Starting phenix.real_space_refine on Fri Mar 15 15:31:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6esf_3947/03_2024/6esf_3947.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6esf_3947/03_2024/6esf_3947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6esf_3947/03_2024/6esf_3947.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6esf_3947/03_2024/6esf_3947.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6esf_3947/03_2024/6esf_3947.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6esf_3947/03_2024/6esf_3947.pdb" } resolution = 3.7 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= 0.001 sd= 0.011 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 6680 2.51 5 N 2275 2.21 5 O 2830 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-5265/modules/chem_data/mon_lib" Total number of atoms: 12091 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 678 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "C" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 804 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 683 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "G" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 811 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} 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: 6.13, per 1000 atoms: 0.51 Number of scatterers: 12091 At special positions: 0 Unit cell: (82.96, 121.04, 114.24, 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 2830 8.00 N 2275 7.00 C 6680 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: 6.26 Conformation dependent library (CDL) restraints added in 1.0 seconds 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1430 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 8 sheets defined 68.9% alpha, 2.4% beta 142 base pairs and 246 stacking pairs defined. Time for finding SS restraints: 5.18 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.087A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 113 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.546A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.663A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.606A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.681A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 72 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.546A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 79 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.746A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 120 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 113 removed outlier: 3.600A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.549A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.697A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 75 removed outlier: 3.697A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS F 75 " --> pdb=" O THR F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.863A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 46 through 72 Processing helix chain 'G' and resid 79 through 88 Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.518A pdb=" N ASN G 94 " --> pdb=" O ASP G 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 4.309A 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 101 through 120 removed outlier: 3.603A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA H 107 " --> pdb=" O LEU H 103 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.061A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.677A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.780A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.766A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 374 hydrogen bonds defined for protein. 1116 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 363 hydrogen bonds 722 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 246 stacking parallelities Total time for adding SS restraints: 4.18 Time building geometry restraints manager: 6.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1923 1.33 - 1.45: 4420 1.45 - 1.56: 5955 1.56 - 1.68: 586 1.68 - 1.80: 22 Bond restraints: 12906 Sorted by residual: bond pdb=" CB ASP A 106 " pdb=" CG ASP A 106 " ideal model delta sigma weight residual 1.516 1.478 0.038 2.50e-02 1.60e+03 2.37e+00 bond pdb=" C3' DC J 6 " pdb=" O3' DC J 6 " ideal model delta sigma weight residual 1.422 1.376 0.046 3.00e-02 1.11e+03 2.36e+00 bond pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " ideal model delta sigma weight residual 1.422 1.468 -0.046 3.00e-02 1.11e+03 2.31e+00 bond pdb=" C1' DT I 9 " pdb=" N1 DT I 9 " ideal model delta sigma weight residual 1.490 1.446 0.044 3.00e-02 1.11e+03 2.19e+00 bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.465 -0.043 3.00e-02 1.11e+03 2.06e+00 ... (remaining 12901 not shown) Histogram of bond angle deviations from ideal: 97.03 - 104.21: 1130 104.21 - 111.38: 6272 111.38 - 118.55: 4136 118.55 - 125.72: 6188 125.72 - 132.90: 966 Bond angle restraints: 18692 Sorted by residual: angle pdb=" C GLN G 84 " pdb=" N LEU G 85 " pdb=" CA LEU G 85 " ideal model delta sigma weight residual 121.58 115.18 6.40 1.95e+00 2.63e-01 1.08e+01 angle pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sigma weight residual 120.20 125.05 -4.85 1.50e+00 4.44e-01 1.04e+01 angle pdb=" C GLN C 84 " pdb=" N LEU C 85 " pdb=" CA LEU C 85 " ideal model delta sigma weight residual 121.14 115.58 5.56 1.75e+00 3.27e-01 1.01e+01 angle pdb=" C ALA C 60 " pdb=" N GLU C 61 " pdb=" CA GLU C 61 " ideal model delta sigma weight residual 121.14 115.59 5.55 1.75e+00 3.27e-01 1.01e+01 angle pdb=" C3' DT I -59 " pdb=" C2' DT I -59 " pdb=" C1' DT I -59 " ideal model delta sigma weight residual 101.60 97.03 4.57 1.50e+00 4.44e-01 9.27e+00 ... (remaining 18687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 5499 35.90 - 71.80: 1480 71.80 - 107.69: 27 107.69 - 143.59: 1 143.59 - 179.49: 1 Dihedral angle restraints: 7008 sinusoidal: 4794 harmonic: 2214 Sorted by residual: dihedral pdb=" CA LEU E 60 " pdb=" C LEU E 60 " pdb=" N LEU E 61 " pdb=" CA LEU E 61 " ideal model delta harmonic sigma weight residual -180.00 -155.84 -24.16 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA TYR H 34 " pdb=" C TYR H 34 " pdb=" N ALA H 35 " pdb=" CA ALA H 35 " ideal model delta harmonic sigma weight residual 180.00 -155.97 -24.03 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA ILE A 62 " pdb=" C ILE A 62 " pdb=" N ARG A 63 " pdb=" CA ARG A 63 " ideal model delta harmonic sigma weight residual 180.00 -156.16 -23.84 0 5.00e+00 4.00e-02 2.27e+01 ... (remaining 7005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1518 0.053 - 0.106: 514 0.106 - 0.158: 90 0.158 - 0.211: 7 0.211 - 0.264: 1 Chirality restraints: 2130 Sorted by residual: chirality pdb=" CG LEU G 34 " pdb=" CB LEU G 34 " pdb=" CD1 LEU G 34 " pdb=" CD2 LEU G 34 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CG LEU C 34 " pdb=" CB LEU C 34 " pdb=" CD1 LEU C 34 " pdb=" CD2 LEU C 34 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CB ILE D 51 " pdb=" CA ILE D 51 " pdb=" CG1 ILE D 51 " pdb=" CG2 ILE D 51 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 2127 not shown) Planarity restraints: 1345 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 99 " -0.042 5.00e-02 4.00e+02 6.33e-02 6.42e+00 pdb=" N PRO D 100 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO D 100 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 100 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 67 " 0.033 2.00e-02 2.50e+03 1.59e-02 6.32e+00 pdb=" N1 DT I 67 " -0.034 2.00e-02 2.50e+03 pdb=" C2 DT I 67 " -0.001 2.00e-02 2.50e+03 pdb=" O2 DT I 67 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DT I 67 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DT I 67 " 0.009 2.00e-02 2.50e+03 pdb=" O4 DT I 67 " 0.009 2.00e-02 2.50e+03 pdb=" C5 DT I 67 " 0.001 2.00e-02 2.50e+03 pdb=" C7 DT I 67 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DT I 67 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 26 " -0.035 2.00e-02 2.50e+03 1.46e-02 5.86e+00 pdb=" N9 DA I 26 " 0.021 2.00e-02 2.50e+03 pdb=" C8 DA I 26 " 0.017 2.00e-02 2.50e+03 pdb=" N7 DA I 26 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DA I 26 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DA I 26 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA I 26 " -0.012 2.00e-02 2.50e+03 pdb=" N1 DA I 26 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DA I 26 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA I 26 " 0.011 2.00e-02 2.50e+03 pdb=" C4 DA I 26 " 0.005 2.00e-02 2.50e+03 ... (remaining 1342 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2465 2.78 - 3.31: 10427 3.31 - 3.84: 25095 3.84 - 4.37: 27796 4.37 - 4.90: 38509 Nonbonded interactions: 104292 Sorted by model distance: nonbonded pdb=" N2 DG I 73 " pdb=" O2 DC J -73 " model vdw 2.249 2.520 nonbonded pdb=" OH TYR A 99 " pdb=" OE2 GLU A 133 " model vdw 2.275 2.440 nonbonded pdb=" OH TYR C 39 " pdb=" OE1 GLU D 68 " model vdw 2.282 2.440 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.293 2.440 nonbonded pdb=" O VAL H 115 " pdb=" OG1 THR H 119 " model vdw 2.299 2.440 ... (remaining 104287 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 37 and (name N or name CA or name C or name O or name CB \ )) or resid 38 through 134)) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 18 through 101) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 119) } ncs_group { reference = chain 'D' 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: 0.480 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: 1.780 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 36.970 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 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 : 0.008 0.070 12906 Z= 0.456 Angle : 0.973 9.144 18692 Z= 0.554 Chirality : 0.052 0.264 2130 Planarity : 0.007 0.063 1345 Dihedral : 28.705 179.491 5578 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.94 % Allowed : 3.13 % Favored : 95.92 % 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: -4.25 (0.23), residues: 746 helix: -2.79 (0.15), residues: 510 sheet: None (None), residues: 0 loop : -2.41 (0.36), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.002 HIS B 75 PHE 0.033 0.004 PHE C 25 TYR 0.016 0.003 TYR C 50 ARG 0.009 0.001 ARG E 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 282 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.7714 (mmtp) cc_final: 0.7454 (mttm) REVERT: A 123 ASP cc_start: 0.7701 (m-30) cc_final: 0.7458 (m-30) REVERT: C 33 LEU cc_start: 0.8327 (mt) cc_final: 0.7741 (tp) REVERT: C 76 THR cc_start: 0.8924 (p) cc_final: 0.8424 (t) REVERT: D 31 LYS cc_start: 0.7801 (mttt) cc_final: 0.7414 (pttm) REVERT: E 74 ILE cc_start: 0.8944 (mt) cc_final: 0.8636 (mt) REVERT: E 123 ASP cc_start: 0.7765 (m-30) cc_final: 0.7222 (m-30) REVERT: G 33 LEU cc_start: 0.8240 (mt) cc_final: 0.7815 (tp) REVERT: G 34 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8668 (mt) REVERT: G 84 GLN cc_start: 0.8332 (tp40) cc_final: 0.8090 (tp-100) REVERT: G 95 LYS cc_start: 0.8352 (ttmt) cc_final: 0.7804 (tppt) REVERT: H 31 LYS cc_start: 0.8535 (tptp) cc_final: 0.8096 (ttpt) REVERT: H 48 ASP cc_start: 0.8133 (m-30) cc_final: 0.7677 (p0) REVERT: H 90 GLU cc_start: 0.7876 (mp0) cc_final: 0.7655 (mp0) REVERT: H 117 LYS cc_start: 0.8643 (tttm) cc_final: 0.8380 (tttt) outliers start: 6 outliers final: 1 residues processed: 286 average time/residue: 0.2900 time to fit residues: 110.1543 Evaluate side-chains 168 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 166 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 51 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 chunk 90 optimal weight: 7.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 C 24 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12906 Z= 0.216 Angle : 0.653 10.441 18692 Z= 0.381 Chirality : 0.037 0.167 2130 Planarity : 0.006 0.055 1345 Dihedral : 32.214 179.096 4065 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 5.33 % Allowed : 14.26 % Favored : 80.41 % 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: -1.18 (0.28), residues: 746 helix: -0.22 (0.20), residues: 527 sheet: None (None), residues: 0 loop : -1.97 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS F 75 PHE 0.010 0.001 PHE D 67 TYR 0.026 0.002 TYR B 88 ARG 0.008 0.001 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 205 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8039 (mm) cc_final: 0.7753 (mm) REVERT: A 94 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7594 (mm-30) REVERT: A 106 ASP cc_start: 0.7127 (t70) cc_final: 0.6810 (m-30) REVERT: A 123 ASP cc_start: 0.7857 (m-30) cc_final: 0.7542 (m-30) REVERT: C 33 LEU cc_start: 0.8152 (mt) cc_final: 0.7847 (tp) REVERT: C 64 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7591 (tm-30) REVERT: C 76 THR cc_start: 0.8953 (p) cc_final: 0.8496 (t) REVERT: C 85 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7387 (mt) REVERT: C 100 VAL cc_start: 0.9271 (OUTLIER) cc_final: 0.8841 (m) REVERT: D 31 LYS cc_start: 0.7824 (mttt) cc_final: 0.7372 (pttt) REVERT: D 117 LYS cc_start: 0.8371 (tttt) cc_final: 0.8088 (tttt) REVERT: E 123 ASP cc_start: 0.7855 (m-30) cc_final: 0.7006 (m-30) REVERT: G 33 LEU cc_start: 0.8126 (mt) cc_final: 0.7775 (tp) REVERT: G 68 ASN cc_start: 0.8655 (t0) cc_final: 0.7883 (t0) REVERT: H 31 LYS cc_start: 0.8447 (tptp) cc_final: 0.8157 (ttpt) REVERT: H 40 LYS cc_start: 0.8768 (mttt) cc_final: 0.8454 (mttm) REVERT: H 46 HIS cc_start: 0.7479 (m170) cc_final: 0.7225 (m170) REVERT: H 110 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7900 (mm-30) REVERT: H 117 LYS cc_start: 0.8623 (tttm) cc_final: 0.8281 (ttpt) outliers start: 34 outliers final: 23 residues processed: 227 average time/residue: 0.2237 time to fit residues: 72.6869 Evaluate side-chains 194 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 169 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 0.0970 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 90 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 31 optimal weight: 0.6980 chunk 72 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 12906 Z= 0.229 Angle : 0.634 9.215 18692 Z= 0.368 Chirality : 0.036 0.155 2130 Planarity : 0.005 0.050 1345 Dihedral : 32.029 179.842 4065 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 6.43 % Allowed : 17.24 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.30), residues: 746 helix: 0.91 (0.22), residues: 527 sheet: None (None), residues: 0 loop : -1.75 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS F 75 PHE 0.010 0.001 PHE D 67 TYR 0.012 0.002 TYR G 57 ARG 0.007 0.000 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 171 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.8231 (p) cc_final: 0.7945 (p) REVERT: A 123 ASP cc_start: 0.7957 (m-30) cc_final: 0.7677 (m-30) REVERT: B 49 LEU cc_start: 0.8753 (mp) cc_final: 0.8423 (mp) REVERT: B 74 GLU cc_start: 0.8265 (tp30) cc_final: 0.7635 (tp30) REVERT: C 33 LEU cc_start: 0.8320 (mt) cc_final: 0.7870 (tp) REVERT: C 64 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7619 (tm-30) REVERT: C 76 THR cc_start: 0.8845 (p) cc_final: 0.8507 (t) REVERT: C 85 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7233 (mt) REVERT: C 100 VAL cc_start: 0.9202 (OUTLIER) cc_final: 0.8786 (m) REVERT: D 31 LYS cc_start: 0.7861 (mttt) cc_final: 0.7434 (pttt) REVERT: D 36 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.8115 (mt) REVERT: D 59 MET cc_start: 0.8374 (tpp) cc_final: 0.7772 (tpp) REVERT: E 123 ASP cc_start: 0.7857 (m-30) cc_final: 0.7122 (m-30) REVERT: G 33 LEU cc_start: 0.8201 (mt) cc_final: 0.7836 (tp) REVERT: G 68 ASN cc_start: 0.8684 (t0) cc_final: 0.7893 (t0) REVERT: H 31 LYS cc_start: 0.8291 (tptp) cc_final: 0.7855 (ttpt) REVERT: H 39 TYR cc_start: 0.7150 (t80) cc_final: 0.6888 (t80) REVERT: H 40 LYS cc_start: 0.8759 (mttt) cc_final: 0.8505 (mttm) REVERT: H 43 LYS cc_start: 0.8368 (mttt) cc_final: 0.8102 (mptt) REVERT: H 48 ASP cc_start: 0.7577 (p0) cc_final: 0.7209 (p0) REVERT: H 110 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7703 (mm-30) outliers start: 41 outliers final: 29 residues processed: 199 average time/residue: 0.2203 time to fit residues: 64.4887 Evaluate side-chains 192 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 160 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 91 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12906 Z= 0.289 Angle : 0.666 8.140 18692 Z= 0.384 Chirality : 0.037 0.147 2130 Planarity : 0.005 0.047 1345 Dihedral : 31.988 178.952 4063 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 6.27 % Allowed : 19.12 % Favored : 74.61 % 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: 0.48 (0.31), residues: 746 helix: 1.11 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -1.64 (0.43), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 75 PHE 0.012 0.002 PHE D 67 TYR 0.017 0.002 TYR B 88 ARG 0.005 0.001 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 158 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.7403 (t70) cc_final: 0.7156 (t70) REVERT: A 123 ASP cc_start: 0.8007 (m-30) cc_final: 0.7611 (m-30) REVERT: B 74 GLU cc_start: 0.8400 (tp30) cc_final: 0.7675 (tp30) REVERT: C 33 LEU cc_start: 0.8500 (mt) cc_final: 0.8024 (tp) REVERT: C 64 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7675 (tm-30) REVERT: C 76 THR cc_start: 0.8858 (p) cc_final: 0.8550 (t) REVERT: D 31 LYS cc_start: 0.7931 (mttt) cc_final: 0.7483 (pttt) REVERT: D 59 MET cc_start: 0.8434 (tpp) cc_final: 0.7747 (tpp) REVERT: E 123 ASP cc_start: 0.7969 (m-30) cc_final: 0.7175 (m-30) REVERT: G 33 LEU cc_start: 0.8359 (mt) cc_final: 0.8063 (tp) REVERT: G 64 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7715 (tm-30) REVERT: G 68 ASN cc_start: 0.8839 (t0) cc_final: 0.8206 (t0) REVERT: H 31 LYS cc_start: 0.8342 (tptp) cc_final: 0.7903 (ttpt) REVERT: H 34 TYR cc_start: 0.8260 (m-80) cc_final: 0.7811 (m-10) REVERT: H 39 TYR cc_start: 0.7476 (t80) cc_final: 0.7276 (t80) REVERT: H 48 ASP cc_start: 0.7798 (p0) cc_final: 0.7322 (p0) REVERT: H 59 MET cc_start: 0.8422 (tpp) cc_final: 0.8215 (mmm) REVERT: H 110 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7707 (mm-30) REVERT: H 117 LYS cc_start: 0.8907 (ttpt) cc_final: 0.8526 (ttpt) outliers start: 40 outliers final: 34 residues processed: 182 average time/residue: 0.2210 time to fit residues: 59.5963 Evaluate side-chains 182 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 148 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12906 Z= 0.194 Angle : 0.610 9.549 18692 Z= 0.352 Chirality : 0.035 0.154 2130 Planarity : 0.004 0.047 1345 Dihedral : 31.808 177.720 4063 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 5.33 % Allowed : 19.75 % Favored : 74.92 % 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: 0.97 (0.31), residues: 746 helix: 1.51 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -1.54 (0.43), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.008 0.001 PHE D 67 TYR 0.014 0.002 TYR F 88 ARG 0.004 0.000 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 165 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.8069 (p) cc_final: 0.7747 (p) REVERT: A 123 ASP cc_start: 0.7843 (m-30) cc_final: 0.7424 (m-30) REVERT: B 74 GLU cc_start: 0.8425 (tp30) cc_final: 0.7621 (tp30) REVERT: C 33 LEU cc_start: 0.8356 (mt) cc_final: 0.8032 (tp) REVERT: C 56 GLU cc_start: 0.8177 (tt0) cc_final: 0.7570 (tm-30) REVERT: C 64 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7558 (tm-30) REVERT: C 76 THR cc_start: 0.8641 (p) cc_final: 0.8226 (t) REVERT: C 100 VAL cc_start: 0.9153 (OUTLIER) cc_final: 0.8717 (m) REVERT: D 31 LYS cc_start: 0.7588 (mttt) cc_final: 0.7271 (pttt) REVERT: D 59 MET cc_start: 0.8300 (tpp) cc_final: 0.7608 (tpp) REVERT: E 123 ASP cc_start: 0.7870 (m-30) cc_final: 0.7239 (m-30) REVERT: G 33 LEU cc_start: 0.8277 (mt) cc_final: 0.8051 (tp) REVERT: G 64 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7674 (tm-30) REVERT: G 68 ASN cc_start: 0.8691 (t0) cc_final: 0.7913 (t0) REVERT: H 31 LYS cc_start: 0.8266 (tptp) cc_final: 0.7816 (ttpt) REVERT: H 34 TYR cc_start: 0.8306 (m-80) cc_final: 0.7894 (m-10) REVERT: H 48 ASP cc_start: 0.7605 (p0) cc_final: 0.7136 (p0) REVERT: H 59 MET cc_start: 0.8342 (tpp) cc_final: 0.8108 (mmm) REVERT: H 60 ASN cc_start: 0.7875 (t0) cc_final: 0.7656 (t0) REVERT: H 110 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7675 (mm-30) REVERT: H 117 LYS cc_start: 0.8779 (ttpt) cc_final: 0.8419 (ttpt) outliers start: 34 outliers final: 26 residues processed: 185 average time/residue: 0.2067 time to fit residues: 56.6251 Evaluate side-chains 174 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 147 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 93 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12906 Z= 0.187 Angle : 0.602 9.602 18692 Z= 0.346 Chirality : 0.034 0.158 2130 Planarity : 0.004 0.049 1345 Dihedral : 31.671 178.303 4063 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 6.11 % Allowed : 21.47 % Favored : 72.41 % 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: 1.19 (0.31), residues: 746 helix: 1.67 (0.22), residues: 529 sheet: None (None), residues: 0 loop : -1.47 (0.44), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 75 PHE 0.006 0.001 PHE D 67 TYR 0.010 0.001 TYR B 88 ARG 0.004 0.000 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 162 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7678 (mp) REVERT: A 87 SER cc_start: 0.8174 (p) cc_final: 0.7889 (p) REVERT: A 123 ASP cc_start: 0.7751 (m-30) cc_final: 0.7284 (m-30) REVERT: B 34 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8338 (tt) REVERT: B 74 GLU cc_start: 0.8409 (tp30) cc_final: 0.7519 (tp30) REVERT: C 33 LEU cc_start: 0.8416 (mt) cc_final: 0.8039 (tp) REVERT: C 56 GLU cc_start: 0.8148 (tt0) cc_final: 0.7543 (tm-30) REVERT: C 64 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7546 (tm-30) REVERT: C 76 THR cc_start: 0.8512 (p) cc_final: 0.8108 (t) REVERT: C 100 VAL cc_start: 0.9127 (OUTLIER) cc_final: 0.8689 (m) REVERT: D 31 LYS cc_start: 0.7581 (mttt) cc_final: 0.7192 (ttpt) REVERT: D 59 MET cc_start: 0.8334 (tpp) cc_final: 0.7588 (tpp) REVERT: D 117 LYS cc_start: 0.8392 (tttt) cc_final: 0.8052 (ttmt) REVERT: E 123 ASP cc_start: 0.7824 (m-30) cc_final: 0.7070 (m-30) REVERT: G 33 LEU cc_start: 0.8250 (mt) cc_final: 0.8047 (tp) REVERT: G 64 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7680 (tm-30) REVERT: G 68 ASN cc_start: 0.8688 (t0) cc_final: 0.7886 (t0) REVERT: H 31 LYS cc_start: 0.8264 (tptp) cc_final: 0.7801 (ttpt) REVERT: H 34 TYR cc_start: 0.8282 (m-80) cc_final: 0.7924 (m-10) REVERT: H 48 ASP cc_start: 0.7647 (p0) cc_final: 0.7198 (p0) REVERT: H 110 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7651 (mm-30) REVERT: H 117 LYS cc_start: 0.8601 (ttpt) cc_final: 0.8216 (ttpt) outliers start: 39 outliers final: 31 residues processed: 183 average time/residue: 0.2072 time to fit residues: 56.4427 Evaluate side-chains 190 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 156 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12906 Z= 0.236 Angle : 0.623 8.876 18692 Z= 0.358 Chirality : 0.035 0.145 2130 Planarity : 0.005 0.047 1345 Dihedral : 31.675 178.160 4063 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 5.96 % Allowed : 21.47 % Favored : 72.57 % 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: 1.14 (0.31), residues: 746 helix: 1.65 (0.22), residues: 529 sheet: None (None), residues: 0 loop : -1.54 (0.43), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 75 PHE 0.008 0.001 PHE D 67 TYR 0.014 0.002 TYR B 88 ARG 0.004 0.000 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 154 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.8164 (p) cc_final: 0.7845 (p) REVERT: A 123 ASP cc_start: 0.7949 (m-30) cc_final: 0.7509 (m-30) REVERT: B 74 GLU cc_start: 0.8462 (tp30) cc_final: 0.7545 (tp30) REVERT: C 33 LEU cc_start: 0.8506 (mt) cc_final: 0.8089 (tp) REVERT: C 64 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7596 (tm-30) REVERT: C 76 THR cc_start: 0.8512 (p) cc_final: 0.8105 (t) REVERT: D 31 LYS cc_start: 0.7609 (mttt) cc_final: 0.7255 (ttpt) REVERT: D 59 MET cc_start: 0.8411 (tpp) cc_final: 0.7618 (tpp) REVERT: D 88 SER cc_start: 0.8627 (p) cc_final: 0.8353 (t) REVERT: D 117 LYS cc_start: 0.8445 (tttt) cc_final: 0.8099 (ttmt) REVERT: E 123 ASP cc_start: 0.7844 (m-30) cc_final: 0.7065 (m-30) REVERT: G 33 LEU cc_start: 0.8335 (mt) cc_final: 0.8120 (tp) REVERT: G 64 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7609 (tm-30) REVERT: G 68 ASN cc_start: 0.8819 (t0) cc_final: 0.8083 (t0) REVERT: H 31 LYS cc_start: 0.8311 (tptp) cc_final: 0.7800 (ttpt) REVERT: H 48 ASP cc_start: 0.7676 (p0) cc_final: 0.7196 (p0) REVERT: H 59 MET cc_start: 0.8457 (tpp) cc_final: 0.7868 (tpp) REVERT: H 110 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7664 (mm-30) REVERT: H 117 LYS cc_start: 0.8678 (ttpt) cc_final: 0.8311 (ttpt) outliers start: 38 outliers final: 35 residues processed: 175 average time/residue: 0.1943 time to fit residues: 51.4737 Evaluate side-chains 181 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 146 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 75 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12906 Z= 0.180 Angle : 0.599 9.522 18692 Z= 0.342 Chirality : 0.034 0.151 2130 Planarity : 0.004 0.049 1345 Dihedral : 31.587 177.769 4063 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 5.64 % Allowed : 21.79 % Favored : 72.57 % 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: 1.48 (0.31), residues: 746 helix: 1.90 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -1.31 (0.44), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.006 0.001 PHE D 67 TYR 0.013 0.001 TYR B 88 ARG 0.005 0.000 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 166 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.7147 (m-80) cc_final: 0.6842 (m-80) REVERT: A 61 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7640 (mp) REVERT: A 87 SER cc_start: 0.8155 (p) cc_final: 0.7870 (p) REVERT: A 123 ASP cc_start: 0.7761 (m-30) cc_final: 0.7314 (m-30) REVERT: C 33 LEU cc_start: 0.8404 (mt) cc_final: 0.8042 (tp) REVERT: C 56 GLU cc_start: 0.8147 (tt0) cc_final: 0.7462 (tm-30) REVERT: C 64 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7541 (tm-30) REVERT: C 76 THR cc_start: 0.8467 (p) cc_final: 0.8039 (t) REVERT: D 31 LYS cc_start: 0.7496 (mttt) cc_final: 0.7220 (ttpt) REVERT: D 59 MET cc_start: 0.8281 (tpp) cc_final: 0.7950 (tpp) REVERT: D 110 GLU cc_start: 0.8188 (tp30) cc_final: 0.7885 (tt0) REVERT: D 117 LYS cc_start: 0.8439 (tttt) cc_final: 0.8116 (ttmt) REVERT: E 123 ASP cc_start: 0.7792 (m-30) cc_final: 0.7212 (m-30) REVERT: G 33 LEU cc_start: 0.8270 (mt) cc_final: 0.8069 (tp) REVERT: G 64 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7635 (tm-30) REVERT: G 68 ASN cc_start: 0.8660 (t0) cc_final: 0.7844 (t0) REVERT: H 31 LYS cc_start: 0.8254 (tptp) cc_final: 0.7778 (ttpt) REVERT: H 34 TYR cc_start: 0.8261 (m-80) cc_final: 0.7975 (m-10) REVERT: H 48 ASP cc_start: 0.7653 (p0) cc_final: 0.7203 (p0) REVERT: H 59 MET cc_start: 0.8341 (tpp) cc_final: 0.7712 (tpp) REVERT: H 110 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7640 (mm-30) REVERT: H 117 LYS cc_start: 0.8678 (ttpt) cc_final: 0.8322 (ttpt) outliers start: 36 outliers final: 32 residues processed: 185 average time/residue: 0.2056 time to fit residues: 56.8900 Evaluate side-chains 186 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 153 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 94 optimal weight: 8.9990 chunk 57 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12906 Z= 0.214 Angle : 0.626 10.229 18692 Z= 0.353 Chirality : 0.035 0.174 2130 Planarity : 0.004 0.048 1345 Dihedral : 31.581 177.971 4063 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 5.49 % Allowed : 22.26 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.31), residues: 746 helix: 1.89 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.35 (0.43), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.007 0.001 PHE D 67 TYR 0.021 0.002 TYR B 88 ARG 0.004 0.000 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 158 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7720 (mp) REVERT: A 87 SER cc_start: 0.8171 (p) cc_final: 0.7824 (p) REVERT: C 33 LEU cc_start: 0.8473 (mt) cc_final: 0.8087 (tp) REVERT: C 64 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7582 (tm-30) REVERT: C 76 THR cc_start: 0.8482 (p) cc_final: 0.8054 (t) REVERT: D 31 LYS cc_start: 0.7585 (mttt) cc_final: 0.7244 (ttpt) REVERT: D 59 MET cc_start: 0.8349 (tpp) cc_final: 0.7933 (tpp) REVERT: D 88 SER cc_start: 0.8674 (p) cc_final: 0.8386 (t) REVERT: D 110 GLU cc_start: 0.8202 (tp30) cc_final: 0.7889 (tt0) REVERT: D 117 LYS cc_start: 0.8420 (tttt) cc_final: 0.8174 (ttmt) REVERT: E 123 ASP cc_start: 0.7757 (m-30) cc_final: 0.7172 (m-30) REVERT: G 33 LEU cc_start: 0.8316 (mt) cc_final: 0.8114 (tp) REVERT: G 64 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7657 (tm-30) REVERT: G 68 ASN cc_start: 0.8655 (t0) cc_final: 0.7855 (t0) REVERT: H 31 LYS cc_start: 0.8399 (tptp) cc_final: 0.7892 (ttpt) REVERT: H 34 TYR cc_start: 0.8293 (m-80) cc_final: 0.7976 (m-10) REVERT: H 48 ASP cc_start: 0.7591 (p0) cc_final: 0.7003 (p0) REVERT: H 59 MET cc_start: 0.8530 (tpp) cc_final: 0.7802 (tpp) REVERT: H 110 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7643 (mm-30) REVERT: H 117 LYS cc_start: 0.8699 (ttpt) cc_final: 0.8341 (ttpt) outliers start: 35 outliers final: 33 residues processed: 177 average time/residue: 0.2064 time to fit residues: 54.5850 Evaluate side-chains 185 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 151 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 48 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 24 optimal weight: 0.0980 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 85 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12906 Z= 0.177 Angle : 0.614 10.077 18692 Z= 0.345 Chirality : 0.034 0.174 2130 Planarity : 0.005 0.102 1345 Dihedral : 31.485 177.689 4063 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.55 % Allowed : 23.04 % Favored : 72.41 % 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: 1.62 (0.32), residues: 746 helix: 2.01 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.23 (0.43), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 82 PHE 0.008 0.001 PHE A 67 TYR 0.010 0.001 TYR F 51 ARG 0.004 0.000 ARG A 69 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 163 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.7155 (m-80) cc_final: 0.6909 (m-80) REVERT: A 61 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7672 (mp) REVERT: A 73 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8537 (tm-30) REVERT: A 123 ASP cc_start: 0.7336 (m-30) cc_final: 0.7125 (m-30) REVERT: C 33 LEU cc_start: 0.8381 (mt) cc_final: 0.8030 (tp) REVERT: C 56 GLU cc_start: 0.8152 (tt0) cc_final: 0.7371 (tm-30) REVERT: C 64 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7536 (tm-30) REVERT: C 76 THR cc_start: 0.8481 (p) cc_final: 0.8047 (t) REVERT: D 31 LYS cc_start: 0.7471 (mttt) cc_final: 0.7207 (ttpt) REVERT: D 59 MET cc_start: 0.8227 (tpp) cc_final: 0.7916 (tpp) REVERT: D 113 LYS cc_start: 0.9045 (tppt) cc_final: 0.8835 (mtmm) REVERT: G 33 LEU cc_start: 0.8257 (mt) cc_final: 0.8048 (tp) REVERT: G 64 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7673 (tm-30) REVERT: G 68 ASN cc_start: 0.8656 (t0) cc_final: 0.7823 (t0) REVERT: G 100 VAL cc_start: 0.9001 (p) cc_final: 0.8631 (m) REVERT: H 31 LYS cc_start: 0.8342 (tptp) cc_final: 0.7818 (ttpt) REVERT: H 48 ASP cc_start: 0.7576 (p0) cc_final: 0.6998 (p0) REVERT: H 59 MET cc_start: 0.8361 (tpp) cc_final: 0.7645 (tpp) REVERT: H 110 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7636 (mm-30) REVERT: H 117 LYS cc_start: 0.8673 (ttpt) cc_final: 0.8332 (ttpt) outliers start: 29 outliers final: 25 residues processed: 178 average time/residue: 0.2199 time to fit residues: 58.2664 Evaluate side-chains 177 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 151 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** 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 = 0.3769 r_free = 0.3769 target = 0.096718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.080585 restraints weight = 43058.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.082307 restraints weight = 22325.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.083450 restraints weight = 14776.688| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12906 Z= 0.210 Angle : 0.627 9.884 18692 Z= 0.352 Chirality : 0.035 0.166 2130 Planarity : 0.005 0.100 1345 Dihedral : 31.471 177.835 4063 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.23 % Allowed : 24.29 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.32), residues: 746 helix: 1.96 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.20 (0.44), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 113 PHE 0.006 0.001 PHE D 67 TYR 0.012 0.001 TYR F 51 ARG 0.009 0.000 ARG A 116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1949.19 seconds wall clock time: 36 minutes 7.02 seconds (2167.02 seconds total)