Starting phenix.real_space_refine on Thu Sep 26 01:02:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fq6_4298/09_2024/6fq6_4298.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fq6_4298/09_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_4298/09_2024/6fq6_4298.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fq6_4298/09_2024/6fq6_4298.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fq6_4298/09_2024/6fq6_4298.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fq6_4298/09_2024/6fq6_4298.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 6.74, per 1000 atoms: 0.56 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.70 Conformation dependent library (CDL) restraints added in 899.9 milliseconds 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: 6.23 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: 4.85 Time building geometry restraints manager: 3.20 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: 0.00 - 2.13: 17353 2.13 - 4.26: 1079 4.26 - 6.40: 105 6.40 - 8.53: 14 8.53 - 10.66: 4 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 3.040 nonbonded pdb=" OG SER C 18 " pdb=" O PHE C 25 " model vdw 2.272 3.040 nonbonded pdb=" O VAL H 108 " pdb=" OG1 THR H 112 " model vdw 2.307 3.040 nonbonded pdb=" NZ LYS D 43 " pdb=" O PRO D 47 " model vdw 2.321 3.120 nonbonded pdb=" O VAL D 108 " pdb=" OG1 THR D 112 " model vdw 2.333 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 0.250 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: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 32.350 Find NCS groups from input model: 0.260 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.230 ------------------------------------------------------------------------------- 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 : 0.818 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: 0.3114 time to fit residues: 126.4590 Evaluate side-chains 167 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 165 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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: 6.9990 chunk 50 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 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 ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** G 104 GLN H 46 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 12800 Z= 0.346 Angle : 0.762 10.311 18555 Z= 0.446 Chirality : 0.042 0.165 2120 Planarity : 0.006 0.040 1326 Dihedral : 31.746 174.160 4052 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 25.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.83 % Allowed : 19.33 % Favored : 76.84 % 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: 0.21 (0.29), residues: 736 helix: 0.75 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -1.43 (0.38), residues: 196 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 0.017 0.002 TYR G 50 ARG 0.012 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 206 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 182 time to evaluate : 0.927 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 120 MET cc_start: 0.7361 (mtp) cc_final: 0.7001 (mtp) REVERT: B 59 LYS cc_start: 0.9527 (ttpt) cc_final: 0.9181 (tptp) REVERT: B 63 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8364 (mt-10) REVERT: B 88 TYR cc_start: 0.8571 (m-10) cc_final: 0.7993 (m-80) REVERT: C 61 GLU cc_start: 0.9286 (tp30) cc_final: 0.8933 (tm-30) REVERT: D 73 GLU cc_start: 0.9161 (mm-30) cc_final: 0.8838 (tp30) REVERT: D 106 HIS cc_start: 0.8704 (m-70) cc_final: 0.8285 (m90) REVERT: E 93 GLN cc_start: 0.8264 (tt0) cc_final: 0.7212 (tp40) REVERT: E 97 GLU cc_start: 0.7581 (mt-10) cc_final: 0.6700 (mt-10) REVERT: E 100 LEU cc_start: 0.9563 (mt) cc_final: 0.9339 (mm) REVERT: F 25 ASN cc_start: 0.6427 (m110) cc_final: 0.5994 (m-40) REVERT: F 44 LYS cc_start: 0.8000 (tttt) cc_final: 0.7689 (ttpt) REVERT: F 59 LYS cc_start: 0.9337 (tptm) cc_final: 0.8794 (tppt) REVERT: F 88 TYR cc_start: 0.8484 (m-10) cc_final: 0.7983 (m-10) REVERT: G 64 GLU cc_start: 0.9284 (tt0) cc_final: 0.8801 (tp30) REVERT: G 84 GLN cc_start: 0.8649 (tp40) cc_final: 0.8330 (tt0) REVERT: H 39 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.7707 (m-80) REVERT: H 73 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8719 (tp30) REVERT: H 106 HIS cc_start: 0.8720 (m-70) cc_final: 0.8249 (m-70) outliers start: 24 outliers final: 16 residues processed: 192 average time/residue: 0.2522 time to fit residues: 67.8282 Evaluate side-chains 151 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 134 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL 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 42 LEU Chi-restraints excluded: chain D residue 87 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 F residue 51 TYR Chi-restraints excluded: chain F residue 64 ASN 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 87 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 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: 2.9990 chunk 72 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 12800 Z= 0.312 Angle : 0.735 12.751 18555 Z= 0.430 Chirality : 0.041 0.157 2120 Planarity : 0.006 0.055 1326 Dihedral : 31.587 170.463 4048 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 24.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.99 % Allowed : 20.61 % 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: 0.30 (0.29), residues: 736 helix: 0.87 (0.21), residues: 535 sheet: None (None), residues: 0 loop : -1.52 (0.38), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS E 39 PHE 0.026 0.003 PHE D 62 TYR 0.018 0.002 TYR D 37 ARG 0.004 0.001 ARG B 23 *********************** 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 183 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 158 time to evaluate : 2.860 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: A 74 ILE cc_start: 0.7426 (mm) cc_final: 0.7196 (mm) REVERT: A 103 LEU cc_start: 0.9494 (mt) cc_final: 0.9236 (mt) REVERT: A 104 PHE cc_start: 0.9186 (m-80) cc_final: 0.8931 (m-80) REVERT: B 25 ASN cc_start: 0.5910 (m110) cc_final: 0.5424 (m110) REVERT: B 88 TYR cc_start: 0.8523 (m-10) cc_final: 0.8041 (m-80) REVERT: C 61 GLU cc_start: 0.9300 (tp30) cc_final: 0.8874 (tm-30) REVERT: D 73 GLU cc_start: 0.9343 (mm-30) cc_final: 0.8848 (tp30) REVERT: D 106 HIS cc_start: 0.8710 (m-70) cc_final: 0.8197 (m90) REVERT: E 105 GLU cc_start: 0.8708 (pt0) cc_final: 0.8419 (pp20) REVERT: F 59 LYS cc_start: 0.9490 (tptm) cc_final: 0.9041 (tppt) REVERT: F 88 TYR cc_start: 0.8502 (m-10) cc_final: 0.7969 (m-10) REVERT: G 64 GLU cc_start: 0.9222 (tt0) cc_final: 0.8641 (tp30) REVERT: G 84 GLN cc_start: 0.8649 (tp40) cc_final: 0.8361 (tt0) REVERT: G 94 ASN cc_start: 0.8180 (OUTLIER) cc_final: 0.7804 (m110) REVERT: H 73 GLU cc_start: 0.9226 (mm-30) cc_final: 0.8550 (tp30) REVERT: H 106 HIS cc_start: 0.8766 (m-70) cc_final: 0.8347 (m170) outliers start: 25 outliers final: 16 residues processed: 173 average time/residue: 0.2641 time to fit residues: 65.5690 Evaluate side-chains 144 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 127 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 64 ASN 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 87 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 73 THR 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 87 THR 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: 0.6980 chunk 46 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 60 optimal weight: 0.0000 chunk 90 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 overall best weight: 3.5390 ------------------------------------------------------------------------------- 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** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN H 106 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 12800 Z= 0.259 Angle : 0.702 10.253 18555 Z= 0.409 Chirality : 0.039 0.159 2120 Planarity : 0.005 0.054 1326 Dihedral : 31.586 168.536 4048 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 22.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.83 % Allowed : 21.88 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.30), residues: 736 helix: 1.06 (0.22), residues: 529 sheet: None (None), residues: 0 loop : -1.57 (0.37), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 46 PHE 0.019 0.002 PHE D 62 TYR 0.011 0.002 TYR D 37 ARG 0.004 0.000 ARG C 42 *********************** 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 174 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 150 time to evaluate : 0.879 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: A 62 ILE cc_start: 0.7911 (mt) cc_final: 0.7636 (mm) REVERT: A 103 LEU cc_start: 0.9615 (mt) cc_final: 0.9371 (mt) REVERT: B 25 ASN cc_start: 0.5942 (m110) cc_final: 0.5561 (m110) REVERT: B 88 TYR cc_start: 0.8578 (m-10) cc_final: 0.8075 (m-80) REVERT: C 61 GLU cc_start: 0.9291 (tp30) cc_final: 0.8937 (tm-30) REVERT: D 73 GLU cc_start: 0.9434 (mm-30) cc_final: 0.8913 (tp30) REVERT: D 106 HIS cc_start: 0.8696 (m-70) cc_final: 0.8169 (m170) REVERT: F 25 ASN cc_start: 0.5631 (m-40) cc_final: 0.5339 (m-40) REVERT: F 59 LYS cc_start: 0.9491 (tptm) cc_final: 0.9068 (tppt) REVERT: F 88 TYR cc_start: 0.8461 (m-10) cc_final: 0.7954 (m-10) REVERT: G 64 GLU cc_start: 0.9221 (tt0) cc_final: 0.8616 (tp30) REVERT: G 84 GLN cc_start: 0.8620 (tp40) cc_final: 0.8357 (tt0) REVERT: H 73 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8449 (tp30) REVERT: H 77 LEU cc_start: 0.9027 (mm) cc_final: 0.8521 (mm) REVERT: H 106 HIS cc_start: 0.8476 (m90) cc_final: 0.8064 (m170) outliers start: 24 outliers final: 20 residues processed: 162 average time/residue: 0.2300 time to fit residues: 54.6304 Evaluate side-chains 147 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 64 ASN 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 42 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 93 GLN 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 87 THR 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: 10.0000 chunk 1 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.5367 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= 0.310 Angle : 0.739 9.440 18555 Z= 0.430 Chirality : 0.040 0.167 2120 Planarity : 0.006 0.049 1326 Dihedral : 31.770 167.767 4048 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 25.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 5.11 % Allowed : 22.20 % Favored : 72.68 % 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: 0.07 (0.30), residues: 736 helix: 0.71 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -1.66 (0.39), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS F 75 PHE 0.019 0.002 PHE D 62 TYR 0.016 0.002 TYR D 37 ARG 0.007 0.001 ARG G 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 170 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 138 time to evaluate : 0.909 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 62 ILE cc_start: 0.7982 (mt) cc_final: 0.7613 (mm) REVERT: A 103 LEU cc_start: 0.9625 (mt) cc_final: 0.9423 (mt) REVERT: B 25 ASN cc_start: 0.6123 (m110) cc_final: 0.5768 (m110) REVERT: B 88 TYR cc_start: 0.8623 (m-10) cc_final: 0.8104 (m-80) REVERT: C 61 GLU cc_start: 0.9317 (tp30) cc_final: 0.8950 (tm-30) REVERT: D 73 GLU cc_start: 0.9441 (mm-30) cc_final: 0.8895 (tp30) REVERT: D 106 HIS cc_start: 0.8718 (m-70) cc_final: 0.8037 (m90) REVERT: F 59 LYS cc_start: 0.9546 (tptm) cc_final: 0.9067 (tppt) REVERT: F 88 TYR cc_start: 0.8500 (m-10) cc_final: 0.7949 (m-10) REVERT: G 32 ARG cc_start: 0.8428 (ttp-170) cc_final: 0.8185 (ttp-170) REVERT: G 64 GLU cc_start: 0.9244 (tt0) cc_final: 0.8660 (tp30) REVERT: G 84 GLN cc_start: 0.8701 (tp40) cc_final: 0.8350 (tt0) REVERT: H 39 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.7510 (m-80) REVERT: H 73 GLU cc_start: 0.9206 (mm-30) cc_final: 0.8519 (tp30) outliers start: 32 outliers final: 25 residues processed: 158 average time/residue: 0.2148 time to fit residues: 49.3286 Evaluate side-chains 155 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 129 time to evaluate : 0.888 ------------------------------------------------------------------------------- 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 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 42 LEU 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 93 GLN Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 123 ASP 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 49 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 87 THR Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 7 optimal weight: 0.0470 chunk 31 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 overall best weight: 4.0086 ------------------------------------------------------------------------------- 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** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.5607 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= 0.268 Angle : 0.710 10.050 18555 Z= 0.411 Chirality : 0.039 0.216 2120 Planarity : 0.005 0.050 1326 Dihedral : 31.842 167.854 4048 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 22.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.47 % Allowed : 24.12 % Favored : 71.41 % 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: 0.15 (0.30), residues: 736 helix: 0.80 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -1.76 (0.39), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 75 PHE 0.015 0.002 PHE D 62 TYR 0.009 0.002 TYR C 50 ARG 0.005 0.001 ARG C 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 170 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 142 time to evaluate : 1.086 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: A 62 ILE cc_start: 0.7783 (mt) cc_final: 0.7347 (mm) REVERT: A 103 LEU cc_start: 0.9622 (mt) cc_final: 0.9369 (mt) REVERT: B 25 ASN cc_start: 0.6050 (m110) cc_final: 0.5666 (m110) REVERT: B 88 TYR cc_start: 0.8543 (m-10) cc_final: 0.7994 (m-80) REVERT: C 61 GLU cc_start: 0.9313 (tp30) cc_final: 0.8944 (tm-30) REVERT: D 73 GLU cc_start: 0.9438 (mm-30) cc_final: 0.8902 (tp30) REVERT: D 106 HIS cc_start: 0.8755 (m-70) cc_final: 0.8051 (m90) REVERT: F 25 ASN cc_start: 0.5404 (m-40) cc_final: 0.5137 (m-40) REVERT: F 59 LYS cc_start: 0.9531 (tptm) cc_final: 0.9076 (tppt) REVERT: F 88 TYR cc_start: 0.8488 (m-10) cc_final: 0.7955 (m-10) REVERT: G 64 GLU cc_start: 0.9245 (tt0) cc_final: 0.8662 (tp30) REVERT: G 84 GLN cc_start: 0.8734 (tp40) cc_final: 0.8425 (tt0) REVERT: H 73 GLU cc_start: 0.9186 (mm-30) cc_final: 0.8405 (tp30) outliers start: 28 outliers final: 24 residues processed: 158 average time/residue: 0.2161 time to fit residues: 50.3918 Evaluate side-chains 155 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 131 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 80 THR 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 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 42 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain E residue 123 ASP 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 87 THR Chi-restraints excluded: chain H residue 103 LEU 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: 7.9990 chunk 54 optimal weight: 9.9990 chunk 69 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- 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** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 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** H 79 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.5958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 12800 Z= 0.307 Angle : 0.749 11.359 18555 Z= 0.430 Chirality : 0.042 0.468 2120 Planarity : 0.005 0.046 1326 Dihedral : 31.957 167.276 4048 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 26.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 5.27 % Allowed : 25.24 % Favored : 69.49 % 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: 0.61 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.69 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS F 75 PHE 0.014 0.002 PHE D 62 TYR 0.014 0.002 TYR D 37 ARG 0.006 0.001 ARG A 116 *********************** 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 165 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 132 time to evaluate : 1.048 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: A 62 ILE cc_start: 0.7894 (mt) cc_final: 0.7428 (mm) REVERT: B 25 ASN cc_start: 0.6015 (m110) cc_final: 0.5612 (m110) REVERT: B 88 TYR cc_start: 0.8543 (m-10) cc_final: 0.7921 (m-10) REVERT: C 61 GLU cc_start: 0.9315 (tp30) cc_final: 0.8805 (tm-30) REVERT: D 73 GLU cc_start: 0.9442 (mm-30) cc_final: 0.8919 (tp30) REVERT: D 106 HIS cc_start: 0.8721 (m-70) cc_final: 0.8014 (m90) REVERT: F 25 ASN cc_start: 0.5463 (m-40) cc_final: 0.5186 (m-40) REVERT: F 59 LYS cc_start: 0.9544 (tptm) cc_final: 0.9118 (tppt) REVERT: F 88 TYR cc_start: 0.8495 (m-10) cc_final: 0.7940 (m-10) REVERT: G 64 GLU cc_start: 0.9268 (tt0) cc_final: 0.8640 (tp30) REVERT: G 84 GLN cc_start: 0.8780 (tp40) cc_final: 0.8408 (tt0) REVERT: H 73 GLU cc_start: 0.9197 (mm-30) cc_final: 0.8516 (tp30) outliers start: 33 outliers final: 25 residues processed: 152 average time/residue: 0.2066 time to fit residues: 46.6941 Evaluate side-chains 147 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 122 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 123 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 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 87 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain E residue 123 ASP 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 87 THR Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 60 optimal weight: 0.2980 chunk 65 optimal weight: 6.9990 chunk 47 optimal weight: 20.0000 chunk 8 optimal weight: 20.0000 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: 4.8588 ------------------------------------------------------------------------------- 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** ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** E 68 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.6207 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= 0.301 Angle : 0.757 15.276 18555 Z= 0.433 Chirality : 0.043 0.465 2120 Planarity : 0.005 0.049 1326 Dihedral : 32.049 167.569 4048 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 25.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.47 % Allowed : 27.00 % Favored : 68.53 % 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: -0.22 (0.30), residues: 736 helix: 0.49 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.67 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 75 PHE 0.014 0.002 PHE A 78 TYR 0.012 0.002 TYR D 37 ARG 0.005 0.001 ARG C 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 160 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 132 time to evaluate : 0.840 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: A 62 ILE cc_start: 0.7941 (mt) cc_final: 0.7435 (mm) REVERT: A 97 GLU cc_start: 0.8905 (tp30) cc_final: 0.8558 (tp30) REVERT: B 25 ASN cc_start: 0.6030 (m110) cc_final: 0.5581 (m110) REVERT: B 59 LYS cc_start: 0.9472 (tptt) cc_final: 0.9100 (tptt) REVERT: B 88 TYR cc_start: 0.8584 (m-10) cc_final: 0.7987 (m-10) REVERT: C 61 GLU cc_start: 0.9325 (tp30) cc_final: 0.8802 (tm-30) REVERT: D 73 GLU cc_start: 0.9459 (mm-30) cc_final: 0.8955 (tp30) REVERT: D 106 HIS cc_start: 0.8702 (m-70) cc_final: 0.8068 (m90) REVERT: E 93 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7271 (tp40) REVERT: F 25 ASN cc_start: 0.5560 (m-40) cc_final: 0.5265 (m-40) REVERT: F 59 LYS cc_start: 0.9564 (tptm) cc_final: 0.9296 (tptt) REVERT: F 67 ARG cc_start: 0.8757 (ttm110) cc_final: 0.8257 (ttp-170) REVERT: F 88 TYR cc_start: 0.8436 (m-10) cc_final: 0.7837 (m-10) REVERT: G 64 GLU cc_start: 0.9241 (tt0) cc_final: 0.8651 (tp30) REVERT: G 84 GLN cc_start: 0.8769 (tp40) cc_final: 0.8400 (tt0) REVERT: H 73 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8429 (tp30) outliers start: 28 outliers final: 25 residues processed: 152 average time/residue: 0.2238 time to fit residues: 49.7094 Evaluate side-chains 145 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 119 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 123 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 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain E residue 123 ASP 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 87 THR Chi-restraints excluded: chain H residue 103 LEU 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: 9.9990 chunk 38 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS ** E 68 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.6710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 12800 Z= 0.396 Angle : 0.839 13.158 18555 Z= 0.481 Chirality : 0.047 0.439 2120 Planarity : 0.006 0.050 1326 Dihedral : 32.388 166.659 4048 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 34.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.15 % Allowed : 28.12 % Favored : 67.73 % 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: -0.62 (0.29), residues: 736 helix: 0.13 (0.22), residues: 523 sheet: None (None), residues: 0 loop : -1.57 (0.40), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS F 75 PHE 0.023 0.003 PHE F 61 TYR 0.017 0.003 TYR D 118 ARG 0.006 0.001 ARG G 77 *********************** 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 151 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 125 time to evaluate : 0.805 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: A 62 ILE cc_start: 0.8144 (mt) cc_final: 0.7672 (mm) REVERT: B 25 ASN cc_start: 0.6251 (m110) cc_final: 0.5804 (m110) REVERT: B 88 TYR cc_start: 0.8560 (m-10) cc_final: 0.7854 (m-10) REVERT: C 61 GLU cc_start: 0.9338 (tp30) cc_final: 0.8822 (tm-30) REVERT: D 73 GLU cc_start: 0.9558 (mm-30) cc_final: 0.9027 (tp30) REVERT: D 82 LYS cc_start: 0.9394 (mtmm) cc_final: 0.9182 (mmtt) REVERT: D 106 HIS cc_start: 0.8503 (m90) cc_final: 0.7948 (m90) REVERT: E 60 LEU cc_start: 0.7691 (mt) cc_final: 0.7276 (mt) REVERT: F 25 ASN cc_start: 0.5710 (m-40) cc_final: 0.5388 (m-40) REVERT: F 59 LYS cc_start: 0.9580 (tptm) cc_final: 0.9315 (tppt) REVERT: F 67 ARG cc_start: 0.8729 (ttm110) cc_final: 0.8250 (ttp-170) REVERT: F 88 TYR cc_start: 0.8422 (m-10) cc_final: 0.7814 (m-10) REVERT: G 84 GLN cc_start: 0.8733 (tp40) cc_final: 0.8171 (tm-30) REVERT: H 73 GLU cc_start: 0.9173 (mm-30) cc_final: 0.8432 (tp30) REVERT: H 106 HIS cc_start: 0.8478 (m90) cc_final: 0.8043 (m90) outliers start: 26 outliers final: 26 residues processed: 142 average time/residue: 0.2117 time to fit residues: 44.1098 Evaluate side-chains 143 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 117 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 123 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 51 TYR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain E residue 123 ASP 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 87 THR Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 10.0000 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: 4.9990 chunk 60 optimal weight: 0.7980 chunk 48 optimal weight: 9.9990 chunk 62 optimal weight: 30.0000 chunk 83 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- 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** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.6806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 12800 Z= 0.323 Angle : 0.797 13.114 18555 Z= 0.455 Chirality : 0.045 0.434 2120 Planarity : 0.005 0.046 1326 Dihedral : 32.370 167.782 4048 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 28.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.31 % Allowed : 28.12 % Favored : 67.57 % 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: -0.55 (0.30), residues: 736 helix: 0.21 (0.22), residues: 521 sheet: None (None), residues: 0 loop : -1.63 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS F 75 PHE 0.020 0.002 PHE F 61 TYR 0.014 0.002 TYR D 37 ARG 0.007 0.001 ARG C 29 ********************** 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 153 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 126 time to evaluate : 0.914 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: A 62 ILE cc_start: 0.8106 (mt) cc_final: 0.7637 (mm) REVERT: B 25 ASN cc_start: 0.6170 (m110) cc_final: 0.5731 (m110) REVERT: B 88 TYR cc_start: 0.8560 (m-10) cc_final: 0.7962 (m-10) REVERT: C 57 TYR cc_start: 0.8146 (t80) cc_final: 0.7860 (t80) REVERT: C 61 GLU cc_start: 0.9328 (tp30) cc_final: 0.8809 (tm-30) REVERT: D 56 MET cc_start: 0.7995 (tpt) cc_final: 0.7515 (tpt) REVERT: D 73 GLU cc_start: 0.9459 (mm-30) cc_final: 0.8947 (tp30) REVERT: D 106 HIS cc_start: 0.8517 (m90) cc_final: 0.7984 (m90) REVERT: E 105 GLU cc_start: 0.8493 (pp20) cc_final: 0.8059 (pm20) REVERT: F 25 ASN cc_start: 0.5666 (m-40) cc_final: 0.5355 (m-40) REVERT: F 59 LYS cc_start: 0.9571 (tptm) cc_final: 0.9343 (tppt) REVERT: F 88 TYR cc_start: 0.8447 (m-10) cc_final: 0.7837 (m-10) REVERT: G 84 GLN cc_start: 0.8688 (tp40) cc_final: 0.8210 (tt0) REVERT: H 73 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8450 (tp30) outliers start: 27 outliers final: 27 residues processed: 142 average time/residue: 0.2080 time to fit residues: 43.7848 Evaluate side-chains 150 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 123 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 123 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 51 TYR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 123 ASP 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 87 THR Chi-restraints excluded: chain H residue 103 LEU 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: 10.0000 chunk 21 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 32 optimal weight: 0.2980 chunk 80 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 overall best weight: 3.2186 ------------------------------------------------------------------------------- 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** B 27 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.055050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.048137 restraints weight = 113616.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.049278 restraints weight = 70148.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.050067 restraints weight = 48043.360| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.6841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12800 Z= 0.252 Angle : 0.757 18.646 18555 Z= 0.429 Chirality : 0.042 0.401 2120 Planarity : 0.005 0.046 1326 Dihedral : 32.153 168.547 4048 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 22.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.51 % Allowed : 29.87 % Favored : 66.61 % 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: -0.40 (0.31), residues: 736 helix: 0.36 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.78 (0.41), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.018 0.002 PHE F 61 TYR 0.015 0.002 TYR D 37 ARG 0.007 0.001 ARG F 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1837.77 seconds wall clock time: 38 minutes 36.61 seconds (2316.61 seconds total)