Starting phenix.real_space_refine on Sun Mar 10 20:06:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rtb_4996/03_2024/6rtb_4996.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rtb_4996/03_2024/6rtb_4996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rtb_4996/03_2024/6rtb_4996.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rtb_4996/03_2024/6rtb_4996.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rtb_4996/03_2024/6rtb_4996.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rtb_4996/03_2024/6rtb_4996.pdb" } resolution = 3.46 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 3 Type Number sf(0) Gaussians C 2895 2.51 5 N 829 2.21 5 O 957 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 35": "OE1" <-> "OE2" Residue "I GLU 20": "OE1" <-> "OE2" Residue "J GLU 20": "OE1" <-> "OE2" Residue "E GLU 35": "OE1" <-> "OE2" Residue "E GLU 46": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4681 Number of models: 1 Model: "" Number of chains: 10 Chain: "H" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 469 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain breaks: 2 Chain: "C" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 469 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain breaks: 2 Chain: "I" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 469 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain breaks: 2 Chain: "D" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 460 Classifications: {'peptide': 69} Link IDs: {'TRANS': 68} Chain breaks: 2 Chain: "J" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 469 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain breaks: 2 Chain: "E" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 469 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain breaks: 2 Chain: "G" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 469 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain breaks: 2 Chain: "B" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 469 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain breaks: 2 Chain: "F" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 469 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain breaks: 2 Chain: "A" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 469 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain breaks: 2 Time building chain proxies: 2.71, per 1000 atoms: 0.58 Number of scatterers: 4681 At special positions: 0 Unit cell: (104.24, 132.431, 41.9584, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 957 8.00 N 829 7.00 C 2895 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: 1.78 Conformation dependent library (CDL) restraints added in 902.1 milliseconds 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1178 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 15 sheets defined 0.0% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'J' and resid 15 through 17 removed outlier: 6.428A pdb=" N VAL H 15 " --> pdb=" O VAL G 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 37 through 43 removed outlier: 6.129A pdb=" N GLY I 36 " --> pdb=" O VAL J 37 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N TYR J 39 " --> pdb=" O GLY I 36 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU I 38 " --> pdb=" O TYR J 39 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N GLY J 41 " --> pdb=" O LEU I 38 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL I 40 " --> pdb=" O GLY J 41 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N LYS J 43 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N SER I 42 " --> pdb=" O LYS J 43 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL G 37 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N VAL F 40 " --> pdb=" O VAL G 37 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TYR G 39 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N SER F 42 " --> pdb=" O TYR G 39 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY G 41 " --> pdb=" O SER F 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 48 through 50 removed outlier: 6.537A pdb=" N VAL H 48 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL G 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 65 through 66 removed outlier: 6.779A pdb=" N ASN H 65 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASN G 65 " --> pdb=" O VAL F 66 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 70 through 72 removed outlier: 6.593A pdb=" N VAL G 71 " --> pdb=" O THR F 72 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 75 through 79 removed outlier: 6.403A pdb=" N ALA H 76 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N GLN G 79 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA H 78 " --> pdb=" O GLN G 79 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ALA G 76 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N GLN F 79 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA G 78 " --> pdb=" O GLN F 79 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 82 through 83 removed outlier: 6.722A pdb=" N VAL H 82 " --> pdb=" O GLU G 83 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL G 82 " --> pdb=" O GLU F 83 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 89 through 91 removed outlier: 6.262A pdb=" N ALA H 89 " --> pdb=" O ALA I 90 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA I 89 " --> pdb=" O ALA J 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 15 through 17 removed outlier: 6.424A pdb=" N VAL C 15 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL B 15 " --> pdb=" O VAL A 16 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 37 through 43 removed outlier: 6.463A pdb=" N LEU D 38 " --> pdb=" O TYR E 39 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N GLY E 41 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL D 40 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N LYS E 43 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N SER D 42 " --> pdb=" O LYS E 43 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU C 38 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N GLY D 41 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL C 40 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N LYS D 43 " --> pdb=" O VAL C 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 47 through 52 removed outlier: 6.859A pdb=" N VAL E 52 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL D 52 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL C 48 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N GLY B 51 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N HIS C 50 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL B 48 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N GLY A 51 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N HIS B 50 " --> pdb=" O GLY A 51 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 70 through 72 removed outlier: 6.196A pdb=" N VAL D 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL C 70 " --> pdb=" O VAL D 71 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 75 through 79 removed outlier: 6.346A pdb=" N THR D 75 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ALA E 78 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL D 77 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N THR C 75 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ALA D 78 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL C 77 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 88 through 89 removed outlier: 6.494A pdb=" N SER C 87 " --> pdb=" O ILE D 88 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 89 through 90 79 hydrogen bonds defined for protein. 237 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.09 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 837 1.29 - 1.35: 733 1.35 - 1.42: 127 1.42 - 1.49: 864 1.49 - 1.56: 2110 Bond restraints: 4671 Sorted by residual: bond pdb=" CB VAL G 16 " pdb=" CG2 VAL G 16 " ideal model delta sigma weight residual 1.521 1.443 0.078 3.30e-02 9.18e+02 5.57e+00 bond pdb=" N ALA C 19 " pdb=" CA ALA C 19 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.29e-02 6.01e+03 4.59e+00 bond pdb=" CA THR D 92 " pdb=" CB THR D 92 " ideal model delta sigma weight residual 1.534 1.497 0.037 1.78e-02 3.16e+03 4.32e+00 bond pdb=" N ALA B 19 " pdb=" CA ALA B 19 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.29e-02 6.01e+03 4.29e+00 bond pdb=" CB VAL F 16 " pdb=" CG1 VAL F 16 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.16e+00 ... (remaining 4666 not shown) Histogram of bond angle deviations from ideal: 101.49 - 107.52: 148 107.52 - 113.56: 2824 113.56 - 119.59: 1154 119.59 - 125.62: 2126 125.62 - 131.66: 36 Bond angle restraints: 6288 Sorted by residual: angle pdb=" N VAL E 74 " pdb=" CA VAL E 74 " pdb=" C VAL E 74 " ideal model delta sigma weight residual 112.96 104.63 8.33 1.00e+00 1.00e+00 6.94e+01 angle pdb=" CG1 VAL G 16 " pdb=" CB VAL G 16 " pdb=" CG2 VAL G 16 " ideal model delta sigma weight residual 110.80 101.49 9.31 2.20e+00 2.07e-01 1.79e+01 angle pdb=" CG1 VAL H 16 " pdb=" CB VAL H 16 " pdb=" CG2 VAL H 16 " ideal model delta sigma weight residual 110.80 101.54 9.26 2.20e+00 2.07e-01 1.77e+01 angle pdb=" C ALA F 18 " pdb=" N ALA F 19 " pdb=" CA ALA F 19 " ideal model delta sigma weight residual 121.54 129.41 -7.87 1.91e+00 2.74e-01 1.70e+01 angle pdb=" C ALA C 18 " pdb=" N ALA C 19 " pdb=" CA ALA C 19 " ideal model delta sigma weight residual 121.54 129.21 -7.67 1.91e+00 2.74e-01 1.61e+01 ... (remaining 6283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.64: 2404 16.64 - 33.29: 265 33.29 - 49.93: 50 49.93 - 66.58: 8 66.58 - 83.22: 7 Dihedral angle restraints: 2734 sinusoidal: 877 harmonic: 1857 Sorted by residual: dihedral pdb=" CA ALA G 19 " pdb=" C ALA G 19 " pdb=" N GLU G 20 " pdb=" CA GLU G 20 " ideal model delta harmonic sigma weight residual 180.00 113.95 66.05 0 5.00e+00 4.00e-02 1.74e+02 dihedral pdb=" CA ALA C 19 " pdb=" C ALA C 19 " pdb=" N GLU C 20 " pdb=" CA GLU C 20 " ideal model delta harmonic sigma weight residual 180.00 128.01 51.99 0 5.00e+00 4.00e-02 1.08e+02 dihedral pdb=" CA ALA I 19 " pdb=" C ALA I 19 " pdb=" N GLU I 20 " pdb=" CA GLU I 20 " ideal model delta harmonic sigma weight residual 180.00 128.78 51.22 0 5.00e+00 4.00e-02 1.05e+02 ... (remaining 2731 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 494 0.057 - 0.115: 260 0.115 - 0.172: 68 0.172 - 0.230: 10 0.230 - 0.287: 7 Chirality restraints: 839 Sorted by residual: chirality pdb=" CB THR I 81 " pdb=" CA THR I 81 " pdb=" OG1 THR I 81 " pdb=" CG2 THR I 81 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB THR B 92 " pdb=" CA THR B 92 " pdb=" OG1 THR B 92 " pdb=" CG2 THR B 92 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB THR D 92 " pdb=" CA THR D 92 " pdb=" OG1 THR D 92 " pdb=" CG2 THR D 92 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 836 not shown) Planarity restraints: 778 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA G 18 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.04e+00 pdb=" C ALA G 18 " 0.042 2.00e-02 2.50e+03 pdb=" O ALA G 18 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA G 19 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA J 19 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.65e+00 pdb=" C ALA J 19 " 0.041 2.00e-02 2.50e+03 pdb=" O ALA J 19 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU J 20 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA F 18 " 0.011 2.00e-02 2.50e+03 2.31e-02 5.32e+00 pdb=" C ALA F 18 " -0.040 2.00e-02 2.50e+03 pdb=" O ALA F 18 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA F 19 " 0.013 2.00e-02 2.50e+03 ... (remaining 775 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 141 2.68 - 3.23: 3871 3.23 - 3.79: 6452 3.79 - 4.34: 8026 4.34 - 4.90: 15387 Nonbonded interactions: 33877 Sorted by model distance: nonbonded pdb=" OG SER G 87 " pdb=" O ALA F 18 " model vdw 2.122 2.440 nonbonded pdb=" O SER E 9 " pdb=" OG SER E 9 " model vdw 2.294 2.440 nonbonded pdb=" O SER C 9 " pdb=" OG SER C 9 " model vdw 2.297 2.440 nonbonded pdb=" O SER B 9 " pdb=" OG SER B 9 " model vdw 2.299 2.440 nonbonded pdb=" O SER D 9 " pdb=" OG SER D 9 " model vdw 2.301 2.440 ... (remaining 33872 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 'A' and (resid 9 through 24 or resid 36 through 93)) selection = (chain 'B' and (resid 9 through 24 or resid 36 through 93)) selection = (chain 'C' and (resid 9 through 24 or resid 36 through 93)) selection = chain 'D' selection = (chain 'E' and (resid 9 through 24 or resid 36 through 93)) selection = (chain 'F' and (resid 9 through 24 or resid 36 through 93)) selection = (chain 'G' and (resid 9 through 24 or resid 36 through 93)) selection = (chain 'H' and (resid 9 through 24 or resid 36 through 93)) selection = (chain 'I' and (resid 9 through 24 or resid 36 through 93)) selection = (chain 'J' and (resid 9 through 24 or resid 36 through 93)) } 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 individual isotropic 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: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.650 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 16.570 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 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 : 0.009 0.078 4671 Z= 0.610 Angle : 1.226 9.311 6288 Z= 0.718 Chirality : 0.072 0.287 839 Planarity : 0.005 0.025 778 Dihedral : 15.078 83.221 1556 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.16 % Allowed : 18.94 % Favored : 80.91 % Rotamer: Outliers : 2.61 % Allowed : 11.33 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.94 % 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: -4.64 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.53 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS E 50 TYR 0.028 0.005 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: H 13 GLU cc_start: 0.6861 (mt-10) cc_final: 0.6179 (mp0) REVERT: C 43 LYS cc_start: 0.8320 (tttt) cc_final: 0.8085 (tttp) REVERT: I 13 GLU cc_start: 0.7516 (mt-10) cc_final: 0.6740 (tt0) REVERT: D 43 LYS cc_start: 0.8128 (tttt) cc_final: 0.7667 (mptt) REVERT: D 80 LYS cc_start: 0.8668 (mtpt) cc_final: 0.8183 (ttmt) REVERT: J 12 LYS cc_start: 0.7253 (mttt) cc_final: 0.5327 (tmtt) REVERT: J 13 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7571 (tt0) REVERT: J 46 GLU cc_start: 0.8331 (tm-30) cc_final: 0.7883 (tm-30) REVERT: J 83 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7619 (mp0) REVERT: G 13 GLU cc_start: 0.6893 (mt-10) cc_final: 0.6421 (mp0) REVERT: B 43 LYS cc_start: 0.8343 (tttt) cc_final: 0.8125 (tttp) REVERT: B 80 LYS cc_start: 0.8613 (mtpt) cc_final: 0.8200 (ttmt) REVERT: F 13 GLU cc_start: 0.6671 (mt-10) cc_final: 0.5959 (tt0) REVERT: F 24 GLN cc_start: 0.7623 (mt0) cc_final: 0.7284 (tm-30) REVERT: F 83 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6867 (mt-10) REVERT: A 80 LYS cc_start: 0.8559 (mtpt) cc_final: 0.8310 (ttmt) outliers start: 12 outliers final: 8 residues processed: 104 average time/residue: 0.1924 time to fit residues: 24.5259 Evaluate side-chains 91 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 83 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain A residue 15 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 0.0970 chunk 17 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 62 optimal weight: 8.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 ASN C 50 HIS C 62 GLN C 79 GLN ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 79 GLN D 79 GLN ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 GLN F 62 GLN A 50 HIS ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4671 Z= 0.235 Angle : 0.719 5.769 6288 Z= 0.403 Chirality : 0.051 0.139 839 Planarity : 0.002 0.018 778 Dihedral : 9.262 48.664 687 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.47 % Favored : 81.53 % Rotamer: Outliers : 6.97 % Allowed : 11.98 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.20 % 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: -4.38 (0.28), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 TYR 0.014 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 82 time to evaluate : 0.528 Fit side-chains REVERT: H 13 GLU cc_start: 0.6550 (mt-10) cc_final: 0.6226 (mp0) REVERT: C 80 LYS cc_start: 0.8218 (mtpt) cc_final: 0.7892 (ttmt) REVERT: C 92 THR cc_start: 0.7589 (p) cc_final: 0.7123 (p) REVERT: I 13 GLU cc_start: 0.7369 (mt-10) cc_final: 0.6720 (tt0) REVERT: D 43 LYS cc_start: 0.8121 (tttt) cc_final: 0.7608 (mptt) REVERT: D 80 LYS cc_start: 0.8478 (mtpt) cc_final: 0.7874 (mttp) REVERT: D 92 THR cc_start: 0.7911 (OUTLIER) cc_final: 0.7585 (p) REVERT: J 12 LYS cc_start: 0.7070 (mttt) cc_final: 0.5568 (tmtt) REVERT: J 13 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7349 (tt0) REVERT: J 46 GLU cc_start: 0.8320 (tm-30) cc_final: 0.8014 (tm-30) REVERT: J 81 THR cc_start: 0.7404 (OUTLIER) cc_final: 0.7093 (p) REVERT: J 83 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7572 (mp0) REVERT: G 13 GLU cc_start: 0.6443 (mt-10) cc_final: 0.6160 (mp0) REVERT: B 80 LYS cc_start: 0.8405 (mtpt) cc_final: 0.8016 (mttp) REVERT: F 13 GLU cc_start: 0.6527 (mt-10) cc_final: 0.5904 (mm-30) REVERT: F 24 GLN cc_start: 0.7509 (mt0) cc_final: 0.7256 (tm-30) REVERT: F 83 GLU cc_start: 0.7048 (mt-10) cc_final: 0.6708 (mt-10) REVERT: A 80 LYS cc_start: 0.8346 (mtpt) cc_final: 0.7883 (ttmt) outliers start: 32 outliers final: 21 residues processed: 103 average time/residue: 0.1583 time to fit residues: 20.7767 Evaluate side-chains 98 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 75 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 22 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 4.9990 chunk 19 optimal weight: 0.0970 chunk 52 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 67 optimal weight: 0.7980 chunk 55 optimal weight: 0.4980 chunk 21 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 47 optimal weight: 5.9990 overall best weight: 1.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 HIS ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4671 Z= 0.209 Angle : 0.658 5.718 6288 Z= 0.369 Chirality : 0.051 0.205 839 Planarity : 0.002 0.010 778 Dihedral : 8.330 40.255 687 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.81 % Favored : 84.19 % Rotamer: Outliers : 6.97 % Allowed : 14.60 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.60 % 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: -4.60 (0.30), residues: 639 helix: None (None), residues: 0 sheet: -3.47 (0.48), residues: 117 loop : -3.26 (0.24), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 50 TYR 0.013 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 76 time to evaluate : 0.463 Fit side-chains REVERT: H 13 GLU cc_start: 0.6511 (mt-10) cc_final: 0.5920 (mp0) REVERT: C 80 LYS cc_start: 0.8238 (mtpt) cc_final: 0.7754 (ttmt) REVERT: C 92 THR cc_start: 0.7663 (p) cc_final: 0.7345 (p) REVERT: I 13 GLU cc_start: 0.7350 (mt-10) cc_final: 0.6774 (tt0) REVERT: D 43 LYS cc_start: 0.8078 (tttt) cc_final: 0.7566 (mptt) REVERT: D 80 LYS cc_start: 0.8266 (mtpt) cc_final: 0.8004 (mtmt) REVERT: J 12 LYS cc_start: 0.7031 (mttt) cc_final: 0.5540 (tmtt) REVERT: J 13 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7291 (tt0) REVERT: J 81 THR cc_start: 0.7220 (OUTLIER) cc_final: 0.6966 (p) REVERT: J 83 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7560 (mp0) REVERT: G 13 GLU cc_start: 0.6471 (mt-10) cc_final: 0.6195 (mp0) REVERT: B 80 LYS cc_start: 0.8214 (mtpt) cc_final: 0.7925 (mtmt) REVERT: B 83 GLU cc_start: 0.7995 (mp0) cc_final: 0.7795 (mp0) REVERT: F 13 GLU cc_start: 0.6474 (mt-10) cc_final: 0.5868 (tt0) REVERT: F 83 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6732 (mt-10) outliers start: 32 outliers final: 20 residues processed: 103 average time/residue: 0.1499 time to fit residues: 20.0412 Evaluate side-chains 93 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 72 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 88 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 62 optimal weight: 0.2980 chunk 66 optimal weight: 0.1980 chunk 59 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 37 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 overall best weight: 2.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 HIS ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN F 62 GLN ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 4671 Z= 0.344 Angle : 0.720 5.471 6288 Z= 0.406 Chirality : 0.052 0.152 839 Planarity : 0.002 0.008 778 Dihedral : 8.658 38.434 686 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.97 % Favored : 79.03 % Rotamer: Outliers : 7.19 % Allowed : 16.12 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.60 % 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: -4.35 (0.28), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.30 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 50 TYR 0.017 0.003 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 68 time to evaluate : 0.540 Fit side-chains REVERT: H 13 GLU cc_start: 0.6671 (mt-10) cc_final: 0.6039 (mp0) REVERT: I 13 GLU cc_start: 0.7479 (mt-10) cc_final: 0.6846 (tt0) REVERT: D 43 LYS cc_start: 0.8168 (tttt) cc_final: 0.7597 (mptt) REVERT: D 80 LYS cc_start: 0.8316 (mtpt) cc_final: 0.7882 (mttp) REVERT: D 83 GLU cc_start: 0.7823 (mp0) cc_final: 0.7584 (mp0) REVERT: J 12 LYS cc_start: 0.7199 (mttt) cc_final: 0.5770 (tmtt) REVERT: J 13 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7432 (tt0) REVERT: J 81 THR cc_start: 0.7518 (OUTLIER) cc_final: 0.7095 (p) REVERT: J 83 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7535 (mp0) REVERT: G 13 GLU cc_start: 0.6572 (mt-10) cc_final: 0.6295 (mp0) REVERT: G 46 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.6673 (tm-30) REVERT: B 80 LYS cc_start: 0.8211 (mtpt) cc_final: 0.7924 (mtmt) REVERT: F 83 GLU cc_start: 0.7060 (mt-10) cc_final: 0.6755 (mt-10) REVERT: A 83 GLU cc_start: 0.7932 (mp0) cc_final: 0.7594 (mp0) outliers start: 33 outliers final: 26 residues processed: 95 average time/residue: 0.1466 time to fit residues: 18.3234 Evaluate side-chains 95 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 67 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain A residue 22 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 59 optimal weight: 0.4980 chunk 16 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 ASN ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 4671 Z= 0.491 Angle : 0.820 5.594 6288 Z= 0.467 Chirality : 0.055 0.148 839 Planarity : 0.003 0.015 778 Dihedral : 9.322 39.566 686 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.79 % Favored : 76.21 % Rotamer: Outliers : 7.63 % Allowed : 16.34 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.05 % 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: -4.68 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.56 (0.20), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 50 TYR 0.022 0.003 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 65 time to evaluate : 0.514 Fit side-chains REVERT: H 13 GLU cc_start: 0.6763 (mt-10) cc_final: 0.6302 (mp0) REVERT: H 46 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.6678 (tm-30) REVERT: I 13 GLU cc_start: 0.7532 (mt-10) cc_final: 0.6855 (tt0) REVERT: D 43 LYS cc_start: 0.8261 (tttt) cc_final: 0.8031 (tttp) REVERT: D 80 LYS cc_start: 0.8311 (mtpt) cc_final: 0.8039 (mttp) REVERT: J 12 LYS cc_start: 0.7321 (mttt) cc_final: 0.5547 (tmtt) REVERT: J 13 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7634 (tt0) REVERT: J 81 THR cc_start: 0.7705 (OUTLIER) cc_final: 0.7104 (p) REVERT: J 83 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7419 (mp0) REVERT: G 13 GLU cc_start: 0.6775 (mt-10) cc_final: 0.6423 (mp0) REVERT: G 46 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.6606 (tm-30) REVERT: B 80 LYS cc_start: 0.8280 (mtpt) cc_final: 0.7876 (mttp) REVERT: F 83 GLU cc_start: 0.7057 (mt-10) cc_final: 0.6794 (mt-10) REVERT: A 12 LYS cc_start: 0.6925 (OUTLIER) cc_final: 0.6592 (mtmt) outliers start: 35 outliers final: 26 residues processed: 92 average time/residue: 0.1445 time to fit residues: 17.3588 Evaluate side-chains 95 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 65 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 22 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 0.5980 chunk 16 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 4671 Z= 0.338 Angle : 0.733 5.678 6288 Z= 0.415 Chirality : 0.052 0.138 839 Planarity : 0.002 0.009 778 Dihedral : 8.705 38.960 686 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.34 % Favored : 79.66 % Rotamer: Outliers : 7.63 % Allowed : 16.78 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.45 % 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: -4.56 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.46 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 50 TYR 0.016 0.003 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 70 time to evaluate : 0.519 Fit side-chains REVERT: H 13 GLU cc_start: 0.6671 (mt-10) cc_final: 0.6002 (mp0) REVERT: H 46 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.6503 (tm-30) REVERT: C 80 LYS cc_start: 0.8349 (mtpt) cc_final: 0.7849 (mtmt) REVERT: I 13 GLU cc_start: 0.7390 (mt-10) cc_final: 0.6730 (tt0) REVERT: I 46 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.6844 (tm-30) REVERT: D 43 LYS cc_start: 0.8217 (tttt) cc_final: 0.7974 (tttp) REVERT: D 80 LYS cc_start: 0.8361 (mtpt) cc_final: 0.8033 (mttp) REVERT: J 12 LYS cc_start: 0.7198 (mttt) cc_final: 0.5788 (tmtt) REVERT: J 13 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7477 (tt0) REVERT: J 46 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.6729 (tm-30) REVERT: J 81 THR cc_start: 0.7603 (OUTLIER) cc_final: 0.7174 (p) REVERT: J 83 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7590 (mp0) REVERT: G 13 GLU cc_start: 0.6679 (mt-10) cc_final: 0.6388 (mp0) REVERT: B 80 LYS cc_start: 0.8273 (mtpt) cc_final: 0.7897 (mttp) REVERT: F 83 GLU cc_start: 0.7138 (mt-10) cc_final: 0.6799 (mt-10) REVERT: A 83 GLU cc_start: 0.7911 (mp0) cc_final: 0.7633 (mp0) outliers start: 35 outliers final: 26 residues processed: 96 average time/residue: 0.1375 time to fit residues: 17.4173 Evaluate side-chains 100 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 70 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain A residue 22 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 3.9990 chunk 37 optimal weight: 0.4980 chunk 56 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 41 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 20 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN C 62 GLN ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN G 62 GLN B 62 GLN F 62 GLN ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 4671 Z= 0.253 Angle : 0.683 5.665 6288 Z= 0.384 Chirality : 0.051 0.138 839 Planarity : 0.002 0.009 778 Dihedral : 8.200 39.005 686 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.56 % Favored : 80.44 % Rotamer: Outliers : 8.28 % Allowed : 16.99 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -4.39 (0.28), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.34 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 50 TYR 0.012 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 65 time to evaluate : 0.505 Fit side-chains REVERT: H 13 GLU cc_start: 0.6563 (mt-10) cc_final: 0.6171 (tt0) REVERT: H 46 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.6583 (tm-30) REVERT: C 80 LYS cc_start: 0.8327 (mtpt) cc_final: 0.7797 (mtmt) REVERT: I 13 GLU cc_start: 0.7297 (mt-10) cc_final: 0.6662 (tt0) REVERT: I 46 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.6812 (tm-30) REVERT: D 43 LYS cc_start: 0.8189 (tttt) cc_final: 0.7972 (tttp) REVERT: D 80 LYS cc_start: 0.8331 (mtpt) cc_final: 0.8002 (mttp) REVERT: J 13 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7426 (tt0) REVERT: J 46 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.6718 (tm-30) REVERT: J 81 THR cc_start: 0.7469 (OUTLIER) cc_final: 0.7066 (p) REVERT: J 83 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7567 (mp0) REVERT: G 13 GLU cc_start: 0.6597 (mt-10) cc_final: 0.6220 (tt0) REVERT: G 46 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.6645 (tm-30) REVERT: B 80 LYS cc_start: 0.8265 (mtpt) cc_final: 0.7879 (mttp) REVERT: F 83 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6696 (mt-10) REVERT: A 12 LYS cc_start: 0.6863 (mtmt) cc_final: 0.6589 (mtmt) REVERT: A 83 GLU cc_start: 0.7930 (mp0) cc_final: 0.7608 (mp0) outliers start: 38 outliers final: 27 residues processed: 97 average time/residue: 0.1473 time to fit residues: 18.6777 Evaluate side-chains 97 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 65 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 62 GLN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain A residue 22 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 12 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 63 optimal weight: 0.0870 chunk 58 optimal weight: 5.9990 chunk 61 optimal weight: 20.0000 chunk 37 optimal weight: 4.9990 overall best weight: 2.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN F 62 GLN ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 4671 Z= 0.331 Angle : 0.725 5.671 6288 Z= 0.408 Chirality : 0.052 0.136 839 Planarity : 0.002 0.010 778 Dihedral : 8.417 39.250 686 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.91 % Favored : 78.09 % Rotamer: Outliers : 7.41 % Allowed : 18.30 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -4.41 (0.28), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 TYR 0.016 0.003 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 68 time to evaluate : 0.528 Fit side-chains REVERT: H 13 GLU cc_start: 0.6640 (mt-10) cc_final: 0.6015 (mp0) REVERT: H 46 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.6583 (tm-30) REVERT: H 62 GLN cc_start: 0.7661 (mp10) cc_final: 0.7369 (mp10) REVERT: C 80 LYS cc_start: 0.8334 (mtpt) cc_final: 0.7827 (mtmt) REVERT: I 13 GLU cc_start: 0.7339 (mt-10) cc_final: 0.6698 (tt0) REVERT: I 46 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.6826 (tm-30) REVERT: D 43 LYS cc_start: 0.8226 (tttt) cc_final: 0.8005 (tttp) REVERT: D 80 LYS cc_start: 0.8373 (mtpt) cc_final: 0.8023 (mttp) REVERT: J 13 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7446 (tt0) REVERT: J 46 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.6711 (tm-30) REVERT: J 81 THR cc_start: 0.7575 (OUTLIER) cc_final: 0.7073 (p) REVERT: J 83 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7575 (mp0) REVERT: G 13 GLU cc_start: 0.6642 (mt-10) cc_final: 0.6270 (tt0) REVERT: G 46 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.6606 (tm-30) REVERT: B 80 LYS cc_start: 0.8290 (mtpt) cc_final: 0.7900 (mttp) REVERT: F 83 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6817 (mt-10) REVERT: A 12 LYS cc_start: 0.6859 (mtmt) cc_final: 0.6625 (mtmt) REVERT: A 83 GLU cc_start: 0.7939 (mp0) cc_final: 0.7604 (mp0) outliers start: 34 outliers final: 26 residues processed: 94 average time/residue: 0.1389 time to fit residues: 17.2703 Evaluate side-chains 100 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 69 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain A residue 22 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 56 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN C 62 GLN ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 62 GLN B 62 GLN F 62 GLN ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 4671 Z= 0.308 Angle : 0.721 5.628 6288 Z= 0.406 Chirality : 0.053 0.172 839 Planarity : 0.002 0.010 778 Dihedral : 8.316 38.957 686 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.97 % Favored : 79.03 % Rotamer: Outliers : 8.06 % Allowed : 17.21 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -4.36 (0.28), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 50 TYR 0.015 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 66 time to evaluate : 0.511 Fit side-chains REVERT: H 13 GLU cc_start: 0.6616 (mt-10) cc_final: 0.6002 (mp0) REVERT: H 46 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.6580 (tm-30) REVERT: C 80 LYS cc_start: 0.8332 (mtpt) cc_final: 0.7810 (mtmt) REVERT: C 92 THR cc_start: 0.6822 (OUTLIER) cc_final: 0.6593 (p) REVERT: I 13 GLU cc_start: 0.7316 (mt-10) cc_final: 0.6690 (tt0) REVERT: I 46 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.6828 (tm-30) REVERT: D 43 LYS cc_start: 0.8235 (tttt) cc_final: 0.8018 (tttp) REVERT: D 80 LYS cc_start: 0.8375 (mtpt) cc_final: 0.8024 (mttp) REVERT: D 92 THR cc_start: 0.7956 (OUTLIER) cc_final: 0.7620 (p) REVERT: J 13 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7464 (tt0) REVERT: J 46 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.6699 (tm-30) REVERT: J 81 THR cc_start: 0.7571 (OUTLIER) cc_final: 0.7054 (p) REVERT: J 83 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7555 (mp0) REVERT: G 13 GLU cc_start: 0.6622 (mt-10) cc_final: 0.6203 (tt0) REVERT: G 46 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.6612 (tm-30) REVERT: B 80 LYS cc_start: 0.8291 (mtpt) cc_final: 0.7912 (mttp) REVERT: B 92 THR cc_start: 0.7468 (p) cc_final: 0.7191 (p) REVERT: F 83 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6833 (mt-10) REVERT: A 12 LYS cc_start: 0.6786 (mtmt) cc_final: 0.6566 (mtmt) REVERT: A 83 GLU cc_start: 0.7919 (mp0) cc_final: 0.7575 (mp0) outliers start: 37 outliers final: 27 residues processed: 95 average time/residue: 0.1403 time to fit residues: 17.6269 Evaluate side-chains 100 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 66 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 62 GLN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain A residue 22 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 33 optimal weight: 0.3980 chunk 43 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN C 62 GLN ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 4671 Z= 0.423 Angle : 0.798 5.877 6288 Z= 0.451 Chirality : 0.054 0.166 839 Planarity : 0.003 0.012 778 Dihedral : 8.774 39.112 686 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.88 % Favored : 75.12 % Rotamer: Outliers : 7.41 % Allowed : 18.52 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -4.54 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.45 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 50 TYR 0.019 0.003 TYR D 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 68 time to evaluate : 0.547 Fit side-chains REVERT: H 13 GLU cc_start: 0.6760 (mt-10) cc_final: 0.6328 (mp0) REVERT: H 46 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.6582 (tm-30) REVERT: C 80 LYS cc_start: 0.8382 (mtpt) cc_final: 0.7871 (mtmt) REVERT: C 92 THR cc_start: 0.6854 (OUTLIER) cc_final: 0.6643 (p) REVERT: I 13 GLU cc_start: 0.7387 (mt-10) cc_final: 0.6721 (tt0) REVERT: I 46 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.6856 (tm-30) REVERT: D 43 LYS cc_start: 0.8294 (tttt) cc_final: 0.8072 (tttp) REVERT: D 80 LYS cc_start: 0.8403 (mtpt) cc_final: 0.8047 (mttp) REVERT: D 92 THR cc_start: 0.7957 (OUTLIER) cc_final: 0.7630 (p) REVERT: J 13 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7591 (tt0) REVERT: J 46 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.6699 (tm-30) REVERT: J 81 THR cc_start: 0.7673 (OUTLIER) cc_final: 0.7098 (p) REVERT: J 83 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7521 (mp0) REVERT: G 13 GLU cc_start: 0.6770 (mt-10) cc_final: 0.6314 (tt0) REVERT: G 46 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.6610 (tm-30) REVERT: B 80 LYS cc_start: 0.8321 (mtpt) cc_final: 0.7905 (mttp) REVERT: B 92 THR cc_start: 0.7495 (p) cc_final: 0.7213 (p) REVERT: F 83 GLU cc_start: 0.7142 (mt-10) cc_final: 0.6810 (mt-10) REVERT: A 12 LYS cc_start: 0.6804 (mtmt) cc_final: 0.6581 (mtmt) outliers start: 34 outliers final: 26 residues processed: 94 average time/residue: 0.1437 time to fit residues: 17.7143 Evaluate side-chains 102 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 69 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 62 GLN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain A residue 22 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 36 optimal weight: 7.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN C 62 GLN ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.158772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.136714 restraints weight = 6882.672| |-----------------------------------------------------------------------------| r_work (start): 0.4191 rms_B_bonded: 2.40 r_work: 0.4114 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3982 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 4671 Z= 0.321 Angle : 0.742 6.143 6288 Z= 0.418 Chirality : 0.053 0.149 839 Planarity : 0.002 0.011 778 Dihedral : 8.434 38.707 686 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.28 % Favored : 78.72 % Rotamer: Outliers : 7.63 % Allowed : 18.30 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -4.45 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.38 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 50 TYR 0.015 0.003 TYR D 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1381.10 seconds wall clock time: 25 minutes 45.45 seconds (1545.45 seconds total)