Starting phenix.real_space_refine on Fri Feb 16 14:47:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf3_13366/02_2024/7pf3_13366.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf3_13366/02_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf3_13366/02_2024/7pf3_13366.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf3_13366/02_2024/7pf3_13366.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf3_13366/02_2024/7pf3_13366.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf3_13366/02_2024/7pf3_13366.pdb" } 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 Residue "k GLU 94": "OE1" <-> "OE2" Residue "k GLU 97": "OE1" <-> "OE2" Residue "k PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 92": "OE1" <-> "OE2" Residue "n GLU 35": "OE1" <-> "OE2" Residue "n ASP 51": "OD1" <-> "OD2" Residue "o GLU 94": "OE1" <-> "OE2" Residue "o GLU 133": "OE1" <-> "OE2" Residue "p GLU 53": "OE1" <-> "OE2" Residue "p TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 76": "OE1" <-> "OE2" Residue "s GLU 41": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 7.20, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 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: 7.60 Conformation dependent library (CDL) restraints added in 1.4 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: 6.40 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: 5.76 Time building geometry restraints manager: 7.95 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: 95.64 - 103.04: 676 103.04 - 110.43: 5823 110.43 - 117.83: 5895 117.83 - 125.23: 7327 125.23 - 132.63: 1132 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 2.440 nonbonded pdb=" OH TYR m 39 " pdb=" OE1 GLU n 71 " model vdw 2.271 2.440 nonbonded pdb=" NH1 ARG p 35 " pdb=" OP2 DC I 663 " model vdw 2.273 2.520 nonbonded pdb=" OD2 ASP p 68 " pdb=" NH2 ARG p 92 " model vdw 2.308 2.520 nonbonded pdb=" NH1 ARG m 42 " pdb=" OG1 THR n 88 " model vdw 2.320 2.520 ... (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 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: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 6.210 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 44.120 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.550 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 1 poor density : 185 time to evaluate : 0.994 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: 0.2954 time to fit residues: 75.4259 Evaluate side-chains 141 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.082 ------------------------------------------------------------------------------- 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: 5.9990 chunk 84 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 44 optimal weight: 0.2980 chunk 87 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 49 HIS ** n 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14386 Z= 0.257 Angle : 0.657 9.994 20853 Z= 0.384 Chirality : 0.036 0.153 2376 Planarity : 0.005 0.055 1478 Dihedral : 32.261 179.875 4581 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.73 % Allowed : 9.52 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.93 (0.28), residues: 825 helix: 1.30 (0.21), residues: 584 sheet: -2.58 (1.42), residues: 10 loop : -0.90 (0.34), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS p 75 PHE 0.022 0.001 PHE r 65 TYR 0.021 0.002 TYR p 88 ARG 0.007 0.000 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 171 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 159 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 50 GLU cc_start: 0.9435 (mt-10) cc_final: 0.8905 (mt-10) REVERT: k 120 MET cc_start: 0.8703 (mtm) cc_final: 0.7846 (mtt) REVERT: l 59 LYS cc_start: 0.9495 (tttp) cc_final: 0.9048 (ttpp) REVERT: l 63 GLU cc_start: 0.9222 (pt0) cc_final: 0.8963 (pt0) REVERT: l 84 MET cc_start: 0.8563 (tpp) cc_final: 0.8191 (tpp) REVERT: n 51 ASP cc_start: 0.9064 (p0) cc_final: 0.8758 (p0) REVERT: n 68 ASP cc_start: 0.9534 (t70) cc_final: 0.9305 (t70) REVERT: n 113 GLU cc_start: 0.9316 (mm-30) cc_final: 0.9004 (mm-30) REVERT: n 116 LYS cc_start: 0.9505 (mtmm) cc_final: 0.9141 (ptpp) REVERT: o 60 LEU cc_start: 0.9011 (mt) cc_final: 0.8807 (mt) REVERT: o 90 MET cc_start: 0.9384 (mmp) cc_final: 0.8973 (mmm) REVERT: o 93 GLN cc_start: 0.9197 (tt0) cc_final: 0.8389 (tp40) REVERT: o 105 GLU cc_start: 0.9036 (tp30) cc_final: 0.8792 (tp30) REVERT: p 59 LYS cc_start: 0.9489 (tppt) cc_final: 0.9124 (tppt) REVERT: p 63 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8655 (pm20) REVERT: p 85 ASP cc_start: 0.8954 (m-30) cc_final: 0.8594 (m-30) REVERT: p 93 GLN cc_start: 0.9060 (tm-30) cc_final: 0.8693 (tm-30) REVERT: q 36 LYS cc_start: 0.9143 (mmtt) cc_final: 0.8919 (mmtt) REVERT: q 92 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8260 (mt-10) REVERT: q 104 GLN cc_start: 0.8838 (mm-40) cc_final: 0.8567 (mm-40) REVERT: r 106 LEU cc_start: 0.9729 (mt) cc_final: 0.9471 (mt) REVERT: s 51 LYS cc_start: 0.5171 (OUTLIER) cc_final: 0.4344 (mmmt) REVERT: s 107 ASN cc_start: 0.8145 (t0) cc_final: 0.7910 (t0) outliers start: 12 outliers final: 7 residues processed: 166 average time/residue: 0.2711 time to fit residues: 63.8056 Evaluate side-chains 145 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 136 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain k residue 80 THR Chi-restraints excluded: chain k residue 124 ILE Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain n residue 44 VAL Chi-restraints excluded: chain o residue 96 SER 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 51 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 8.9990 chunk 31 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 109 optimal weight: 0.0870 chunk 89 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 overall best weight: 3.3964 ------------------------------------------------------------------------------- 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 l 75 HIS ** m 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 49 HIS ** o 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 14386 Z= 0.330 Angle : 0.658 9.598 20853 Z= 0.384 Chirality : 0.036 0.154 2376 Planarity : 0.005 0.055 1478 Dihedral : 31.966 177.640 4581 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.60 % Allowed : 14.43 % Favored : 82.97 % 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: 1.48 (0.28), residues: 825 helix: 1.78 (0.21), residues: 584 sheet: -2.45 (1.54), residues: 10 loop : -0.92 (0.35), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS l 75 PHE 0.008 0.001 PHE l 100 TYR 0.016 0.002 TYR q 57 ARG 0.005 0.001 ARG p 39 *********************** 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 166 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 148 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: k 50 GLU cc_start: 0.9470 (mt-10) cc_final: 0.8955 (mt-10) REVERT: k 120 MET cc_start: 0.8773 (mtm) cc_final: 0.7931 (mtt) REVERT: l 25 ASN cc_start: 0.8796 (OUTLIER) cc_final: 0.7750 (t0) REVERT: l 59 LYS cc_start: 0.9505 (tttp) cc_final: 0.9025 (ttpp) REVERT: l 84 MET cc_start: 0.8729 (tpp) cc_final: 0.8332 (tpp) REVERT: n 68 ASP cc_start: 0.9541 (t70) cc_final: 0.9318 (t70) REVERT: n 113 GLU cc_start: 0.9314 (mm-30) cc_final: 0.9075 (mm-30) REVERT: o 51 ILE cc_start: 0.9465 (OUTLIER) cc_final: 0.9215 (mm) REVERT: o 93 GLN cc_start: 0.9193 (tt0) cc_final: 0.8335 (tp40) REVERT: o 105 GLU cc_start: 0.9035 (tp30) cc_final: 0.8731 (tp30) REVERT: p 59 LYS cc_start: 0.9449 (tppt) cc_final: 0.8675 (tppp) REVERT: p 63 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8432 (mp0) REVERT: p 93 GLN cc_start: 0.9212 (tm-30) cc_final: 0.8863 (tm-30) REVERT: q 104 GLN cc_start: 0.8948 (mm-40) cc_final: 0.8693 (mm-40) REVERT: r 76 GLU cc_start: 0.9115 (tp30) cc_final: 0.8835 (tp30) REVERT: r 106 LEU cc_start: 0.9720 (mt) cc_final: 0.9450 (mp) outliers start: 18 outliers final: 9 residues processed: 160 average time/residue: 0.2761 time to fit residues: 63.9127 Evaluate side-chains 141 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 129 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain k residue 80 THR Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain k residue 96 SER Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 79 LYS Chi-restraints excluded: chain o residue 51 ILE Chi-restraints excluded: chain o residue 80 THR Chi-restraints excluded: chain o residue 96 SER 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 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: 4.9990 chunk 11 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 101 optimal weight: 6.9990 chunk 107 optimal weight: 30.0000 chunk 96 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2599 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= 0.246 Angle : 0.628 10.462 20853 Z= 0.366 Chirality : 0.035 0.196 2376 Planarity : 0.004 0.053 1478 Dihedral : 31.709 179.863 4581 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.73 % Allowed : 18.04 % Favored : 80.23 % 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: 1.99 (0.21), residues: 584 sheet: -2.18 (1.65), residues: 10 loop : -0.87 (0.36), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS l 75 PHE 0.009 0.001 PHE k 67 TYR 0.014 0.001 TYR l 98 ARG 0.004 0.000 ARG p 39 *********************** 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 161 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 149 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 50 GLU cc_start: 0.9481 (mt-10) cc_final: 0.8956 (mt-10) REVERT: k 90 MET cc_start: 0.9315 (mmm) cc_final: 0.8990 (mmm) REVERT: k 105 GLU cc_start: 0.9129 (pp20) cc_final: 0.8764 (pp20) REVERT: k 106 ASP cc_start: 0.9061 (m-30) cc_final: 0.8718 (m-30) REVERT: k 120 MET cc_start: 0.8713 (mtm) cc_final: 0.7821 (mtt) REVERT: l 84 MET cc_start: 0.8801 (tpp) cc_final: 0.8273 (tpp) REVERT: n 68 ASP cc_start: 0.9547 (t70) cc_final: 0.9339 (t0) REVERT: n 113 GLU cc_start: 0.9313 (mm-30) cc_final: 0.9072 (mm-30) REVERT: o 93 GLN cc_start: 0.9134 (tt0) cc_final: 0.8436 (tp40) REVERT: o 105 GLU cc_start: 0.9046 (tp30) cc_final: 0.8778 (tp30) REVERT: o 120 MET cc_start: 0.8179 (mtt) cc_final: 0.7960 (mtt) REVERT: p 59 LYS cc_start: 0.9449 (tppt) cc_final: 0.9131 (tppp) REVERT: p 84 MET cc_start: 0.9041 (tpp) cc_final: 0.8642 (tpp) REVERT: p 93 GLN cc_start: 0.9253 (tm-30) cc_final: 0.8840 (tm-30) REVERT: q 36 LYS cc_start: 0.9240 (mmtt) cc_final: 0.8924 (mmtm) REVERT: r 85 LYS cc_start: 0.9734 (mmmm) cc_final: 0.9503 (mmmm) outliers start: 12 outliers final: 11 residues processed: 155 average time/residue: 0.2577 time to fit residues: 57.2702 Evaluate side-chains 147 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 136 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain k residue 80 THR Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain k residue 92 LEU Chi-restraints excluded: chain l residue 79 LYS Chi-restraints excluded: chain m residue 114 VAL Chi-restraints excluded: chain o residue 96 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 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: 0.9980 overall best weight: 3.5986 ------------------------------------------------------------------------------- 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** ** q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 14386 Z= 0.346 Angle : 0.656 10.205 20853 Z= 0.382 Chirality : 0.036 0.155 2376 Planarity : 0.004 0.051 1478 Dihedral : 31.667 177.697 4581 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.74 % Allowed : 19.19 % 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 (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: 1.66 (0.28), residues: 825 helix: 1.93 (0.21), residues: 586 sheet: -1.98 (1.73), residues: 10 loop : -0.97 (0.36), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS p 75 PHE 0.008 0.001 PHE l 100 TYR 0.013 0.002 TYR r 83 ARG 0.004 0.000 ARG r 31 *********************** 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 159 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 140 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 50 GLU cc_start: 0.9482 (mt-10) cc_final: 0.8958 (mt-10) REVERT: k 105 GLU cc_start: 0.9107 (pp20) cc_final: 0.8722 (pp20) REVERT: k 106 ASP cc_start: 0.9044 (m-30) cc_final: 0.8671 (m-30) REVERT: k 120 MET cc_start: 0.8722 (mtm) cc_final: 0.7789 (mtt) REVERT: l 52 GLU cc_start: 0.8815 (pm20) cc_final: 0.8121 (pm20) REVERT: l 53 GLU cc_start: 0.8712 (pm20) cc_final: 0.8322 (pm20) REVERT: l 84 MET cc_start: 0.8863 (tpp) cc_final: 0.8376 (tpp) REVERT: n 68 ASP cc_start: 0.9544 (t70) cc_final: 0.9334 (t0) REVERT: n 108 LYS cc_start: 0.9603 (ptpp) cc_final: 0.9386 (ptpp) REVERT: n 113 GLU cc_start: 0.9355 (mm-30) cc_final: 0.9122 (mm-30) REVERT: o 51 ILE cc_start: 0.9425 (OUTLIER) cc_final: 0.9188 (mm) REVERT: o 93 GLN cc_start: 0.9148 (tt0) cc_final: 0.8403 (tp40) REVERT: p 59 LYS cc_start: 0.9441 (tppt) cc_final: 0.9120 (tppp) REVERT: p 84 MET cc_start: 0.9094 (tpp) cc_final: 0.8629 (tpp) REVERT: p 93 GLN cc_start: 0.9284 (tm-30) cc_final: 0.8876 (tm-30) REVERT: r 83 TYR cc_start: 0.8916 (t80) cc_final: 0.8610 (t80) outliers start: 19 outliers final: 12 residues processed: 151 average time/residue: 0.2688 time to fit residues: 58.0938 Evaluate side-chains 146 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 133 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain k residue 77 ASP Chi-restraints excluded: chain k residue 80 THR Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain k residue 92 LEU Chi-restraints excluded: chain k residue 96 SER Chi-restraints excluded: chain l residue 79 LYS Chi-restraints excluded: chain m residue 114 VAL Chi-restraints excluded: chain o residue 51 ILE Chi-restraints excluded: chain o residue 96 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 12 optimal weight: 0.0970 chunk 61 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** ** l 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 84 ASN ** 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: 0.8629 moved from start: 0.3250 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= 0.189 Angle : 0.630 12.619 20853 Z= 0.360 Chirality : 0.034 0.143 2376 Planarity : 0.004 0.054 1478 Dihedral : 31.425 179.061 4581 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.88 % Allowed : 21.50 % 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: 1.78 (0.29), residues: 825 helix: 1.98 (0.21), residues: 586 sheet: -1.92 (1.72), residues: 10 loop : -0.79 (0.37), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS k 113 PHE 0.008 0.001 PHE o 67 TYR 0.012 0.001 TYR l 98 ARG 0.005 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 166 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 153 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 50 GLU cc_start: 0.9484 (mt-10) cc_final: 0.8952 (mt-10) REVERT: k 90 MET cc_start: 0.9261 (mmm) cc_final: 0.8947 (mmm) REVERT: k 120 MET cc_start: 0.8700 (mtm) cc_final: 0.7884 (mtt) REVERT: l 52 GLU cc_start: 0.8758 (pm20) cc_final: 0.8075 (pm20) REVERT: l 53 GLU cc_start: 0.8549 (pm20) cc_final: 0.8167 (pm20) REVERT: l 84 MET cc_start: 0.8924 (tpp) cc_final: 0.8379 (tpp) REVERT: m 56 GLU cc_start: 0.9378 (tt0) cc_final: 0.8668 (tt0) REVERT: n 93 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8680 (mt-10) REVERT: n 113 GLU cc_start: 0.9343 (mm-30) cc_final: 0.9096 (mm-30) REVERT: o 51 ILE cc_start: 0.9387 (OUTLIER) cc_final: 0.9124 (mm) REVERT: o 93 GLN cc_start: 0.9040 (tt0) cc_final: 0.8353 (tp40) REVERT: o 105 GLU cc_start: 0.9121 (tp30) cc_final: 0.8914 (tp30) REVERT: p 59 LYS cc_start: 0.9399 (tppt) cc_final: 0.9062 (tppp) REVERT: p 84 MET cc_start: 0.9075 (tpp) cc_final: 0.8443 (tpp) REVERT: p 93 GLN cc_start: 0.9269 (tm-30) cc_final: 0.8801 (tm-30) REVERT: q 64 GLU cc_start: 0.9415 (tm-30) cc_final: 0.9209 (pp20) REVERT: r 57 LYS cc_start: 0.9475 (mtpt) cc_final: 0.9252 (ttmm) REVERT: r 83 TYR cc_start: 0.8682 (t80) cc_final: 0.8270 (t80) REVERT: r 85 LYS cc_start: 0.9749 (mmmm) cc_final: 0.9461 (mmmm) outliers start: 13 outliers final: 10 residues processed: 157 average time/residue: 0.2646 time to fit residues: 59.7567 Evaluate side-chains 148 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 137 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain k residue 92 LEU Chi-restraints excluded: chain l residue 79 LYS Chi-restraints excluded: chain m residue 16 THR Chi-restraints excluded: chain m residue 114 VAL Chi-restraints excluded: chain n residue 44 VAL Chi-restraints excluded: chain n residue 80 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 7.9990 chunk 60 optimal weight: 0.4980 chunk 90 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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** ** l 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 14386 Z= 0.197 Angle : 0.627 13.204 20853 Z= 0.358 Chirality : 0.033 0.208 2376 Planarity : 0.004 0.053 1478 Dihedral : 31.264 179.271 4581 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.16 % Allowed : 22.37 % Favored : 75.47 % 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: 1.75 (0.29), residues: 825 helix: 1.96 (0.21), residues: 586 sheet: -2.04 (1.72), residues: 10 loop : -0.79 (0.38), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS p 75 PHE 0.011 0.001 PHE k 104 TYR 0.011 0.001 TYR l 98 ARG 0.004 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 160 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 145 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 50 GLU cc_start: 0.9488 (mt-10) cc_final: 0.8949 (mt-10) REVERT: k 104 PHE cc_start: 0.9314 (m-80) cc_final: 0.9101 (m-80) REVERT: k 120 MET cc_start: 0.8656 (mtm) cc_final: 0.7742 (mtt) REVERT: l 23 ARG cc_start: 0.8128 (ptp90) cc_final: 0.7760 (pmt-80) REVERT: l 52 GLU cc_start: 0.8641 (pm20) cc_final: 0.7974 (pm20) REVERT: l 53 GLU cc_start: 0.8481 (pm20) cc_final: 0.8110 (pm20) REVERT: l 84 MET cc_start: 0.8915 (tpp) cc_final: 0.8349 (tpp) REVERT: m 56 GLU cc_start: 0.9383 (tt0) cc_final: 0.8876 (tt0) REVERT: n 93 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8718 (mt-10) REVERT: n 113 GLU cc_start: 0.9345 (mm-30) cc_final: 0.9106 (mm-30) REVERT: o 50 GLU cc_start: 0.9069 (OUTLIER) cc_final: 0.8551 (pp20) REVERT: o 51 ILE cc_start: 0.9392 (OUTLIER) cc_final: 0.9095 (mm) REVERT: o 93 GLN cc_start: 0.9034 (tt0) cc_final: 0.8308 (tp40) REVERT: p 59 LYS cc_start: 0.9411 (tppt) cc_final: 0.9051 (tppp) REVERT: p 84 MET cc_start: 0.9092 (tpp) cc_final: 0.8383 (tpp) REVERT: p 93 GLN cc_start: 0.9254 (tm-30) cc_final: 0.8793 (tm-30) REVERT: q 36 LYS cc_start: 0.9162 (mmtt) cc_final: 0.8912 (mmtt) REVERT: q 94 ASN cc_start: 0.8999 (m-40) cc_final: 0.8744 (m-40) REVERT: r 57 LYS cc_start: 0.9481 (mtpt) cc_final: 0.9246 (ttmm) REVERT: r 83 TYR cc_start: 0.8704 (t80) cc_final: 0.8279 (t80) REVERT: r 85 LYS cc_start: 0.9733 (mmmm) cc_final: 0.9449 (mmmm) outliers start: 15 outliers final: 9 residues processed: 154 average time/residue: 0.2675 time to fit residues: 58.8304 Evaluate side-chains 145 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 134 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain k residue 80 THR Chi-restraints excluded: chain k residue 92 LEU Chi-restraints excluded: chain l residue 79 LYS Chi-restraints excluded: chain m residue 16 THR Chi-restraints excluded: chain m residue 114 VAL Chi-restraints excluded: chain o residue 50 GLU Chi-restraints excluded: chain 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: 0.7980 chunk 20 optimal weight: 0.0000 chunk 68 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 52 optimal weight: 0.0970 chunk 9 optimal weight: 0.3980 chunk 84 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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** ** l 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14386 Z= 0.220 Angle : 0.645 13.749 20853 Z= 0.367 Chirality : 0.034 0.240 2376 Planarity : 0.004 0.053 1478 Dihedral : 31.241 179.331 4581 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.73 % Allowed : 23.23 % Favored : 75.04 % 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: 1.79 (0.29), residues: 825 helix: 1.98 (0.21), residues: 584 sheet: -2.11 (1.72), residues: 10 loop : -0.72 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS p 75 PHE 0.011 0.001 PHE q 25 TYR 0.034 0.001 TYR r 40 ARG 0.005 0.000 ARG r 33 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 140 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 50 GLU cc_start: 0.9490 (mt-10) cc_final: 0.8953 (mt-10) REVERT: k 90 MET cc_start: 0.9288 (mmm) cc_final: 0.8970 (mmm) REVERT: k 120 MET cc_start: 0.8955 (mtm) cc_final: 0.8072 (mtp) REVERT: l 23 ARG cc_start: 0.8066 (ptp90) cc_final: 0.7730 (pmt-80) REVERT: l 52 GLU cc_start: 0.8645 (pm20) cc_final: 0.7996 (pm20) REVERT: l 53 GLU cc_start: 0.8492 (pm20) cc_final: 0.8173 (pm20) REVERT: l 84 MET cc_start: 0.8931 (tpp) cc_final: 0.8354 (tpp) REVERT: m 56 GLU cc_start: 0.9379 (tt0) cc_final: 0.9055 (tt0) REVERT: n 93 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8719 (mt-10) REVERT: n 113 GLU cc_start: 0.9362 (mm-30) cc_final: 0.9125 (mm-30) REVERT: o 50 GLU cc_start: 0.9072 (OUTLIER) cc_final: 0.8547 (pp20) REVERT: o 51 ILE cc_start: 0.9400 (OUTLIER) cc_final: 0.9104 (mm) REVERT: o 93 GLN cc_start: 0.9055 (tt0) cc_final: 0.8380 (tp40) REVERT: p 59 LYS cc_start: 0.9401 (tppt) cc_final: 0.9058 (tppp) REVERT: p 84 MET cc_start: 0.9071 (tpp) cc_final: 0.8324 (tpp) REVERT: p 93 GLN cc_start: 0.9244 (tm-30) cc_final: 0.8791 (tm-30) REVERT: q 94 ASN cc_start: 0.9011 (m-40) cc_final: 0.8783 (m-40) REVERT: r 40 TYR cc_start: 0.8574 (m-80) cc_final: 0.8350 (m-10) REVERT: r 57 LYS cc_start: 0.9500 (mtpt) cc_final: 0.9258 (ttmm) REVERT: r 83 TYR cc_start: 0.8780 (t80) cc_final: 0.8346 (t80) outliers start: 12 outliers final: 8 residues processed: 146 average time/residue: 0.2612 time to fit residues: 54.7320 Evaluate side-chains 150 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 140 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain k residue 92 LEU Chi-restraints excluded: chain l residue 79 LYS Chi-restraints excluded: chain m residue 16 THR Chi-restraints excluded: chain m residue 114 VAL Chi-restraints excluded: chain o residue 50 GLU Chi-restraints excluded: chain 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 65 optimal weight: 0.3980 chunk 105 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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** ** l 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 14386 Z= 0.215 Angle : 0.649 14.895 20853 Z= 0.367 Chirality : 0.034 0.210 2376 Planarity : 0.004 0.052 1478 Dihedral : 31.219 179.519 4581 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.88 % Allowed : 22.66 % Favored : 75.47 % 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: 1.72 (0.29), residues: 825 helix: 1.92 (0.21), residues: 586 sheet: -2.14 (1.69), residues: 10 loop : -0.73 (0.38), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS p 75 PHE 0.019 0.001 PHE k 104 TYR 0.025 0.001 TYR r 40 ARG 0.006 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 152 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 139 time to evaluate : 1.027 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: 0.9491 (mt-10) cc_final: 0.8949 (mt-10) REVERT: k 90 MET cc_start: 0.9288 (mmm) cc_final: 0.9023 (mmm) REVERT: k 104 PHE cc_start: 0.9305 (m-80) cc_final: 0.9063 (m-80) REVERT: k 120 MET cc_start: 0.8919 (mtm) cc_final: 0.7968 (mtp) REVERT: l 23 ARG cc_start: 0.8076 (ptp90) cc_final: 0.7729 (pmt-80) REVERT: l 52 GLU cc_start: 0.8593 (pm20) cc_final: 0.7918 (pm20) REVERT: l 53 GLU cc_start: 0.8439 (pm20) cc_final: 0.8108 (pm20) REVERT: l 74 GLU cc_start: 0.9188 (pt0) cc_final: 0.8905 (mt-10) REVERT: l 84 MET cc_start: 0.8935 (tpp) cc_final: 0.8348 (tpp) REVERT: m 56 GLU cc_start: 0.9364 (tt0) cc_final: 0.9113 (tt0) REVERT: n 113 GLU cc_start: 0.9362 (mm-30) cc_final: 0.9126 (mm-30) REVERT: o 50 GLU cc_start: 0.9072 (OUTLIER) cc_final: 0.8542 (pp20) REVERT: o 51 ILE cc_start: 0.9384 (OUTLIER) cc_final: 0.9084 (mm) REVERT: o 90 MET cc_start: 0.9258 (mmm) cc_final: 0.8772 (mmm) REVERT: o 93 GLN cc_start: 0.9073 (tt0) cc_final: 0.8287 (tp40) REVERT: p 59 LYS cc_start: 0.9397 (tppt) cc_final: 0.9038 (tppp) REVERT: p 84 MET cc_start: 0.9039 (tpp) cc_final: 0.8239 (tpp) REVERT: p 93 GLN cc_start: 0.9231 (tm-30) cc_final: 0.8771 (tm-30) REVERT: q 94 ASN cc_start: 0.9014 (m-40) cc_final: 0.8741 (m-40) REVERT: r 57 LYS cc_start: 0.9518 (mtpt) cc_final: 0.9269 (ttmm) REVERT: r 83 TYR cc_start: 0.8751 (t80) cc_final: 0.8388 (t80) outliers start: 13 outliers final: 9 residues processed: 146 average time/residue: 0.2679 time to fit residues: 55.6708 Evaluate side-chains 145 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 134 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain k residue 92 LEU Chi-restraints excluded: chain l residue 79 LYS Chi-restraints excluded: chain m residue 16 THR Chi-restraints excluded: chain m residue 114 VAL Chi-restraints excluded: chain o residue 50 GLU Chi-restraints excluded: chain 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 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 50 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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** ** l 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 84 ASN ** 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: 0.8688 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 14386 Z= 0.341 Angle : 0.692 15.608 20853 Z= 0.394 Chirality : 0.037 0.199 2376 Planarity : 0.005 0.054 1478 Dihedral : 31.444 176.090 4581 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 20.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.02 % Allowed : 22.66 % Favored : 75.32 % 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: 1.67 (0.29), residues: 825 helix: 1.87 (0.21), residues: 586 sheet: -2.16 (1.68), residues: 10 loop : -0.72 (0.39), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS l 75 PHE 0.007 0.001 PHE l 100 TYR 0.011 0.002 TYR p 51 ARG 0.007 0.001 ARG r 33 ********************** 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 145 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 131 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 50 GLU cc_start: 0.9493 (mt-10) cc_final: 0.8968 (mt-10) REVERT: k 120 MET cc_start: 0.8965 (mtm) cc_final: 0.7979 (mtt) REVERT: l 23 ARG cc_start: 0.8042 (ptp90) cc_final: 0.7731 (pmt-80) REVERT: l 24 ASP cc_start: 0.8368 (t0) cc_final: 0.8156 (t0) REVERT: l 84 MET cc_start: 0.8948 (tpp) cc_final: 0.8396 (tpp) REVERT: m 56 GLU cc_start: 0.9384 (tt0) cc_final: 0.9153 (tt0) REVERT: n 34 LYS cc_start: 0.9411 (tppt) cc_final: 0.8937 (mmtt) REVERT: n 113 GLU cc_start: 0.9404 (mm-30) cc_final: 0.9132 (mm-30) REVERT: o 50 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.8588 (pp20) REVERT: o 51 ILE cc_start: 0.9406 (OUTLIER) cc_final: 0.9104 (mm) REVERT: o 93 GLN cc_start: 0.9141 (tt0) cc_final: 0.8401 (tp40) REVERT: p 59 LYS cc_start: 0.9418 (tppt) cc_final: 0.9063 (tppp) REVERT: p 84 MET cc_start: 0.9079 (tpp) cc_final: 0.8399 (tpp) REVERT: p 93 GLN cc_start: 0.9229 (tm-30) cc_final: 0.8800 (tm-30) REVERT: q 94 ASN cc_start: 0.9019 (m-40) cc_final: 0.8795 (m-40) REVERT: r 57 LYS cc_start: 0.9540 (mtpt) cc_final: 0.9282 (ttmm) REVERT: r 83 TYR cc_start: 0.8983 (t80) cc_final: 0.8616 (t80) outliers start: 14 outliers final: 8 residues processed: 138 average time/residue: 0.2747 time to fit residues: 54.2656 Evaluate side-chains 136 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 126 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 79 LYS Chi-restraints excluded: chain m residue 16 THR Chi-restraints excluded: chain m residue 114 VAL Chi-restraints excluded: chain o residue 50 GLU Chi-restraints excluded: chain o residue 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 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 81 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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** ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.029102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2480 r_free = 0.2480 target = 0.021489 restraints weight = 140417.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.022276 restraints weight = 69987.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.022771 restraints weight = 45509.688| |-----------------------------------------------------------------------------| r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 14386 Z= 0.294 Angle : 0.680 15.540 20853 Z= 0.385 Chirality : 0.036 0.201 2376 Planarity : 0.005 0.062 1478 Dihedral : 31.509 179.911 4581 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.88 % Allowed : 22.80 % Favored : 75.32 % 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: 1.61 (0.29), residues: 825 helix: 1.80 (0.21), residues: 586 sheet: -2.12 (1.66), residues: 10 loop : -0.66 (0.40), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS p 75 PHE 0.008 0.001 PHE q 25 TYR 0.010 0.001 TYR p 51 ARG 0.008 0.000 ARG r 33 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2096.51 seconds wall clock time: 39 minutes 34.38 seconds (2374.38 seconds total)