Starting phenix.real_space_refine on Tue Dec 31 06:54:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pf3_13366/12_2024/7pf3_13366.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pf3_13366/12_2024/7pf3_13366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pf3_13366/12_2024/7pf3_13366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pf3_13366/12_2024/7pf3_13366.map" model { file = "/net/cci-nas-00/data/ceres_data/7pf3_13366/12_2024/7pf3_13366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pf3_13366/12_2024/7pf3_13366.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 8.06, per 1000 atoms: 0.60 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: 3.64 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 7.17 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: 6.31 Time building geometry restraints manager: 4.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2465 1.33 - 1.45: 4950 1.45 - 1.57: 6285 1.57 - 1.69: 666 1.69 - 1.81: 20 Bond restraints: 14386 Sorted by residual: bond pdb=" CG GLU l 53 " pdb=" CD GLU l 53 " ideal model delta sigma weight residual 1.516 1.462 0.054 2.50e-02 1.60e+03 4.59e+00 bond pdb=" CD GLU q 61 " pdb=" OE1 GLU q 61 " ideal model delta sigma weight residual 1.249 1.210 0.039 1.90e-02 2.77e+03 4.31e+00 bond pdb=" CB ASP k 81 " pdb=" CG ASP k 81 " ideal model delta sigma weight residual 1.516 1.567 -0.051 2.50e-02 1.60e+03 4.22e+00 bond pdb=" CB GLU l 53 " pdb=" CG GLU l 53 " ideal model delta sigma weight residual 1.520 1.461 0.059 3.00e-02 1.11e+03 3.86e+00 bond pdb=" C3' DG I 709 " pdb=" O3' DG I 709 " ideal model delta sigma weight residual 1.422 1.481 -0.059 3.00e-02 1.11e+03 3.82e+00 ... (remaining 14381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 20464 2.70 - 5.40: 334 5.40 - 8.10: 42 8.10 - 10.80: 10 10.80 - 13.50: 3 Bond angle restraints: 20853 Sorted by residual: angle pdb=" CB ARG r 79 " pdb=" CG ARG r 79 " pdb=" CD ARG r 79 " ideal model delta sigma weight residual 111.30 123.37 -12.07 2.30e+00 1.89e-01 2.76e+01 angle pdb=" N GLU q 61 " pdb=" CA GLU q 61 " pdb=" CB GLU q 61 " ideal model delta sigma weight residual 110.28 118.14 -7.86 1.55e+00 4.16e-01 2.57e+01 angle pdb=" N GLU p 63 " pdb=" CA GLU p 63 " pdb=" CB GLU p 63 " ideal model delta sigma weight residual 110.28 117.74 -7.46 1.55e+00 4.16e-01 2.32e+01 angle pdb=" CB MET n 62 " pdb=" CG MET n 62 " pdb=" SD MET n 62 " ideal model delta sigma weight residual 112.70 126.20 -13.50 3.00e+00 1.11e-01 2.02e+01 angle pdb=" CA LYS m 36 " pdb=" CB LYS m 36 " pdb=" CG LYS m 36 " ideal model delta sigma weight residual 114.10 122.23 -8.13 2.00e+00 2.50e-01 1.65e+01 ... (remaining 20848 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 6098 35.99 - 71.98: 1671 71.98 - 107.96: 26 107.96 - 143.95: 2 143.95 - 179.94: 2 Dihedral angle restraints: 7799 sinusoidal: 5368 harmonic: 2431 Sorted by residual: dihedral pdb=" CA GLU o 50 " pdb=" C GLU o 50 " pdb=" N ILE o 51 " pdb=" CA ILE o 51 " ideal model delta harmonic sigma weight residual 180.00 153.59 26.41 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA ILE l 50 " pdb=" C ILE l 50 " pdb=" N TYR l 51 " pdb=" CA TYR l 51 " ideal model delta harmonic sigma weight residual 180.00 -157.18 -22.82 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA HIS r 82 " pdb=" C HIS r 82 " pdb=" N TYR r 83 " pdb=" CA TYR r 83 " ideal model delta harmonic sigma weight residual -180.00 -158.35 -21.65 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 7796 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1773 0.050 - 0.100: 476 0.100 - 0.150: 107 0.150 - 0.200: 17 0.200 - 0.250: 3 Chirality restraints: 2376 Sorted by residual: chirality pdb=" CA GLU o 50 " pdb=" N GLU o 50 " pdb=" C GLU o 50 " pdb=" CB GLU o 50 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA ILE q 79 " pdb=" N ILE q 79 " pdb=" C ILE q 79 " pdb=" CB ILE q 79 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB THR l 54 " pdb=" CA THR l 54 " pdb=" OG1 THR l 54 " pdb=" CG2 THR l 54 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 2373 not shown) Planarity restraints: 1478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP k 81 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.80e+00 pdb=" C ASP k 81 " -0.054 2.00e-02 2.50e+03 pdb=" O ASP k 81 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU k 82 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR p 88 " 0.015 2.00e-02 2.50e+03 2.11e-02 8.90e+00 pdb=" CG TYR p 88 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR p 88 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR p 88 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR p 88 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR p 88 " 0.019 2.00e-02 2.50e+03 pdb=" CZ TYR p 88 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR p 88 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG r 33 " -0.203 9.50e-02 1.11e+02 9.25e-02 8.74e+00 pdb=" NE ARG r 33 " 0.001 2.00e-02 2.50e+03 pdb=" CZ ARG r 33 " 0.036 2.00e-02 2.50e+03 pdb=" NH1 ARG r 33 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG r 33 " -0.018 2.00e-02 2.50e+03 ... (remaining 1475 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2974 2.79 - 3.32: 12723 3.32 - 3.85: 29001 3.85 - 4.37: 32233 4.37 - 4.90: 44479 Nonbonded interactions: 121410 Sorted by model distance: nonbonded pdb=" OG SER m 40 " pdb=" O ARG m 42 " model vdw 2.266 3.040 nonbonded pdb=" OH TYR m 39 " pdb=" OE1 GLU n 71 " model vdw 2.271 3.040 nonbonded pdb=" NH1 ARG p 35 " pdb=" OP2 DC I 663 " model vdw 2.273 3.120 nonbonded pdb=" OD2 ASP p 68 " pdb=" NH2 ARG p 92 " model vdw 2.308 3.120 nonbonded pdb=" NH1 ARG m 42 " pdb=" OG1 THR n 88 " model vdw 2.320 3.120 ... (remaining 121405 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'k' selection = chain 'o' } ncs_group { reference = chain 'l' selection = chain 'p' } ncs_group { reference = chain 'm' selection = chain 'q' } ncs_group { reference = chain 'n' selection = chain 'r' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 39.160 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.070 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 14386 Z= 0.433 Angle : 0.944 13.497 20853 Z= 0.529 Chirality : 0.049 0.250 2376 Planarity : 0.008 0.115 1478 Dihedral : 29.233 179.937 6233 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.14 % Allowed : 0.43 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.009 0.002 HIS p 75 PHE 0.037 0.003 PHE r 70 TYR 0.041 0.004 TYR p 88 ARG 0.033 0.001 ARG r 33 *********************** 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 : 1.021 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: 0.8134 (mtt) REVERT: l 31 LYS cc_start: 0.9221 (ttmm) cc_final: 0.8954 (ttmm) REVERT: l 49 LEU cc_start: 0.9607 (tp) cc_final: 0.8614 (tp) REVERT: l 59 LYS cc_start: 0.9510 (tttp) cc_final: 0.9057 (ttpp) REVERT: l 63 GLU cc_start: 0.9320 (pt0) cc_final: 0.9078 (pt0) REVERT: n 51 ASP cc_start: 0.9015 (p0) cc_final: 0.8718 (p0) REVERT: n 68 ASP cc_start: 0.9574 (t70) cc_final: 0.9285 (t0) REVERT: n 108 LYS cc_start: 0.9711 (ptpt) cc_final: 0.9505 (ptpp) REVERT: n 113 GLU cc_start: 0.9317 (mm-30) cc_final: 0.8991 (mm-30) REVERT: n 116 LYS cc_start: 0.9525 (mtmm) cc_final: 0.9106 (ptpp) REVERT: o 54 TYR cc_start: 0.9479 (m-80) cc_final: 0.8860 (m-80) REVERT: o 90 MET cc_start: 0.9418 (mmp) cc_final: 0.8987 (mmm) REVERT: o 93 GLN cc_start: 0.9262 (tt0) cc_final: 0.8518 (tp40) REVERT: o 97 GLU cc_start: 0.9192 (mp0) cc_final: 0.8499 (mp0) REVERT: p 59 LYS cc_start: 0.9606 (tppt) cc_final: 0.9255 (tppt) REVERT: p 63 GLU cc_start: 0.9228 (pm20) cc_final: 0.8879 (pm20) REVERT: p 85 ASP cc_start: 0.8948 (m-30) cc_final: 0.8745 (m-30) REVERT: p 93 GLN cc_start: 0.9099 (tm-30) cc_final: 0.8642 (tm-30) REVERT: q 36 LYS cc_start: 0.9244 (mmtt) cc_final: 0.8927 (mmtm) REVERT: q 62 ILE cc_start: 0.9846 (pt) cc_final: 0.9251 (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: 0.8370 (mt-10) REVERT: q 104 GLN cc_start: 0.8809 (mm-40) cc_final: 0.8445 (mm-40) REVERT: q 118 LYS cc_start: 0.8094 (mttt) cc_final: 0.7886 (mmmt) REVERT: r 83 TYR cc_start: 0.7545 (m-80) cc_final: 0.6734 (m-80) REVERT: r 84 ASN cc_start: 0.9195 (m-40) cc_final: 0.8784 (m-40) REVERT: r 95 GLN cc_start: 0.9692 (tt0) cc_final: 0.9446 (tt0) REVERT: r 106 LEU cc_start: 0.9743 (mt) cc_final: 0.9270 (mt) REVERT: s 72 VAL cc_start: 0.9120 (p) cc_final: 0.8627 (p) REVERT: s 107 ASN cc_start: 0.8073 (t0) cc_final: 0.7858 (t0) outliers start: 1 outliers final: 0 residues processed: 185 average time/residue: 0.3011 time to fit residues: 77.0503 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 : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 87 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** k 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 25 ASN ** m 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 49 HIS n 84 ASN ** o 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14386 Z= 0.242 Angle : 0.650 11.257 20853 Z= 0.379 Chirality : 0.036 0.158 2376 Planarity : 0.005 0.058 1478 Dihedral : 32.106 176.069 4581 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.72 % Allowed : 9.81 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.28), residues: 825 helix: 1.31 (0.21), residues: 586 sheet: -2.54 (1.50), residues: 10 loop : -0.89 (0.34), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS p 75 PHE 0.025 0.002 PHE r 65 TYR 0.015 0.002 TYR p 88 ARG 0.008 0.001 ARG n 99 *********************** 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 174 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 169 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 50 GLU cc_start: 0.9501 (mt-10) cc_final: 0.9051 (mt-10) REVERT: k 120 MET cc_start: 0.8652 (mtm) cc_final: 0.7857 (mtt) REVERT: l 25 ASN cc_start: 0.8536 (OUTLIER) cc_final: 0.7961 (t0) REVERT: l 59 LYS cc_start: 0.9479 (tttp) cc_final: 0.9022 (ttpp) REVERT: l 63 GLU cc_start: 0.9203 (pt0) cc_final: 0.8949 (pt0) REVERT: l 84 MET cc_start: 0.8626 (tpp) cc_final: 0.8188 (tpp) REVERT: n 51 ASP cc_start: 0.9050 (p0) cc_final: 0.8722 (p0) REVERT: n 68 ASP cc_start: 0.9543 (t70) cc_final: 0.9334 (t70) REVERT: n 113 GLU cc_start: 0.9312 (mm-30) cc_final: 0.9009 (mm-30) REVERT: n 116 LYS cc_start: 0.9516 (mtmm) cc_final: 0.9127 (ptpp) REVERT: o 90 MET cc_start: 0.9373 (mmp) cc_final: 0.8977 (mmm) REVERT: o 93 GLN cc_start: 0.9160 (tt0) cc_final: 0.8366 (tp40) REVERT: o 105 GLU cc_start: 0.9046 (tp30) cc_final: 0.8790 (tp30) REVERT: o 126 LEU cc_start: 0.9451 (tp) cc_final: 0.9179 (tt) REVERT: p 59 LYS cc_start: 0.9470 (tppt) cc_final: 0.9113 (tppp) REVERT: p 63 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8638 (pm20) REVERT: p 85 ASP cc_start: 0.9015 (m-30) cc_final: 0.8787 (m-30) REVERT: p 93 GLN cc_start: 0.9080 (tm-30) cc_final: 0.8705 (tm-30) REVERT: q 36 LYS cc_start: 0.9196 (mmtt) cc_final: 0.8976 (mmtt) REVERT: q 90 ASP cc_start: 0.9046 (t70) cc_final: 0.8634 (t70) REVERT: q 94 ASN cc_start: 0.9220 (t0) cc_final: 0.8895 (m-40) REVERT: q 104 GLN cc_start: 0.8863 (mm-40) cc_final: 0.8635 (mm-40) REVERT: s 107 ASN cc_start: 0.8069 (t0) cc_final: 0.7784 (t0) outliers start: 5 outliers final: 1 residues processed: 172 average time/residue: 0.2826 time to fit residues: 69.0647 Evaluate side-chains 139 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 136 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain n residue 44 VAL Chi-restraints excluded: chain p residue 63 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** k 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 113 HIS l 25 ASN l 75 HIS ** m 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 49 HIS ** o 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 108 ASN ** q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 14386 Z= 0.383 Angle : 0.687 9.649 20853 Z= 0.398 Chirality : 0.038 0.176 2376 Planarity : 0.005 0.056 1478 Dihedral : 31.850 177.486 4581 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.02 % Allowed : 13.13 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.28), residues: 825 helix: 1.70 (0.20), residues: 586 sheet: -2.33 (1.62), residues: 10 loop : -1.01 (0.35), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS p 75 PHE 0.011 0.002 PHE k 104 TYR 0.013 0.002 TYR l 98 ARG 0.005 0.001 ARG q 29 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 50 GLU cc_start: 0.9493 (mt-10) cc_final: 0.9068 (mt-10) REVERT: k 60 LEU cc_start: 0.9010 (mt) cc_final: 0.8737 (mp) REVERT: k 105 GLU cc_start: 0.8929 (pp20) cc_final: 0.8551 (pp20) REVERT: k 106 ASP cc_start: 0.8999 (m-30) cc_final: 0.8793 (m-30) REVERT: k 120 MET cc_start: 0.8796 (mtm) cc_final: 0.7966 (mtt) REVERT: l 59 LYS cc_start: 0.9493 (tttp) cc_final: 0.9015 (ttpp) REVERT: l 79 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8799 (pttm) REVERT: l 84 MET cc_start: 0.8809 (tpp) cc_final: 0.8366 (tpp) REVERT: n 51 ASP cc_start: 0.9123 (p0) cc_final: 0.8853 (p0) REVERT: n 68 ASP cc_start: 0.9551 (t70) cc_final: 0.9335 (t70) REVERT: n 76 GLU cc_start: 0.9207 (mm-30) cc_final: 0.9006 (mm-30) REVERT: n 113 GLU cc_start: 0.9320 (mm-30) cc_final: 0.9081 (mm-30) REVERT: o 51 ILE cc_start: 0.9399 (OUTLIER) cc_final: 0.9183 (mm) REVERT: o 93 GLN cc_start: 0.9175 (tt0) cc_final: 0.8449 (tp40) REVERT: o 105 GLU cc_start: 0.9009 (tp30) cc_final: 0.8741 (tp30) REVERT: p 59 LYS cc_start: 0.9474 (tppt) cc_final: 0.9168 (tppp) REVERT: p 84 MET cc_start: 0.9161 (tpp) cc_final: 0.8877 (tpp) REVERT: p 93 GLN cc_start: 0.9220 (tm-30) cc_final: 0.8838 (tm-30) REVERT: q 36 LYS cc_start: 0.9232 (mmtt) cc_final: 0.9005 (mmtt) REVERT: q 90 ASP cc_start: 0.9068 (t70) cc_final: 0.8745 (t70) REVERT: q 94 ASN cc_start: 0.9254 (t0) cc_final: 0.8820 (m-40) REVERT: q 104 GLN cc_start: 0.8829 (mm-40) cc_final: 0.8609 (mm-40) REVERT: r 76 GLU cc_start: 0.9154 (tp30) cc_final: 0.8932 (tp30) REVERT: s 107 ASN cc_start: 0.8267 (t0) cc_final: 0.8058 (t0) outliers start: 14 outliers final: 7 residues processed: 156 average time/residue: 0.2744 time to fit residues: 61.2829 Evaluate side-chains 144 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain k residue 100 LEU Chi-restraints excluded: chain l residue 79 LYS Chi-restraints excluded: chain m residue 24 GLN Chi-restraints excluded: chain m residue 114 VAL Chi-restraints excluded: chain n residue 44 VAL Chi-restraints excluded: chain o residue 51 ILE Chi-restraints excluded: chain o residue 97 GLU Chi-restraints excluded: chain p residue 63 GLU Chi-restraints excluded: chain s residue 92 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 107 optimal weight: 0.0670 chunk 96 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 overall best weight: 1.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14386 Z= 0.227 Angle : 0.626 10.397 20853 Z= 0.363 Chirality : 0.034 0.146 2376 Planarity : 0.004 0.053 1478 Dihedral : 31.644 178.847 4581 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.16 % Allowed : 14.29 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.28), residues: 825 helix: 1.97 (0.21), residues: 586 sheet: -2.05 (1.71), residues: 10 loop : -0.96 (0.36), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS l 75 PHE 0.007 0.001 PHE k 67 TYR 0.014 0.001 TYR l 98 ARG 0.003 0.000 ARG r 33 *********************** 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: 15 poor density : 151 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 50 GLU cc_start: 0.9495 (mt-10) cc_final: 0.9075 (mt-10) REVERT: k 90 MET cc_start: 0.9395 (mmm) cc_final: 0.9030 (mmm) REVERT: k 105 GLU cc_start: 0.9037 (pp20) cc_final: 0.8559 (pp20) REVERT: k 106 ASP cc_start: 0.9079 (m-30) cc_final: 0.8751 (m-30) REVERT: k 120 MET cc_start: 0.8809 (mtm) cc_final: 0.8021 (mtt) REVERT: l 52 GLU cc_start: 0.8745 (pm20) cc_final: 0.8066 (pm20) REVERT: l 53 GLU cc_start: 0.8636 (pm20) cc_final: 0.8170 (pm20) REVERT: l 79 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8788 (pttm) REVERT: l 84 MET cc_start: 0.8927 (tpp) cc_final: 0.8456 (tpp) REVERT: n 51 ASP cc_start: 0.9070 (p0) cc_final: 0.8763 (p0) REVERT: n 93 GLU cc_start: 0.8974 (mt-10) cc_final: 0.8520 (mt-10) REVERT: n 113 GLU cc_start: 0.9325 (mm-30) cc_final: 0.9086 (mm-30) REVERT: o 51 ILE cc_start: 0.9368 (OUTLIER) cc_final: 0.9151 (mm) REVERT: o 59 GLU cc_start: 0.9382 (pm20) cc_final: 0.9147 (pm20) REVERT: o 93 GLN cc_start: 0.9072 (tt0) cc_final: 0.8315 (tp40) REVERT: o 105 GLU cc_start: 0.9036 (tp30) cc_final: 0.8718 (tp30) REVERT: p 59 LYS cc_start: 0.9429 (tppt) cc_final: 0.9123 (tppp) REVERT: p 93 GLN cc_start: 0.9224 (tm-30) cc_final: 0.8782 (tm-30) REVERT: q 36 LYS cc_start: 0.9251 (mmtt) cc_final: 0.9045 (mmtt) REVERT: q 64 GLU cc_start: 0.9424 (tm-30) cc_final: 0.9210 (pp20) REVERT: q 90 ASP cc_start: 0.8995 (t70) cc_final: 0.8745 (t70) REVERT: q 94 ASN cc_start: 0.9246 (t0) cc_final: 0.8827 (m-40) REVERT: r 85 LYS cc_start: 0.9697 (mmmm) cc_final: 0.9458 (mmmm) REVERT: s 107 ASN cc_start: 0.8232 (t0) cc_final: 0.7893 (t0) outliers start: 15 outliers final: 9 residues processed: 159 average time/residue: 0.2698 time to fit residues: 61.7419 Evaluate side-chains 141 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain k residue 100 LEU Chi-restraints excluded: chain l residue 79 LYS Chi-restraints excluded: chain m residue 16 THR Chi-restraints excluded: chain m residue 24 GLN Chi-restraints excluded: chain m residue 114 VAL Chi-restraints excluded: chain n residue 44 VAL Chi-restraints excluded: chain o residue 51 ILE Chi-restraints excluded: chain o residue 80 THR Chi-restraints excluded: chain o residue 97 GLU Chi-restraints excluded: chain p residue 63 GLU Chi-restraints excluded: chain r residue 82 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: k 93 GLN ** k 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 108 ASN ** q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 14386 Z= 0.334 Angle : 0.657 10.688 20853 Z= 0.380 Chirality : 0.036 0.142 2376 Planarity : 0.004 0.051 1478 Dihedral : 31.605 177.388 4581 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.89 % Allowed : 17.17 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.28), residues: 825 helix: 1.97 (0.20), residues: 586 sheet: -1.85 (1.77), residues: 10 loop : -0.99 (0.36), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS p 75 PHE 0.009 0.001 PHE q 25 TYR 0.026 0.002 TYR q 57 ARG 0.004 0.000 ARG r 33 *********************** 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 158 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 50 GLU cc_start: 0.9498 (mt-10) cc_final: 0.9062 (mt-10) REVERT: k 120 MET cc_start: 0.8755 (mtm) cc_final: 0.7890 (mtt) REVERT: l 52 GLU cc_start: 0.8637 (pm20) cc_final: 0.7891 (pm20) REVERT: l 53 GLU cc_start: 0.8595 (pm20) cc_final: 0.8083 (pm20) REVERT: l 84 MET cc_start: 0.8947 (tpp) cc_final: 0.8474 (tpp) REVERT: n 51 ASP cc_start: 0.9148 (p0) cc_final: 0.8897 (p0) REVERT: n 108 LYS cc_start: 0.9594 (ptpp) cc_final: 0.9278 (ptpp) REVERT: n 113 GLU cc_start: 0.9350 (mm-30) cc_final: 0.9116 (mm-30) REVERT: o 51 ILE cc_start: 0.9370 (OUTLIER) cc_final: 0.9162 (mm) REVERT: o 82 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.9012 (mm) REVERT: o 90 MET cc_start: 0.9237 (mmm) cc_final: 0.9005 (mmp) REVERT: o 93 GLN cc_start: 0.9134 (tt0) cc_final: 0.8344 (tp40) REVERT: o 105 GLU cc_start: 0.9044 (tp30) cc_final: 0.8713 (tp30) REVERT: o 120 MET cc_start: 0.8180 (mtt) cc_final: 0.7976 (mtt) REVERT: p 59 LYS cc_start: 0.9443 (tppt) cc_final: 0.9134 (tppp) REVERT: p 84 MET cc_start: 0.9129 (tpp) cc_final: 0.8601 (tpp) REVERT: p 93 GLN cc_start: 0.9254 (tm-30) cc_final: 0.8810 (tm-30) REVERT: q 90 ASP cc_start: 0.9059 (t70) cc_final: 0.8779 (t70) REVERT: q 94 ASN cc_start: 0.9281 (t0) cc_final: 0.8835 (m-40) REVERT: q 104 GLN cc_start: 0.8831 (mm-40) cc_final: 0.8220 (mm-40) REVERT: r 57 LYS cc_start: 0.9559 (mtpt) cc_final: 0.9289 (ttmm) REVERT: s 107 ASN cc_start: 0.8380 (t0) cc_final: 0.8019 (t0) outliers start: 20 outliers final: 11 residues processed: 150 average time/residue: 0.2643 time to fit residues: 57.2516 Evaluate side-chains 143 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain k residue 100 LEU Chi-restraints excluded: chain m residue 16 THR Chi-restraints excluded: chain m residue 24 GLN Chi-restraints excluded: chain m residue 114 VAL Chi-restraints excluded: chain n residue 44 VAL Chi-restraints excluded: chain o residue 51 ILE Chi-restraints excluded: chain o residue 80 THR 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 r residue 82 HIS Chi-restraints excluded: chain s residue 92 LEU Chi-restraints excluded: chain s residue 93 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14386 Z= 0.228 Angle : 0.640 12.691 20853 Z= 0.366 Chirality : 0.035 0.202 2376 Planarity : 0.004 0.059 1478 Dihedral : 31.526 179.547 4581 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.28), residues: 825 helix: 1.99 (0.20), residues: 586 sheet: -1.68 (1.78), residues: 10 loop : -0.97 (0.37), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS p 75 PHE 0.011 0.001 PHE k 67 TYR 0.018 0.001 TYR q 57 ARG 0.004 0.000 ARG r 33 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 50 GLU cc_start: 0.9503 (mt-10) cc_final: 0.9109 (mt-10) REVERT: k 106 ASP cc_start: 0.9027 (m-30) cc_final: 0.8641 (m-30) REVERT: k 108 ASN cc_start: 0.9721 (t0) cc_final: 0.9517 (t0) REVERT: k 120 MET cc_start: 0.8690 (mtm) cc_final: 0.7879 (mtt) REVERT: l 52 GLU cc_start: 0.8589 (pm20) cc_final: 0.7880 (pm20) REVERT: l 53 GLU cc_start: 0.8490 (pm20) cc_final: 0.8093 (pm20) REVERT: l 79 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8862 (pttm) REVERT: l 84 MET cc_start: 0.9012 (tpp) cc_final: 0.8479 (tpp) REVERT: n 51 ASP cc_start: 0.9074 (p0) cc_final: 0.8807 (p0) REVERT: n 93 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8631 (mt-10) REVERT: n 108 LYS cc_start: 0.9596 (ptpp) cc_final: 0.9317 (ptpp) REVERT: n 113 GLU cc_start: 0.9337 (mm-30) cc_final: 0.9102 (mm-30) REVERT: o 51 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.9107 (mm) REVERT: o 93 GLN cc_start: 0.9096 (tt0) cc_final: 0.8336 (tp40) REVERT: o 105 GLU cc_start: 0.9092 (tp30) cc_final: 0.8845 (tp30) REVERT: p 45 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.7827 (mtm180) REVERT: p 59 LYS cc_start: 0.9413 (tppt) cc_final: 0.9086 (tppp) REVERT: p 84 MET cc_start: 0.9143 (tpp) cc_final: 0.8600 (tpp) REVERT: p 88 TYR cc_start: 0.8847 (m-80) cc_final: 0.8564 (m-80) REVERT: p 93 GLN cc_start: 0.9246 (tm-30) cc_final: 0.8775 (tm-30) REVERT: q 38 ASN cc_start: 0.8356 (m110) cc_final: 0.7714 (p0) REVERT: q 90 ASP cc_start: 0.8924 (t70) cc_final: 0.8666 (t70) REVERT: q 94 ASN cc_start: 0.9228 (t0) cc_final: 0.8814 (m-40) REVERT: q 104 GLN cc_start: 0.8884 (mm-40) cc_final: 0.8666 (mm-40) REVERT: r 83 TYR cc_start: 0.8699 (t80) cc_final: 0.8457 (t80) REVERT: r 85 LYS cc_start: 0.9705 (mmmm) cc_final: 0.9441 (mmmm) REVERT: r 93 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8706 (mm-30) REVERT: s 107 ASN cc_start: 0.8485 (t0) cc_final: 0.8096 (t0) outliers start: 15 outliers final: 9 residues processed: 156 average time/residue: 0.2832 time to fit residues: 62.6123 Evaluate side-chains 149 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 79 LYS Chi-restraints excluded: chain m residue 16 THR Chi-restraints excluded: chain m residue 24 GLN Chi-restraints excluded: chain m residue 114 VAL Chi-restraints excluded: chain o residue 51 ILE Chi-restraints excluded: chain o residue 80 THR Chi-restraints excluded: chain o residue 97 GLU Chi-restraints excluded: chain o residue 108 ASN Chi-restraints excluded: chain p residue 45 ARG Chi-restraints excluded: chain p residue 63 GLU 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 78 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 49 optimal weight: 0.0980 chunk 42 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 14386 Z= 0.283 Angle : 0.655 13.221 20853 Z= 0.374 Chirality : 0.035 0.193 2376 Planarity : 0.004 0.055 1478 Dihedral : 31.484 178.002 4581 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.30 % Allowed : 20.92 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.28), residues: 825 helix: 2.04 (0.21), residues: 584 sheet: -1.80 (1.75), residues: 10 loop : -0.92 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS p 75 PHE 0.009 0.001 PHE k 67 TYR 0.016 0.002 TYR q 57 ARG 0.003 0.000 ARG r 33 *********************** 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 143 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 50 GLU cc_start: 0.9504 (mt-10) cc_final: 0.9098 (mt-10) REVERT: k 73 GLU cc_start: 0.9313 (tt0) cc_final: 0.8775 (pt0) REVERT: k 104 PHE cc_start: 0.9365 (m-80) cc_final: 0.9136 (m-80) REVERT: k 120 MET cc_start: 0.8677 (mtm) cc_final: 0.7841 (mtt) REVERT: l 52 GLU cc_start: 0.8563 (pm20) cc_final: 0.7923 (pm20) REVERT: l 53 GLU cc_start: 0.8397 (pm20) cc_final: 0.8060 (pm20) REVERT: l 84 MET cc_start: 0.9011 (tpp) cc_final: 0.8471 (tpp) REVERT: n 51 ASP cc_start: 0.9137 (p0) cc_final: 0.8896 (p0) REVERT: n 108 LYS cc_start: 0.9595 (ptpp) cc_final: 0.9338 (ptpp) REVERT: n 113 GLU cc_start: 0.9360 (mm-30) cc_final: 0.9131 (mm-30) REVERT: o 51 ILE cc_start: 0.9350 (OUTLIER) cc_final: 0.9126 (mm) REVERT: o 59 GLU cc_start: 0.9414 (pm20) cc_final: 0.9110 (pm20) REVERT: o 93 GLN cc_start: 0.9081 (tt0) cc_final: 0.8267 (tp40) REVERT: o 105 GLU cc_start: 0.9078 (tp30) cc_final: 0.8821 (tp30) REVERT: p 59 LYS cc_start: 0.9414 (tppt) cc_final: 0.9088 (tppp) REVERT: p 84 MET cc_start: 0.9141 (tpp) cc_final: 0.8584 (tpp) REVERT: p 93 GLN cc_start: 0.9242 (tm-30) cc_final: 0.8788 (tm-30) REVERT: q 36 LYS cc_start: 0.9140 (mmtt) cc_final: 0.8917 (mmtm) REVERT: q 38 ASN cc_start: 0.8384 (m110) cc_final: 0.7734 (p0) REVERT: q 90 ASP cc_start: 0.8918 (t70) cc_final: 0.8662 (t70) REVERT: q 94 ASN cc_start: 0.9253 (t0) cc_final: 0.8822 (m-40) REVERT: r 57 LYS cc_start: 0.9575 (mtpt) cc_final: 0.9334 (ttmm) REVERT: r 83 TYR cc_start: 0.8804 (t80) cc_final: 0.8555 (t80) REVERT: r 93 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8726 (mm-30) REVERT: s 107 ASN cc_start: 0.8474 (t0) cc_final: 0.8035 (t0) outliers start: 9 outliers final: 7 residues processed: 138 average time/residue: 0.2662 time to fit residues: 53.2622 Evaluate side-chains 138 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 16 THR Chi-restraints excluded: chain m residue 24 GLN Chi-restraints excluded: chain m residue 114 VAL Chi-restraints excluded: chain o residue 51 ILE Chi-restraints excluded: chain o residue 97 GLU Chi-restraints excluded: chain p residue 63 GLU Chi-restraints excluded: chain r residue 82 HIS Chi-restraints excluded: chain s residue 86 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.1980 chunk 68 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 108 ASN ** q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 14386 Z= 0.400 Angle : 0.708 14.048 20853 Z= 0.404 Chirality : 0.039 0.233 2376 Planarity : 0.005 0.053 1478 Dihedral : 31.820 176.991 4581 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.16 % Allowed : 21.21 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.28), residues: 825 helix: 1.94 (0.20), residues: 584 sheet: -2.21 (1.72), residues: 10 loop : -0.99 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS p 75 PHE 0.012 0.002 PHE k 104 TYR 0.015 0.002 TYR q 57 ARG 0.006 0.001 ARG n 31 *********************** 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 144 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 50 GLU cc_start: 0.9509 (mt-10) cc_final: 0.9063 (mt-10) REVERT: k 93 GLN cc_start: 0.9314 (tt0) cc_final: 0.8933 (tp40) REVERT: k 120 MET cc_start: 0.8649 (mtm) cc_final: 0.7739 (mtt) REVERT: l 52 GLU cc_start: 0.8572 (pm20) cc_final: 0.7912 (pm20) REVERT: l 53 GLU cc_start: 0.8427 (pm20) cc_final: 0.8086 (pm20) REVERT: l 79 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8793 (pttm) REVERT: l 84 MET cc_start: 0.8979 (tpp) cc_final: 0.8460 (tpp) REVERT: n 34 LYS cc_start: 0.8954 (mmtt) cc_final: 0.8744 (mmtt) REVERT: n 93 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8653 (mt-10) REVERT: n 113 GLU cc_start: 0.9395 (mm-30) cc_final: 0.9118 (mm-30) REVERT: o 51 ILE cc_start: 0.9372 (OUTLIER) cc_final: 0.9166 (mm) REVERT: o 93 GLN cc_start: 0.9106 (tt0) cc_final: 0.8365 (tp40) REVERT: o 105 GLU cc_start: 0.9082 (tp30) cc_final: 0.8789 (tp30) REVERT: p 45 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8224 (ttp80) REVERT: p 59 LYS cc_start: 0.9407 (tppt) cc_final: 0.9073 (tppp) REVERT: p 84 MET cc_start: 0.9146 (tpp) cc_final: 0.8634 (tpp) REVERT: p 93 GLN cc_start: 0.9238 (tm-30) cc_final: 0.8782 (tm-30) REVERT: q 36 LYS cc_start: 0.9154 (mmtt) cc_final: 0.8826 (mmtm) REVERT: q 95 LYS cc_start: 0.9367 (mmtt) cc_final: 0.8942 (mtpp) REVERT: r 57 LYS cc_start: 0.9570 (mtpt) cc_final: 0.9358 (ttmm) REVERT: r 83 TYR cc_start: 0.8978 (t80) cc_final: 0.8778 (t80) REVERT: r 93 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8667 (mm-30) REVERT: s 107 ASN cc_start: 0.8565 (t0) cc_final: 0.8127 (t0) outliers start: 15 outliers final: 10 residues processed: 137 average time/residue: 0.2915 time to fit residues: 56.1886 Evaluate side-chains 136 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 79 LYS Chi-restraints excluded: chain m residue 16 THR Chi-restraints excluded: chain m residue 24 GLN Chi-restraints excluded: chain m residue 114 VAL Chi-restraints excluded: chain o residue 51 ILE Chi-restraints excluded: chain o residue 56 LYS Chi-restraints excluded: chain o residue 97 GLU Chi-restraints excluded: chain o residue 108 ASN Chi-restraints excluded: chain p residue 45 ARG Chi-restraints excluded: chain p residue 63 GLU Chi-restraints excluded: chain r residue 82 HIS Chi-restraints excluded: chain r residue 94 ILE Chi-restraints excluded: chain s residue 86 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 89 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14386 Z= 0.243 Angle : 0.674 14.795 20853 Z= 0.380 Chirality : 0.036 0.179 2376 Planarity : 0.004 0.053 1478 Dihedral : 31.731 179.770 4581 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.59 % Allowed : 21.36 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.28), residues: 825 helix: 2.00 (0.21), residues: 584 sheet: -2.26 (1.66), residues: 10 loop : -0.93 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS p 75 PHE 0.010 0.001 PHE k 67 TYR 0.012 0.001 TYR q 57 ARG 0.003 0.000 ARG r 33 *********************** 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 148 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 50 GLU cc_start: 0.9503 (mt-10) cc_final: 0.9056 (mt-10) REVERT: k 73 GLU cc_start: 0.9209 (tt0) cc_final: 0.8734 (pt0) REVERT: k 93 GLN cc_start: 0.9225 (tt0) cc_final: 0.8822 (tp40) REVERT: k 104 PHE cc_start: 0.9393 (m-80) cc_final: 0.9180 (m-80) REVERT: k 105 GLU cc_start: 0.9002 (pp20) cc_final: 0.8483 (pp20) REVERT: k 106 ASP cc_start: 0.9049 (m-30) cc_final: 0.8714 (m-30) REVERT: k 120 MET cc_start: 0.8574 (mtm) cc_final: 0.7749 (mtt) REVERT: l 52 GLU cc_start: 0.8578 (pm20) cc_final: 0.7967 (pm20) REVERT: l 53 GLU cc_start: 0.8419 (pm20) cc_final: 0.8145 (pm20) REVERT: l 79 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8781 (pttm) REVERT: l 84 MET cc_start: 0.9028 (tpp) cc_final: 0.8454 (tpp) REVERT: m 64 GLU cc_start: 0.9422 (tm-30) cc_final: 0.9169 (pp20) REVERT: n 34 LYS cc_start: 0.9016 (mmtt) cc_final: 0.8776 (mmtt) REVERT: n 93 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8666 (mt-10) REVERT: n 108 LYS cc_start: 0.9591 (ptpp) cc_final: 0.9356 (ptpp) REVERT: n 113 GLU cc_start: 0.9388 (mm-30) cc_final: 0.9115 (mm-30) REVERT: o 93 GLN cc_start: 0.9021 (tt0) cc_final: 0.8252 (tp40) REVERT: o 105 GLU cc_start: 0.9041 (tp30) cc_final: 0.8777 (tp30) REVERT: p 59 LYS cc_start: 0.9405 (tppt) cc_final: 0.9079 (tppp) REVERT: p 84 MET cc_start: 0.9157 (tpp) cc_final: 0.8503 (tpp) REVERT: p 93 GLN cc_start: 0.9238 (tm-30) cc_final: 0.8760 (tm-30) REVERT: q 36 LYS cc_start: 0.9187 (mmtt) cc_final: 0.8864 (mmtm) REVERT: q 38 ASN cc_start: 0.8375 (m110) cc_final: 0.7713 (p0) REVERT: r 57 LYS cc_start: 0.9558 (mtpt) cc_final: 0.9316 (ttmm) REVERT: r 83 TYR cc_start: 0.8901 (t80) cc_final: 0.8462 (t80) REVERT: r 85 LYS cc_start: 0.9724 (mmmm) cc_final: 0.9494 (mmmm) REVERT: r 93 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8681 (mm-30) REVERT: s 107 ASN cc_start: 0.8554 (t0) cc_final: 0.8165 (t0) outliers start: 11 outliers final: 7 residues processed: 142 average time/residue: 0.2847 time to fit residues: 57.5596 Evaluate side-chains 136 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 79 LYS Chi-restraints excluded: chain m residue 16 THR Chi-restraints excluded: chain m residue 24 GLN Chi-restraints excluded: chain m residue 114 VAL Chi-restraints excluded: chain o residue 97 GLU Chi-restraints excluded: chain p residue 63 GLU Chi-restraints excluded: chain r residue 82 HIS Chi-restraints excluded: chain s residue 86 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 108 ASN ** q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.120 14386 Z= 0.332 Angle : 0.701 14.714 20853 Z= 0.396 Chirality : 0.037 0.180 2376 Planarity : 0.005 0.051 1478 Dihedral : 31.700 178.770 4581 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.44 % Allowed : 22.22 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.29), residues: 825 helix: 1.97 (0.21), residues: 586 sheet: -2.50 (1.62), residues: 10 loop : -0.95 (0.39), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS p 75 PHE 0.009 0.001 PHE q 25 TYR 0.012 0.002 TYR q 57 ARG 0.005 0.000 ARG p 39 ********************** 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 136 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 1.031 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: 0.9509 (mt-10) cc_final: 0.9059 (mt-10) REVERT: k 93 GLN cc_start: 0.9199 (tt0) cc_final: 0.8868 (tp40) REVERT: k 120 MET cc_start: 0.8645 (mtm) cc_final: 0.7758 (mtt) REVERT: l 52 GLU cc_start: 0.8551 (pm20) cc_final: 0.7949 (pm20) REVERT: l 53 GLU cc_start: 0.8422 (pm20) cc_final: 0.8146 (pm20) REVERT: l 79 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8784 (pttm) REVERT: l 84 MET cc_start: 0.9011 (tpp) cc_final: 0.8461 (tpp) REVERT: m 64 GLU cc_start: 0.9439 (tm-30) cc_final: 0.9186 (pp20) REVERT: n 34 LYS cc_start: 0.9039 (mmtt) cc_final: 0.8752 (mmtt) REVERT: n 71 GLU cc_start: 0.9053 (tp30) cc_final: 0.8852 (tp30) REVERT: n 108 LYS cc_start: 0.9582 (ptpp) cc_final: 0.9358 (ptpp) REVERT: n 113 GLU cc_start: 0.9397 (mm-30) cc_final: 0.9121 (mm-30) REVERT: o 93 GLN cc_start: 0.9028 (tt0) cc_final: 0.8294 (tp40) REVERT: o 105 GLU cc_start: 0.9102 (tp30) cc_final: 0.8818 (tp30) REVERT: p 59 LYS cc_start: 0.9400 (tppt) cc_final: 0.9076 (tppp) REVERT: p 84 MET cc_start: 0.9160 (tpp) cc_final: 0.8502 (tpp) REVERT: p 93 GLN cc_start: 0.9241 (tm-30) cc_final: 0.8793 (tm-30) REVERT: q 36 LYS cc_start: 0.9192 (mmtt) cc_final: 0.8870 (mmtm) REVERT: q 38 ASN cc_start: 0.8379 (m110) cc_final: 0.7764 (p0) REVERT: q 95 LYS cc_start: 0.9337 (mmtt) cc_final: 0.8868 (mtpp) REVERT: r 57 LYS cc_start: 0.9558 (mtpt) cc_final: 0.9319 (ttmm) REVERT: r 83 TYR cc_start: 0.8951 (t80) cc_final: 0.8577 (t80) REVERT: r 85 LYS cc_start: 0.9747 (mmmm) cc_final: 0.9473 (mmmm) REVERT: r 93 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8695 (mm-30) REVERT: s 107 ASN cc_start: 0.8642 (t0) cc_final: 0.8252 (t0) outliers start: 10 outliers final: 8 residues processed: 131 average time/residue: 0.2787 time to fit residues: 52.3180 Evaluate side-chains 134 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 79 LYS Chi-restraints excluded: chain m residue 16 THR Chi-restraints excluded: chain m residue 24 GLN Chi-restraints excluded: chain m residue 114 VAL 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 r residue 82 HIS Chi-restraints excluded: chain s residue 86 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 88 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 108 ASN ** r 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.029189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2486 r_free = 0.2486 target = 0.021639 restraints weight = 136471.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.022436 restraints weight = 66535.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.022969 restraints weight = 42609.108| |-----------------------------------------------------------------------------| r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 14386 Z= 0.232 Angle : 0.679 15.154 20853 Z= 0.380 Chirality : 0.035 0.206 2376 Planarity : 0.004 0.050 1478 Dihedral : 31.627 179.148 4581 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.44 % Allowed : 21.79 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.29), residues: 825 helix: 2.05 (0.21), residues: 584 sheet: -2.49 (1.66), residues: 10 loop : -0.87 (0.39), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS p 75 PHE 0.010 0.001 PHE k 67 TYR 0.011 0.001 TYR p 51 ARG 0.006 0.000 ARG p 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2152.02 seconds wall clock time: 40 minutes 34.09 seconds (2434.09 seconds total)