Starting phenix.real_space_refine on Thu Feb 15 10:24:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fq6_4298/02_2024/6fq6_4298.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fq6_4298/02_2024/6fq6_4298.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/6fq6_4298/02_2024/6fq6_4298.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fq6_4298/02_2024/6fq6_4298.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fq6_4298/02_2024/6fq6_4298.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fq6_4298/02_2024/6fq6_4298.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= 0.003 sd= 0.027 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: 5 Type Number sf(0) Gaussians P 294 5.49 5 S 12 5.16 5 C 6620 2.51 5 N 2249 2.21 5 O 2812 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None 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: 11987 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "B" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 668 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 832 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "E" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "F" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 832 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 690 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "I" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Time building chain proxies: 5.95, per 1000 atoms: 0.50 Number of scatterers: 11987 At special positions: 0 Unit cell: (77, 121.8, 112, 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 12 16.00 P 294 15.00 O 2812 8.00 N 2249 7.00 C 6620 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: 7.44 Conformation dependent library (CDL) restraints added in 1.1 seconds 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1412 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 9 sheets defined 73.5% alpha, 2.4% beta 147 base pairs and 260 stacking pairs defined. Time for finding SS restraints: 6.42 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.744A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 28 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 47 through 76 removed outlier: 3.940A pdb=" N TYR B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLU B 52 " --> pdb=" O GLY B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.802A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 36 removed outlier: 3.596A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.492A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.684A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.754A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 120 removed outlier: 3.691A pdb=" N ALA D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.685A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 28 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 47 through 76 removed outlier: 4.048A pdb=" N TYR F 51 " --> pdb=" O SER F 47 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLU F 52 " --> pdb=" O GLY F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.708A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.426A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.872A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.511A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.567A pdb=" N ALA H 104 " --> pdb=" O PRO H 100 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.515A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.551A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.727A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.915A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.823A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.634A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.657A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 395 hydrogen bonds defined for protein. 1167 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 376 hydrogen bonds 744 hydrogen bond angles 0 basepair planarities 147 basepair parallelities 260 stacking parallelities Total time for adding SS restraints: 4.92 Time building geometry restraints manager: 7.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1413 1.32 - 1.44: 4792 1.44 - 1.56: 5985 1.56 - 1.68: 588 1.68 - 1.80: 22 Bond restraints: 12800 Sorted by residual: bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.496 -0.074 3.00e-02 1.11e+03 6.07e+00 bond pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " ideal model delta sigma weight residual 1.422 1.492 -0.070 3.00e-02 1.11e+03 5.50e+00 bond pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " ideal model delta sigma weight residual 1.422 1.491 -0.069 3.00e-02 1.11e+03 5.32e+00 bond pdb=" C3' DG J 52 " pdb=" O3' DG J 52 " ideal model delta sigma weight residual 1.422 1.488 -0.066 3.00e-02 1.11e+03 4.78e+00 bond pdb=" C2 DC I 61 " pdb=" O2 DC I 61 " ideal model delta sigma weight residual 1.237 1.196 0.041 2.00e-02 2.50e+03 4.22e+00 ... (remaining 12795 not shown) Histogram of bond angle deviations from ideal: 97.48 - 104.56: 1104 104.56 - 111.63: 6439 111.63 - 118.71: 4061 118.71 - 125.78: 6021 125.78 - 132.86: 930 Bond angle restraints: 18555 Sorted by residual: angle pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sigma weight residual 120.20 127.48 -7.28 1.50e+00 4.44e-01 2.35e+01 angle pdb=" O4' DC I -26 " pdb=" C1' DC I -26 " pdb=" N1 DC I -26 " ideal model delta sigma weight residual 108.40 101.87 6.53 1.50e+00 4.44e-01 1.90e+01 angle pdb=" O4' DG I 4 " pdb=" C1' DG I 4 " pdb=" N9 DG I 4 " ideal model delta sigma weight residual 108.40 114.63 -6.23 1.50e+00 4.44e-01 1.72e+01 angle pdb=" O4' DC I -28 " pdb=" C1' DC I -28 " pdb=" N1 DC I -28 " ideal model delta sigma weight residual 108.40 102.36 6.04 1.50e+00 4.44e-01 1.62e+01 angle pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " pdb=" P DC I -58 " ideal model delta sigma weight residual 120.20 126.24 -6.04 1.50e+00 4.44e-01 1.62e+01 ... (remaining 18550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.22: 5496 32.22 - 64.45: 1400 64.45 - 96.67: 36 96.67 - 128.90: 4 128.90 - 161.12: 2 Dihedral angle restraints: 6938 sinusoidal: 4752 harmonic: 2186 Sorted by residual: dihedral pdb=" C4' DT I -59 " pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " pdb=" P DC I -58 " ideal model delta sinusoidal sigma weight residual 220.00 58.88 161.12 1 3.50e+01 8.16e-04 1.53e+01 dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual 220.00 64.07 155.93 1 3.50e+01 8.16e-04 1.50e+01 dihedral pdb=" C4' DC I 52 " pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " pdb=" P DC I 53 " ideal model delta sinusoidal sigma weight residual 220.00 103.74 116.26 1 3.50e+01 8.16e-04 1.13e+01 ... (remaining 6935 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1771 0.088 - 0.176: 322 0.176 - 0.263: 24 0.263 - 0.351: 2 0.351 - 0.439: 1 Chirality restraints: 2120 Sorted by residual: chirality pdb=" C1' DG I 4 " pdb=" O4' DG I 4 " pdb=" C2' DG I 4 " pdb=" N9 DG I 4 " both_signs ideal model delta sigma weight residual False 2.42 1.98 0.44 2.00e-01 2.50e+01 4.81e+00 chirality pdb=" C1' DG I 20 " pdb=" O4' DG I 20 " pdb=" C2' DG I 20 " pdb=" N9 DG I 20 " both_signs ideal model delta sigma weight residual False 2.42 2.11 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" C1' DG I -21 " pdb=" O4' DG I -21 " pdb=" C2' DG I -21 " pdb=" N9 DG I -21 " both_signs ideal model delta sigma weight residual False 2.42 2.15 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 2117 not shown) Planarity restraints: 1326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC I 61 " 0.001 2.00e-02 2.50e+03 3.07e-02 2.12e+01 pdb=" N1 DC I 61 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DC I 61 " -0.071 2.00e-02 2.50e+03 pdb=" O2 DC I 61 " 0.046 2.00e-02 2.50e+03 pdb=" N3 DC I 61 " 0.008 2.00e-02 2.50e+03 pdb=" C4 DC I 61 " -0.025 2.00e-02 2.50e+03 pdb=" N4 DC I 61 " 0.018 2.00e-02 2.50e+03 pdb=" C5 DC I 61 " 0.008 2.00e-02 2.50e+03 pdb=" C6 DC I 61 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I -28 " 0.065 2.00e-02 2.50e+03 3.01e-02 2.03e+01 pdb=" N1 DC I -28 " -0.040 2.00e-02 2.50e+03 pdb=" C2 DC I -28 " -0.013 2.00e-02 2.50e+03 pdb=" O2 DC I -28 " -0.010 2.00e-02 2.50e+03 pdb=" N3 DC I -28 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DC I -28 " 0.005 2.00e-02 2.50e+03 pdb=" N4 DC I -28 " 0.033 2.00e-02 2.50e+03 pdb=" C5 DC I -28 " -0.009 2.00e-02 2.50e+03 pdb=" C6 DC I -28 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I -26 " 0.060 2.00e-02 2.50e+03 2.99e-02 2.01e+01 pdb=" N1 DC I -26 " -0.047 2.00e-02 2.50e+03 pdb=" C2 DC I -26 " -0.002 2.00e-02 2.50e+03 pdb=" O2 DC I -26 " -0.018 2.00e-02 2.50e+03 pdb=" N3 DC I -26 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DC I -26 " 0.007 2.00e-02 2.50e+03 pdb=" N4 DC I -26 " 0.032 2.00e-02 2.50e+03 pdb=" C5 DC I -26 " -0.029 2.00e-02 2.50e+03 pdb=" C6 DC I -26 " -0.004 2.00e-02 2.50e+03 ... (remaining 1323 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2243 2.79 - 3.32: 11197 3.32 - 3.84: 25040 3.84 - 4.37: 28236 4.37 - 4.90: 39457 Nonbonded interactions: 106173 Sorted by model distance: nonbonded pdb=" OG SER G 18 " pdb=" O PHE G 25 " model vdw 2.261 2.440 nonbonded pdb=" OG SER C 18 " pdb=" O PHE C 25 " model vdw 2.272 2.440 nonbonded pdb=" O VAL H 108 " pdb=" OG1 THR H 112 " model vdw 2.307 2.440 nonbonded pdb=" NZ LYS D 43 " pdb=" O PRO D 47 " model vdw 2.321 2.520 nonbonded pdb=" O VAL D 108 " pdb=" OG1 THR D 112 " model vdw 2.333 2.440 ... (remaining 106168 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' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 20 through 101) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 33 through 121) selection = chain 'H' } 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: 0.260 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: 1.700 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 42.580 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 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 0.074 12800 Z= 0.459 Angle : 1.104 10.662 18555 Z= 0.656 Chirality : 0.066 0.439 2120 Planarity : 0.008 0.040 1326 Dihedral : 26.701 161.124 5526 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.32 % Allowed : 1.44 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.84 (0.27), residues: 736 helix: -0.06 (0.20), residues: 522 sheet: None (None), residues: 0 loop : -1.57 (0.35), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.003 HIS C 82 PHE 0.021 0.004 PHE E 78 TYR 0.032 0.004 TYR A 54 ARG 0.005 0.001 ARG C 11 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 308 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.6281 (mt) cc_final: 0.5838 (mt) REVERT: A 93 GLN cc_start: 0.8110 (tt0) cc_final: 0.6481 (tt0) REVERT: A 100 LEU cc_start: 0.9279 (mt) cc_final: 0.9033 (pp) REVERT: A 120 MET cc_start: 0.7083 (mtp) cc_final: 0.6080 (mtp) REVERT: A 124 ILE cc_start: 0.9470 (mt) cc_final: 0.8921 (mp) REVERT: A 129 ARG cc_start: 0.9134 (mtp180) cc_final: 0.8642 (mmm160) REVERT: B 59 LYS cc_start: 0.9096 (ttpt) cc_final: 0.8878 (tppt) REVERT: B 70 VAL cc_start: 0.9337 (t) cc_final: 0.9073 (t) REVERT: B 88 TYR cc_start: 0.8315 (m-10) cc_final: 0.7667 (m-80) REVERT: B 96 THR cc_start: 0.8707 (m) cc_final: 0.8446 (p) REVERT: C 61 GLU cc_start: 0.9202 (tp30) cc_final: 0.8889 (tm-30) REVERT: C 84 GLN cc_start: 0.8066 (tp40) cc_final: 0.7165 (tp40) REVERT: C 94 ASN cc_start: 0.8432 (t0) cc_final: 0.8117 (t0) REVERT: C 113 SER cc_start: 0.8820 (m) cc_final: 0.8586 (p) REVERT: D 34 TYR cc_start: 0.8699 (m-80) cc_final: 0.8435 (m-10) REVERT: D 41 VAL cc_start: 0.9538 (t) cc_final: 0.9324 (t) REVERT: D 51 ILE cc_start: 0.8376 (pt) cc_final: 0.8030 (tt) REVERT: D 73 GLU cc_start: 0.9177 (mm-30) cc_final: 0.8396 (tt0) REVERT: E 82 LEU cc_start: 0.5668 (mt) cc_final: 0.5353 (mt) REVERT: E 92 LEU cc_start: 0.9246 (mt) cc_final: 0.8990 (mt) REVERT: E 93 GLN cc_start: 0.8743 (tt0) cc_final: 0.7597 (tp-100) REVERT: E 106 ASP cc_start: 0.8654 (m-30) cc_final: 0.8345 (m-30) REVERT: E 120 MET cc_start: 0.7320 (mtp) cc_final: 0.6917 (mtt) REVERT: F 25 ASN cc_start: 0.5810 (m-40) cc_final: 0.5327 (m-40) REVERT: F 44 LYS cc_start: 0.7914 (tttt) cc_final: 0.7452 (tmmt) REVERT: F 70 VAL cc_start: 0.9311 (t) cc_final: 0.9063 (t) REVERT: F 88 TYR cc_start: 0.8243 (m-10) cc_final: 0.7772 (m-10) REVERT: G 35 ARG cc_start: 0.8699 (mtm180) cc_final: 0.8216 (mtp180) REVERT: G 64 GLU cc_start: 0.9426 (tt0) cc_final: 0.9132 (tp30) REVERT: G 94 ASN cc_start: 0.8753 (t0) cc_final: 0.8495 (t0) REVERT: H 34 TYR cc_start: 0.8028 (m-80) cc_final: 0.7797 (m-10) REVERT: H 37 TYR cc_start: 0.7736 (m-80) cc_final: 0.7450 (m-80) REVERT: H 73 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8261 (tt0) REVERT: H 106 HIS cc_start: 0.8454 (m-70) cc_final: 0.8090 (m90) outliers start: 2 outliers final: 2 residues processed: 310 average time/residue: 0.3074 time to fit residues: 125.6260 Evaluate side-chains 167 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 165 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain H residue 113 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 68 GLN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN C 110 ASN ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN F 25 ASN F 27 GLN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 12800 Z= 0.346 Angle : 0.765 10.523 18555 Z= 0.449 Chirality : 0.042 0.167 2120 Planarity : 0.006 0.037 1326 Dihedral : 31.699 174.367 4052 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 30.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 5.11 % Allowed : 17.73 % Favored : 77.16 % 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: 0.29 (0.29), residues: 736 helix: 0.79 (0.21), residues: 537 sheet: None (None), residues: 0 loop : -1.34 (0.39), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS D 79 PHE 0.018 0.003 PHE D 62 TYR 0.018 0.002 TYR G 50 ARG 0.010 0.001 ARG F 23 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 181 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8108 (tttt) cc_final: 0.7905 (tttt) REVERT: A 120 MET cc_start: 0.7312 (mtp) cc_final: 0.7011 (mtp) REVERT: B 59 LYS cc_start: 0.9578 (ttpt) cc_final: 0.9269 (tptp) REVERT: B 63 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8381 (mt-10) REVERT: B 88 TYR cc_start: 0.8572 (m-10) cc_final: 0.8030 (m-80) REVERT: C 61 GLU cc_start: 0.9291 (tp30) cc_final: 0.8934 (tm-30) REVERT: D 73 GLU cc_start: 0.9385 (mm-30) cc_final: 0.9062 (tp30) REVERT: D 106 HIS cc_start: 0.8714 (m-70) cc_final: 0.8286 (m90) REVERT: E 55 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7857 (tm-30) REVERT: E 93 GLN cc_start: 0.8260 (tt0) cc_final: 0.7875 (tp-100) REVERT: E 100 LEU cc_start: 0.9553 (mt) cc_final: 0.9328 (mm) REVERT: E 103 LEU cc_start: 0.9223 (pp) cc_final: 0.8902 (mt) REVERT: F 25 ASN cc_start: 0.6283 (m110) cc_final: 0.6014 (m-40) REVERT: F 44 LYS cc_start: 0.7965 (tttt) cc_final: 0.7680 (ttpt) REVERT: F 59 LYS cc_start: 0.9390 (tptm) cc_final: 0.8811 (tppt) REVERT: F 88 TYR cc_start: 0.8484 (m-10) cc_final: 0.8004 (m-10) REVERT: G 64 GLU cc_start: 0.9284 (tt0) cc_final: 0.8783 (tp30) REVERT: G 84 GLN cc_start: 0.8711 (tp40) cc_final: 0.8439 (tt0) REVERT: H 39 TYR cc_start: 0.8348 (OUTLIER) cc_final: 0.7714 (m-80) REVERT: H 73 GLU cc_start: 0.9273 (mm-30) cc_final: 0.8767 (tp30) REVERT: H 106 HIS cc_start: 0.8743 (m-70) cc_final: 0.8229 (m-70) outliers start: 32 outliers final: 16 residues processed: 193 average time/residue: 0.2529 time to fit residues: 67.8908 Evaluate side-chains 157 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 139 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 51 TYR Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 93 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 90 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 12800 Z= 0.265 Angle : 0.712 13.295 18555 Z= 0.415 Chirality : 0.040 0.160 2120 Planarity : 0.005 0.042 1326 Dihedral : 31.394 170.239 4048 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 25.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.15 % Allowed : 19.97 % Favored : 75.88 % 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: 0.49 (0.29), residues: 736 helix: 1.00 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.41 (0.38), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.024 0.002 PHE D 62 TYR 0.015 0.002 TYR D 37 ARG 0.007 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 160 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LEU cc_start: 0.9513 (mt) cc_final: 0.9309 (mt) REVERT: B 25 ASN cc_start: 0.5936 (m110) cc_final: 0.5441 (m110) REVERT: B 88 TYR cc_start: 0.8468 (m-10) cc_final: 0.7923 (m-80) REVERT: C 61 GLU cc_start: 0.9280 (tp30) cc_final: 0.8972 (tm-30) REVERT: D 73 GLU cc_start: 0.9343 (mm-30) cc_final: 0.8936 (tp30) REVERT: D 106 HIS cc_start: 0.8682 (m-70) cc_final: 0.8189 (m90) REVERT: E 55 GLN cc_start: 0.8471 (tt0) cc_final: 0.8217 (tm-30) REVERT: E 97 GLU cc_start: 0.7632 (mt-10) cc_final: 0.6835 (mt-10) REVERT: E 106 ASP cc_start: 0.9032 (m-30) cc_final: 0.8808 (t70) REVERT: F 25 ASN cc_start: 0.6043 (m110) cc_final: 0.5750 (m-40) REVERT: F 44 LYS cc_start: 0.7967 (tttt) cc_final: 0.7635 (ttpt) REVERT: F 59 LYS cc_start: 0.9504 (tptm) cc_final: 0.9134 (tppt) REVERT: F 88 TYR cc_start: 0.8436 (m-10) cc_final: 0.7934 (m-10) REVERT: G 84 GLN cc_start: 0.8640 (tp40) cc_final: 0.8408 (tt0) REVERT: G 94 ASN cc_start: 0.8305 (OUTLIER) cc_final: 0.8089 (m-40) REVERT: H 39 TYR cc_start: 0.8317 (OUTLIER) cc_final: 0.7680 (m-80) REVERT: H 73 GLU cc_start: 0.9223 (mm-30) cc_final: 0.8558 (tp30) REVERT: H 77 LEU cc_start: 0.9098 (mm) cc_final: 0.8702 (mm) REVERT: H 106 HIS cc_start: 0.8744 (m-70) cc_final: 0.8150 (m170) outliers start: 26 outliers final: 14 residues processed: 175 average time/residue: 0.2401 time to fit residues: 59.6043 Evaluate side-chains 147 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 131 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain H residue 42 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12800 Z= 0.216 Angle : 0.675 10.295 18555 Z= 0.391 Chirality : 0.038 0.153 2120 Planarity : 0.005 0.056 1326 Dihedral : 31.231 167.057 4048 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 22.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.04 % Allowed : 21.57 % Favored : 75.40 % 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: 0.79 (0.30), residues: 736 helix: 1.23 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -1.26 (0.38), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.018 0.002 PHE D 62 TYR 0.016 0.001 TYR D 37 ARG 0.006 0.000 ARG E 116 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 161 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.9084 (m-30) cc_final: 0.8865 (p0) REVERT: B 25 ASN cc_start: 0.5925 (m110) cc_final: 0.5534 (m110) REVERT: B 88 TYR cc_start: 0.8443 (m-10) cc_final: 0.7954 (m-80) REVERT: C 61 GLU cc_start: 0.9249 (tp30) cc_final: 0.8991 (tm-30) REVERT: D 73 GLU cc_start: 0.9301 (mm-30) cc_final: 0.8811 (tp30) REVERT: D 102 GLU cc_start: 0.9279 (tp30) cc_final: 0.8762 (tm-30) REVERT: D 103 LEU cc_start: 0.9512 (mp) cc_final: 0.9238 (mt) REVERT: D 106 HIS cc_start: 0.8673 (m-70) cc_final: 0.8166 (m-70) REVERT: F 59 LYS cc_start: 0.9485 (tptm) cc_final: 0.9043 (tppt) REVERT: F 60 VAL cc_start: 0.9254 (m) cc_final: 0.9049 (m) REVERT: F 88 TYR cc_start: 0.8406 (m-10) cc_final: 0.7902 (m-10) REVERT: H 65 ASP cc_start: 0.8623 (t0) cc_final: 0.8412 (t0) REVERT: H 73 GLU cc_start: 0.9202 (mm-30) cc_final: 0.8666 (tp30) REVERT: H 105 LYS cc_start: 0.9074 (pttp) cc_final: 0.8863 (pttp) REVERT: H 106 HIS cc_start: 0.8604 (m-70) cc_final: 0.8117 (m-70) outliers start: 19 outliers final: 12 residues processed: 174 average time/residue: 0.2320 time to fit residues: 58.9237 Evaluate side-chains 145 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 133 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 42 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.4974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 12800 Z= 0.285 Angle : 0.710 10.330 18555 Z= 0.412 Chirality : 0.039 0.192 2120 Planarity : 0.005 0.049 1326 Dihedral : 31.477 166.083 4048 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 28.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.31 % Allowed : 21.57 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.33 (0.30), residues: 736 helix: 0.82 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -1.30 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS F 75 PHE 0.017 0.002 PHE D 62 TYR 0.019 0.002 TYR D 37 ARG 0.007 0.001 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 137 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.5967 (m110) cc_final: 0.5598 (m110) REVERT: B 88 TYR cc_start: 0.8578 (m-10) cc_final: 0.8076 (m-80) REVERT: C 61 GLU cc_start: 0.9270 (tp30) cc_final: 0.8963 (tm-30) REVERT: D 56 MET cc_start: 0.7956 (tpt) cc_final: 0.7754 (tpt) REVERT: D 73 GLU cc_start: 0.9349 (mm-30) cc_final: 0.8918 (tp30) REVERT: D 106 HIS cc_start: 0.8755 (m-70) cc_final: 0.8206 (m90) REVERT: E 105 GLU cc_start: 0.8340 (pp20) cc_final: 0.8049 (pp20) REVERT: F 25 ASN cc_start: 0.5445 (m-40) cc_final: 0.5191 (m-40) REVERT: F 59 LYS cc_start: 0.9545 (tptm) cc_final: 0.9116 (tppt) REVERT: F 88 TYR cc_start: 0.8449 (m-10) cc_final: 0.7948 (m-10) REVERT: H 73 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8602 (tp30) outliers start: 27 outliers final: 23 residues processed: 155 average time/residue: 0.2045 time to fit residues: 47.2882 Evaluate side-chains 147 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 124 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 44 optimal weight: 0.0770 chunk 7 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 overall best weight: 4.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.5439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 12800 Z= 0.278 Angle : 0.712 13.368 18555 Z= 0.411 Chirality : 0.039 0.149 2120 Planarity : 0.005 0.046 1326 Dihedral : 31.727 166.767 4048 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 27.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 5.11 % Allowed : 22.36 % Favored : 72.52 % 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: 0.10 (0.30), residues: 736 helix: 0.68 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.46 (0.39), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS D 46 PHE 0.018 0.002 PHE B 61 TYR 0.014 0.002 TYR D 37 ARG 0.004 0.001 ARG G 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 131 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.6193 (m110) cc_final: 0.5776 (m110) REVERT: B 88 TYR cc_start: 0.8605 (m-10) cc_final: 0.8114 (m-80) REVERT: C 61 GLU cc_start: 0.9352 (tp30) cc_final: 0.8789 (tm-30) REVERT: D 59 MET cc_start: 0.9120 (mmm) cc_final: 0.8863 (mmm) REVERT: D 73 GLU cc_start: 0.9318 (mm-30) cc_final: 0.8780 (tp30) REVERT: D 106 HIS cc_start: 0.8779 (m-70) cc_final: 0.8216 (m170) REVERT: E 105 GLU cc_start: 0.8285 (pp20) cc_final: 0.7651 (pp20) REVERT: F 59 LYS cc_start: 0.9558 (tptm) cc_final: 0.9130 (tppt) REVERT: F 88 TYR cc_start: 0.8446 (m-10) cc_final: 0.7920 (m-10) REVERT: G 56 GLU cc_start: 0.9364 (tt0) cc_final: 0.8960 (tt0) REVERT: G 57 TYR cc_start: 0.8796 (t80) cc_final: 0.8596 (t80) REVERT: H 73 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8421 (tp30) REVERT: H 77 LEU cc_start: 0.9084 (mm) cc_final: 0.8668 (mm) REVERT: H 106 HIS cc_start: 0.8642 (t-90) cc_final: 0.8421 (t-90) outliers start: 32 outliers final: 23 residues processed: 151 average time/residue: 0.2301 time to fit residues: 50.9821 Evaluate side-chains 146 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 123 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 93 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 10.0000 chunk 10 optimal weight: 0.5980 chunk 54 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.5604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12800 Z= 0.204 Angle : 0.684 11.525 18555 Z= 0.389 Chirality : 0.039 0.363 2120 Planarity : 0.004 0.043 1326 Dihedral : 31.616 166.597 4048 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 20.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.99 % Allowed : 24.76 % Favored : 71.25 % 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: 0.54 (0.30), residues: 736 helix: 1.06 (0.23), residues: 530 sheet: None (None), residues: 0 loop : -1.43 (0.38), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 113 PHE 0.014 0.002 PHE B 61 TYR 0.015 0.001 TYR H 37 ARG 0.006 0.000 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 149 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.6158 (m110) cc_final: 0.5808 (m110) REVERT: B 51 TYR cc_start: 0.8088 (m-80) cc_final: 0.6965 (m-80) REVERT: B 88 TYR cc_start: 0.8558 (m-10) cc_final: 0.7953 (m-10) REVERT: C 61 GLU cc_start: 0.9290 (tp30) cc_final: 0.8848 (tm-30) REVERT: D 34 TYR cc_start: 0.8603 (m-80) cc_final: 0.7716 (m-80) REVERT: D 73 GLU cc_start: 0.9285 (mm-30) cc_final: 0.8770 (tp30) REVERT: D 102 GLU cc_start: 0.9371 (tp30) cc_final: 0.8766 (tm-30) REVERT: D 106 HIS cc_start: 0.8676 (m-70) cc_final: 0.8088 (m170) REVERT: E 55 GLN cc_start: 0.8807 (pt0) cc_final: 0.8485 (pt0) REVERT: E 97 GLU cc_start: 0.7279 (mt-10) cc_final: 0.7055 (mp0) REVERT: F 59 LYS cc_start: 0.9559 (tptm) cc_final: 0.9098 (tppt) REVERT: F 88 TYR cc_start: 0.8382 (m-10) cc_final: 0.7918 (m-10) REVERT: G 56 GLU cc_start: 0.9331 (tt0) cc_final: 0.8862 (tt0) REVERT: G 57 TYR cc_start: 0.8793 (t80) cc_final: 0.8565 (t80) REVERT: H 73 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8485 (tp30) REVERT: H 106 HIS cc_start: 0.8443 (t-90) cc_final: 0.8140 (t-90) outliers start: 25 outliers final: 21 residues processed: 163 average time/residue: 0.2208 time to fit residues: 52.6393 Evaluate side-chains 152 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 93 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 20.0000 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 47 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.5993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 12800 Z= 0.312 Angle : 0.737 13.123 18555 Z= 0.424 Chirality : 0.041 0.420 2120 Planarity : 0.005 0.046 1326 Dihedral : 31.774 166.427 4048 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 31.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.79 % Allowed : 25.40 % Favored : 69.81 % 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: 0.08 (0.30), residues: 736 helix: 0.75 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -1.61 (0.38), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS F 75 PHE 0.017 0.002 PHE B 61 TYR 0.020 0.002 TYR H 37 ARG 0.010 0.001 ARG G 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 125 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.6144 (m110) cc_final: 0.5776 (m110) REVERT: B 88 TYR cc_start: 0.8580 (m-10) cc_final: 0.8076 (m-80) REVERT: C 61 GLU cc_start: 0.9378 (tp30) cc_final: 0.8874 (tm-30) REVERT: D 34 TYR cc_start: 0.8590 (m-80) cc_final: 0.7605 (m-80) REVERT: D 39 TYR cc_start: 0.8931 (OUTLIER) cc_final: 0.7938 (m-80) REVERT: D 56 MET cc_start: 0.8028 (tpt) cc_final: 0.7709 (tpt) REVERT: D 73 GLU cc_start: 0.9354 (mm-30) cc_final: 0.8917 (tp30) REVERT: D 106 HIS cc_start: 0.8773 (m-70) cc_final: 0.8108 (m90) REVERT: F 59 LYS cc_start: 0.9582 (tptm) cc_final: 0.9364 (tptp) REVERT: F 67 ARG cc_start: 0.8654 (ttm110) cc_final: 0.8289 (ttp-170) REVERT: F 88 TYR cc_start: 0.8380 (m-10) cc_final: 0.7981 (m-10) REVERT: G 25 PHE cc_start: 0.7582 (m-80) cc_final: 0.7347 (m-80) REVERT: G 56 GLU cc_start: 0.9293 (tt0) cc_final: 0.8876 (tt0) REVERT: H 73 GLU cc_start: 0.9153 (mm-30) cc_final: 0.8528 (tp30) REVERT: H 106 HIS cc_start: 0.8650 (t-90) cc_final: 0.8378 (t-90) outliers start: 30 outliers final: 25 residues processed: 145 average time/residue: 0.2075 time to fit residues: 45.0726 Evaluate side-chains 149 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 123 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 39 TYR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 93 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.6539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 12800 Z= 0.357 Angle : 0.788 12.779 18555 Z= 0.455 Chirality : 0.044 0.383 2120 Planarity : 0.005 0.046 1326 Dihedral : 32.309 167.925 4048 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 37.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.47 % Allowed : 25.72 % Favored : 69.81 % 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: -0.53 (0.29), residues: 736 helix: 0.26 (0.21), residues: 525 sheet: None (None), residues: 0 loop : -1.74 (0.39), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS F 75 PHE 0.023 0.003 PHE F 61 TYR 0.025 0.002 TYR D 37 ARG 0.007 0.001 ARG G 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 128 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.6267 (m110) cc_final: 0.5840 (m110) REVERT: B 88 TYR cc_start: 0.8571 (m-10) cc_final: 0.8059 (m-80) REVERT: C 61 GLU cc_start: 0.9402 (tp30) cc_final: 0.8972 (tm-30) REVERT: D 34 TYR cc_start: 0.8495 (m-80) cc_final: 0.7420 (m-80) REVERT: D 39 TYR cc_start: 0.8941 (OUTLIER) cc_final: 0.7969 (m-80) REVERT: D 56 MET cc_start: 0.8368 (tpt) cc_final: 0.8140 (tpt) REVERT: D 73 GLU cc_start: 0.9458 (mm-30) cc_final: 0.8998 (tp30) REVERT: D 106 HIS cc_start: 0.8771 (m-70) cc_final: 0.8182 (m170) REVERT: E 60 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7080 (mt) REVERT: F 67 ARG cc_start: 0.8754 (ttm110) cc_final: 0.8370 (mtm110) REVERT: F 88 TYR cc_start: 0.8465 (m-10) cc_final: 0.7930 (m-10) REVERT: G 56 GLU cc_start: 0.9400 (tt0) cc_final: 0.9054 (tt0) REVERT: H 56 MET cc_start: 0.8726 (tpp) cc_final: 0.8335 (tpt) REVERT: H 73 GLU cc_start: 0.9262 (mm-30) cc_final: 0.8443 (tp30) REVERT: H 106 HIS cc_start: 0.8695 (t-90) cc_final: 0.8378 (t-90) outliers start: 28 outliers final: 23 residues processed: 141 average time/residue: 0.2221 time to fit residues: 46.0535 Evaluate side-chains 149 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 124 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 39 TYR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 93 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.5980 chunk 65 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 83 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.6641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 12800 Z= 0.299 Angle : 0.752 11.049 18555 Z= 0.433 Chirality : 0.042 0.387 2120 Planarity : 0.005 0.045 1326 Dihedral : 32.279 168.936 4048 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 31.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.99 % Allowed : 27.16 % Favored : 68.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.30), residues: 736 helix: 0.41 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.78 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 75 PHE 0.023 0.002 PHE C 25 TYR 0.031 0.002 TYR D 37 ARG 0.005 0.001 ARG G 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.6073 (m110) cc_final: 0.5667 (m110) REVERT: B 88 TYR cc_start: 0.8473 (m-10) cc_final: 0.7969 (m-80) REVERT: C 61 GLU cc_start: 0.9376 (tp30) cc_final: 0.8956 (tm-30) REVERT: C 64 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8212 (mm-30) REVERT: D 34 TYR cc_start: 0.8349 (m-80) cc_final: 0.7439 (m-80) REVERT: D 73 GLU cc_start: 0.9343 (mm-30) cc_final: 0.8856 (tp30) REVERT: D 106 HIS cc_start: 0.8732 (m-70) cc_final: 0.8115 (m170) REVERT: F 59 LYS cc_start: 0.9517 (tptt) cc_final: 0.9029 (tppt) REVERT: F 88 TYR cc_start: 0.8423 (m-10) cc_final: 0.7917 (m-10) REVERT: G 56 GLU cc_start: 0.9422 (tt0) cc_final: 0.9009 (tt0) REVERT: G 57 TYR cc_start: 0.8778 (t80) cc_final: 0.8186 (t80) REVERT: H 56 MET cc_start: 0.8594 (tpp) cc_final: 0.8278 (tpt) REVERT: H 73 GLU cc_start: 0.9161 (mm-30) cc_final: 0.8510 (tp30) REVERT: H 106 HIS cc_start: 0.8671 (t-90) cc_final: 0.8391 (t-170) outliers start: 25 outliers final: 22 residues processed: 142 average time/residue: 0.2182 time to fit residues: 45.6794 Evaluate side-chains 147 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 125 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 93 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 14 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 4 optimal weight: 0.4980 chunk 56 optimal weight: 0.7980 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.055060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.048072 restraints weight = 115003.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.049215 restraints weight = 71300.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.049956 restraints weight = 48713.335| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.6734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 12800 Z= 0.254 Angle : 0.728 10.739 18555 Z= 0.417 Chirality : 0.041 0.386 2120 Planarity : 0.005 0.044 1326 Dihedral : 32.190 169.049 4048 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 26.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.67 % Allowed : 28.27 % Favored : 68.05 % 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: -0.18 (0.30), residues: 736 helix: 0.55 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -1.70 (0.39), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.020 0.002 PHE F 61 TYR 0.025 0.002 TYR D 37 ARG 0.007 0.000 ARG B 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1850.04 seconds wall clock time: 34 minutes 55.32 seconds (2095.32 seconds total)