0.022 0.002 TYR r 83 PHE 0.013 0.001 PHE k 104 HIS 0.006 0.001 HIS p 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.18 (14386) covalent geometry : angle 0.89265 / 0.52 (20853) hydrogen bonds : bond 0.04302 / 2.90 ( 849) hydrogen bonds : angle 3.32771 / 2.39 ( 2113) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1809.30 seconds wall clock time: 32 minutes 5.62 seconds (1925.62 seconds total)