Starting phenix.real_space_refine on Thu Sep 26 00:26:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6esf_3947/09_2024/6esf_3947.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6esf_3947/09_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_3947/09_2024/6esf_3947.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6esf_3947/09_2024/6esf_3947.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6esf_3947/09_2024/6esf_3947.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6esf_3947/09_2024/6esf_3947.cif" } 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 7.22, per 1000 atoms: 0.60 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 - 3.00 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: 3.18 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: 5.82 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: 4.33 Time building geometry restraints manager: 3.50 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: 0.00 - 1.83: 17351 1.83 - 3.66: 1211 3.66 - 5.49: 103 5.49 - 7.32: 22 7.32 - 9.14: 5 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 3.120 nonbonded pdb=" OH TYR A 99 " pdb=" OE2 GLU A 133 " model vdw 2.275 3.040 nonbonded pdb=" OH TYR C 39 " pdb=" OE1 GLU D 68 " model vdw 2.282 3.040 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.293 3.040 nonbonded pdb=" O VAL H 115 " pdb=" OG1 THR H 119 " model vdw 2.299 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 0.200 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: 0.450 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 32.730 Find NCS groups from input model: 0.290 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.600 ------------------------------------------------------------------------------- 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 : 0.941 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: 0.2910 time to fit residues: 110.8007 Evaluate side-chains 168 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 166 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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: 0.7980 chunk 25 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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** F 93 GLN G 38 ASN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12906 Z= 0.199 Angle : 0.655 11.374 18692 Z= 0.382 Chirality : 0.037 0.173 2130 Planarity : 0.006 0.057 1345 Dihedral : 32.269 178.294 4065 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.61 % Allowed : 14.89 % Favored : 81.50 % 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: -1.16 (0.28), residues: 746 helix: -0.20 (0.20), residues: 528 sheet: None (None), residues: 0 loop : -1.99 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS H 46 PHE 0.011 0.001 PHE D 67 TYR 0.027 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 236 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 213 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8059 (mm) cc_final: 0.7730 (mm) REVERT: A 94 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7719 (mm-30) REVERT: A 123 ASP cc_start: 0.7969 (m-30) cc_final: 0.7523 (m-30) REVERT: C 25 PHE cc_start: 0.8887 (OUTLIER) cc_final: 0.8662 (m-80) REVERT: C 33 LEU cc_start: 0.8113 (mt) cc_final: 0.7807 (tp) REVERT: C 64 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7444 (tm-30) REVERT: C 76 THR cc_start: 0.8978 (p) cc_final: 0.8551 (t) REVERT: C 85 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7476 (mt) REVERT: C 100 VAL cc_start: 0.9247 (OUTLIER) cc_final: 0.8791 (m) REVERT: D 31 LYS cc_start: 0.7749 (mttt) cc_final: 0.7270 (pttt) REVERT: E 123 ASP cc_start: 0.7913 (m-30) cc_final: 0.7172 (m-30) REVERT: G 33 LEU cc_start: 0.8084 (mt) cc_final: 0.7821 (tp) REVERT: G 57 TYR cc_start: 0.8732 (t80) cc_final: 0.8498 (t80) REVERT: G 64 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7657 (tm-30) REVERT: G 68 ASN cc_start: 0.8532 (t0) cc_final: 0.7822 (t0) REVERT: H 31 LYS cc_start: 0.8282 (tptp) cc_final: 0.7965 (ttpt) REVERT: H 39 TYR cc_start: 0.7601 (t80) cc_final: 0.6992 (t80) REVERT: H 110 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7878 (mm-30) REVERT: H 117 LYS cc_start: 0.8616 (tttm) cc_final: 0.8264 (ttpt) outliers start: 23 outliers final: 14 residues processed: 229 average time/residue: 0.2284 time to fit residues: 74.7284 Evaluate side-chains 181 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 164 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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 82 THR Chi-restraints excluded: chain C residue 25 PHE 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 E residue 51 ILE Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 115 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: 3.9990 chunk 28 optimal weight: 0.7980 chunk 75 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 90 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- 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 ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 12906 Z= 0.327 Angle : 0.710 8.140 18692 Z= 0.409 Chirality : 0.039 0.159 2130 Planarity : 0.006 0.053 1345 Dihedral : 32.206 179.690 4065 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 6.43 % Allowed : 17.55 % Favored : 76.02 % 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: -0.05 (0.30), residues: 746 helix: 0.73 (0.22), residues: 527 sheet: None (None), residues: 0 loop : -1.84 (0.43), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS F 75 PHE 0.013 0.002 PHE D 67 TYR 0.014 0.002 TYR C 39 ARG 0.007 0.001 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 202 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 161 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8001 (mm-30) REVERT: A 106 ASP cc_start: 0.7287 (t70) cc_final: 0.7007 (t70) REVERT: A 108 ASN cc_start: 0.8329 (t0) cc_final: 0.8114 (t0) REVERT: A 123 ASP cc_start: 0.8086 (m-30) cc_final: 0.7687 (m-30) REVERT: B 49 LEU cc_start: 0.8612 (mp) cc_final: 0.8362 (mp) REVERT: B 74 GLU cc_start: 0.8454 (tp30) cc_final: 0.7710 (tp30) REVERT: C 33 LEU cc_start: 0.8504 (mt) cc_final: 0.8057 (tp) REVERT: C 64 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7635 (tm-30) REVERT: C 76 THR cc_start: 0.8994 (p) cc_final: 0.8689 (t) REVERT: D 31 LYS cc_start: 0.7873 (mttt) cc_final: 0.7439 (pttt) REVERT: D 59 MET cc_start: 0.8474 (tpp) cc_final: 0.7832 (tpp) REVERT: D 117 LYS cc_start: 0.8443 (tttt) cc_final: 0.7761 (tttt) REVERT: E 123 ASP cc_start: 0.8118 (m-30) cc_final: 0.7427 (m-30) REVERT: G 33 LEU cc_start: 0.8228 (mt) cc_final: 0.7812 (tp) REVERT: G 57 TYR cc_start: 0.8954 (t80) cc_final: 0.8728 (t80) REVERT: G 61 GLU cc_start: 0.8234 (tp30) cc_final: 0.8021 (tp30) REVERT: G 68 ASN cc_start: 0.8841 (t0) cc_final: 0.8188 (t0) REVERT: H 31 LYS cc_start: 0.8325 (tptp) cc_final: 0.7862 (ttpt) REVERT: H 39 TYR cc_start: 0.7345 (t80) cc_final: 0.7097 (t80) REVERT: H 48 ASP cc_start: 0.7732 (p0) cc_final: 0.7374 (p0) REVERT: H 102 GLU cc_start: 0.7377 (tm-30) cc_final: 0.7166 (tm-30) REVERT: H 110 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7728 (mm-30) outliers start: 41 outliers final: 32 residues processed: 192 average time/residue: 0.2068 time to fit residues: 59.0403 Evaluate side-chains 183 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 151 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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 109 LEU Chi-restraints excluded: chain B residue 34 ILE 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 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 51 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 34 ILE 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 58 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 115 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: 5.9990 chunk 47 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7325 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12906 Z= 0.246 Angle : 0.646 9.066 18692 Z= 0.375 Chirality : 0.036 0.158 2130 Planarity : 0.005 0.052 1345 Dihedral : 32.059 179.044 4065 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 6.11 % Allowed : 18.50 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.31), residues: 746 helix: 1.22 (0.22), residues: 527 sheet: None (None), residues: 0 loop : -1.79 (0.43), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 75 PHE 0.008 0.001 PHE D 67 TYR 0.015 0.002 TYR B 88 ARG 0.005 0.000 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 204 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 165 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.7539 (t70) cc_final: 0.7288 (t70) REVERT: A 123 ASP cc_start: 0.8092 (m-30) cc_final: 0.7327 (m-30) REVERT: B 49 LEU cc_start: 0.8648 (mp) cc_final: 0.8292 (mp) REVERT: B 74 GLU cc_start: 0.8353 (tp30) cc_final: 0.7561 (tp30) REVERT: C 33 LEU cc_start: 0.8480 (mt) cc_final: 0.8025 (tp) REVERT: C 64 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7598 (tm-30) REVERT: C 76 THR cc_start: 0.8968 (p) cc_final: 0.8677 (t) REVERT: D 31 LYS cc_start: 0.7575 (mttt) cc_final: 0.7226 (pttt) REVERT: D 59 MET cc_start: 0.8409 (tpp) cc_final: 0.7713 (tpp) REVERT: D 90 GLU cc_start: 0.8101 (mp0) cc_final: 0.7712 (pm20) REVERT: E 123 ASP cc_start: 0.8107 (m-30) cc_final: 0.7358 (m-30) REVERT: G 33 LEU cc_start: 0.8323 (mt) cc_final: 0.8037 (tp) REVERT: G 57 TYR cc_start: 0.8859 (t80) cc_final: 0.8646 (t80) REVERT: G 61 GLU cc_start: 0.7928 (tp30) cc_final: 0.7685 (tp30) REVERT: G 68 ASN cc_start: 0.8858 (t0) cc_final: 0.8175 (t0) REVERT: H 31 LYS cc_start: 0.8285 (tptp) cc_final: 0.7847 (ttpt) REVERT: H 34 TYR cc_start: 0.8429 (m-80) cc_final: 0.7984 (m-10) REVERT: H 39 TYR cc_start: 0.7499 (t80) cc_final: 0.7079 (t80) REVERT: H 48 ASP cc_start: 0.7861 (p0) cc_final: 0.7435 (p0) REVERT: H 110 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7703 (mm-30) REVERT: H 117 LYS cc_start: 0.8768 (ttpt) cc_final: 0.8518 (ttpt) outliers start: 39 outliers final: 33 residues processed: 192 average time/residue: 0.2093 time to fit residues: 59.7794 Evaluate side-chains 187 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 154 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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 109 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 46 ILE 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 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 86 VAL 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 100 VAL Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 70 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 49 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12906 Z= 0.223 Angle : 0.631 9.153 18692 Z= 0.364 Chirality : 0.036 0.157 2130 Planarity : 0.005 0.053 1345 Dihedral : 31.888 178.169 4063 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 5.49 % Allowed : 20.22 % Favored : 74.29 % 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: 0.89 (0.31), residues: 746 helix: 1.47 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.66 (0.44), residues: 216 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 0.020 0.002 TYR B 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 194 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 159 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.8027 (p) cc_final: 0.7775 (p) REVERT: A 108 ASN cc_start: 0.8218 (t0) cc_final: 0.7791 (t0) REVERT: A 123 ASP cc_start: 0.8063 (m-30) cc_final: 0.7239 (m-30) REVERT: B 53 GLU cc_start: 0.8747 (tp30) cc_final: 0.8512 (tp30) REVERT: B 74 GLU cc_start: 0.8394 (tp30) cc_final: 0.7628 (tp30) REVERT: C 33 LEU cc_start: 0.8423 (mt) cc_final: 0.8030 (tp) REVERT: C 64 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7601 (tm-30) REVERT: C 76 THR cc_start: 0.8878 (p) cc_final: 0.8564 (t) REVERT: D 31 LYS cc_start: 0.7595 (mttt) cc_final: 0.7243 (pttt) REVERT: D 59 MET cc_start: 0.8394 (tpp) cc_final: 0.7674 (tpp) REVERT: D 90 GLU cc_start: 0.7967 (mp0) cc_final: 0.7619 (mp0) REVERT: D 117 LYS cc_start: 0.8411 (tttt) cc_final: 0.7783 (tttt) REVERT: E 94 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8209 (mm-30) REVERT: E 97 GLU cc_start: 0.8411 (pp20) cc_final: 0.8133 (pp20) REVERT: E 123 ASP cc_start: 0.7693 (m-30) cc_final: 0.7050 (m-30) REVERT: G 33 LEU cc_start: 0.8312 (mt) cc_final: 0.8091 (tp) REVERT: G 61 GLU cc_start: 0.7966 (tp30) cc_final: 0.7706 (tp30) REVERT: G 68 ASN cc_start: 0.8715 (t0) cc_final: 0.7998 (t0) REVERT: H 31 LYS cc_start: 0.8115 (tptp) cc_final: 0.7797 (ttpt) REVERT: H 34 TYR cc_start: 0.8353 (m-80) cc_final: 0.7875 (m-10) REVERT: H 48 ASP cc_start: 0.7816 (p0) cc_final: 0.7306 (p0) REVERT: H 59 MET cc_start: 0.8497 (tpp) cc_final: 0.8003 (tpp) REVERT: H 110 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7703 (mm-30) REVERT: H 117 LYS cc_start: 0.8722 (ttpt) cc_final: 0.8451 (ttpt) outliers start: 35 outliers final: 28 residues processed: 179 average time/residue: 0.2169 time to fit residues: 57.1957 Evaluate side-chains 176 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 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 109 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 46 ILE 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 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 82 LEU Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 63 VAL 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: 5.9990 chunk 56 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 44 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 0.0770 chunk 93 optimal weight: 8.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN H 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12906 Z= 0.175 Angle : 0.601 9.504 18692 Z= 0.345 Chirality : 0.034 0.162 2130 Planarity : 0.005 0.056 1345 Dihedral : 31.690 177.929 4063 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.08 % Allowed : 22.88 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.31), residues: 746 helix: 1.70 (0.22), residues: 529 sheet: None (None), residues: 0 loop : -1.56 (0.44), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 82 PHE 0.005 0.001 PHE D 67 TYR 0.011 0.001 TYR G 57 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 204 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 178 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: A 87 SER cc_start: 0.8013 (p) cc_final: 0.7743 (p) REVERT: A 108 ASN cc_start: 0.8072 (t0) cc_final: 0.7740 (t0) REVERT: A 123 ASP cc_start: 0.7906 (m-30) cc_final: 0.7104 (m-30) REVERT: B 53 GLU cc_start: 0.8706 (tp30) cc_final: 0.8420 (tp30) REVERT: C 33 LEU cc_start: 0.8361 (mt) cc_final: 0.8029 (tp) REVERT: C 56 GLU cc_start: 0.8090 (tt0) cc_final: 0.7385 (tm-30) REVERT: C 64 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7532 (tm-30) REVERT: C 76 THR cc_start: 0.8778 (p) cc_final: 0.8563 (t) REVERT: C 100 VAL cc_start: 0.9144 (p) cc_final: 0.8720 (m) REVERT: D 31 LYS cc_start: 0.7475 (mttt) cc_final: 0.7174 (pttt) REVERT: D 59 MET cc_start: 0.8327 (tpp) cc_final: 0.7594 (tpp) REVERT: D 90 GLU cc_start: 0.8016 (mp0) cc_final: 0.7711 (mp0) REVERT: D 117 LYS cc_start: 0.8194 (tttt) cc_final: 0.7729 (tptt) REVERT: E 94 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8272 (mm-30) REVERT: E 123 ASP cc_start: 0.7615 (m-30) cc_final: 0.7156 (m-30) REVERT: G 61 GLU cc_start: 0.7867 (tp30) cc_final: 0.7642 (tp30) REVERT: G 64 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7636 (tm-30) REVERT: G 68 ASN cc_start: 0.8638 (t0) cc_final: 0.7858 (t0) REVERT: G 100 VAL cc_start: 0.9101 (OUTLIER) cc_final: 0.8709 (m) REVERT: H 31 LYS cc_start: 0.8168 (tptp) cc_final: 0.7704 (ttpt) REVERT: H 34 TYR cc_start: 0.8204 (m-80) cc_final: 0.7898 (m-10) REVERT: H 48 ASP cc_start: 0.7760 (p0) cc_final: 0.7295 (p0) REVERT: H 59 MET cc_start: 0.8327 (tpp) cc_final: 0.7803 (tpp) REVERT: H 117 LYS cc_start: 0.8517 (ttpt) cc_final: 0.8064 (ttpt) outliers start: 26 outliers final: 13 residues processed: 194 average time/residue: 0.2110 time to fit residues: 60.3250 Evaluate side-chains 171 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 157 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 84 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: 0.0050 chunk 70 optimal weight: 0.0370 chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.8078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12906 Z= 0.213 Angle : 0.627 10.000 18692 Z= 0.356 Chirality : 0.035 0.156 2130 Planarity : 0.005 0.054 1345 Dihedral : 31.633 178.237 4063 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.08 % Allowed : 23.82 % Favored : 72.10 % 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: 1.17 (0.31), residues: 746 helix: 1.66 (0.22), residues: 529 sheet: None (None), residues: 0 loop : -1.50 (0.44), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 75 PHE 0.012 0.001 PHE H 67 TYR 0.019 0.002 TYR D 80 ARG 0.003 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 185 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 159 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: A 41 TYR cc_start: 0.7060 (m-80) cc_final: 0.6768 (m-80) REVERT: A 87 SER cc_start: 0.8178 (p) cc_final: 0.7864 (p) REVERT: A 108 ASN cc_start: 0.8149 (t0) cc_final: 0.7737 (t0) REVERT: A 123 ASP cc_start: 0.7924 (m-30) cc_final: 0.7072 (m-30) REVERT: C 33 LEU cc_start: 0.8427 (mt) cc_final: 0.8062 (tp) REVERT: C 64 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7602 (tm-30) REVERT: C 76 THR cc_start: 0.8730 (p) cc_final: 0.8505 (t) REVERT: D 31 LYS cc_start: 0.7501 (mttt) cc_final: 0.7225 (pttt) REVERT: D 59 MET cc_start: 0.8382 (tpp) cc_final: 0.7604 (tpp) REVERT: D 90 GLU cc_start: 0.8019 (mp0) cc_final: 0.7726 (mp0) REVERT: D 117 LYS cc_start: 0.8254 (tttt) cc_final: 0.7761 (tptt) REVERT: E 123 ASP cc_start: 0.7935 (m-30) cc_final: 0.7439 (m-30) REVERT: G 68 ASN cc_start: 0.8517 (t0) cc_final: 0.7874 (t0) REVERT: G 92 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7431 (pt0) REVERT: H 31 LYS cc_start: 0.8201 (tptp) cc_final: 0.7751 (ttpt) REVERT: H 34 TYR cc_start: 0.8306 (m-80) cc_final: 0.7907 (m-10) REVERT: H 48 ASP cc_start: 0.7801 (p0) cc_final: 0.7285 (p0) REVERT: H 59 MET cc_start: 0.8561 (tpp) cc_final: 0.8018 (tpp) REVERT: H 90 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7432 (pm20) REVERT: H 117 LYS cc_start: 0.8537 (ttpt) cc_final: 0.8079 (ttpt) outliers start: 26 outliers final: 19 residues processed: 174 average time/residue: 0.2058 time to fit residues: 53.3114 Evaluate side-chains 169 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 148 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 18 SER 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 F residue 34 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 90 GLU 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: 4.9990 chunk 18 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 65 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 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: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12906 Z= 0.232 Angle : 0.646 9.443 18692 Z= 0.364 Chirality : 0.036 0.153 2130 Planarity : 0.005 0.053 1345 Dihedral : 31.630 177.972 4063 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.55 % Allowed : 24.29 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.31), residues: 746 helix: 1.64 (0.22), residues: 529 sheet: None (None), residues: 0 loop : -1.53 (0.43), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 75 PHE 0.009 0.001 PHE H 67 TYR 0.037 0.002 TYR D 80 ARG 0.003 0.000 ARG C 77 *********************** 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 183 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 154 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: A 87 SER cc_start: 0.8170 (p) cc_final: 0.7857 (p) REVERT: A 108 ASN cc_start: 0.8394 (t0) cc_final: 0.8023 (t0) REVERT: A 123 ASP cc_start: 0.7924 (m-30) cc_final: 0.7047 (m-30) REVERT: C 33 LEU cc_start: 0.8451 (mt) cc_final: 0.8107 (tp) REVERT: C 64 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7622 (tm-30) REVERT: C 76 THR cc_start: 0.8670 (p) cc_final: 0.8447 (t) REVERT: D 31 LYS cc_start: 0.7540 (mttt) cc_final: 0.7254 (pttt) REVERT: D 59 MET cc_start: 0.8370 (tpp) cc_final: 0.7586 (tpp) REVERT: D 117 LYS cc_start: 0.8294 (tttt) cc_final: 0.7791 (tptt) REVERT: E 94 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8175 (mm-30) REVERT: E 123 ASP cc_start: 0.7956 (m-30) cc_final: 0.7481 (m-30) REVERT: G 64 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7720 (tm-30) REVERT: G 68 ASN cc_start: 0.8628 (t0) cc_final: 0.7830 (t0) REVERT: H 31 LYS cc_start: 0.8331 (tptp) cc_final: 0.7855 (ttpt) REVERT: H 34 TYR cc_start: 0.8302 (m-80) cc_final: 0.7813 (m-10) REVERT: H 48 ASP cc_start: 0.7739 (p0) cc_final: 0.7199 (p0) REVERT: H 58 ILE cc_start: 0.9143 (tt) cc_final: 0.8891 (tt) REVERT: H 59 MET cc_start: 0.8663 (tpp) cc_final: 0.8054 (tpp) REVERT: H 110 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7676 (mm-30) REVERT: H 117 LYS cc_start: 0.8598 (ttpt) cc_final: 0.8149 (ttpt) outliers start: 29 outliers final: 25 residues processed: 172 average time/residue: 0.2188 time to fit residues: 57.1628 Evaluate side-chains 173 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 148 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 34 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 18 SER 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 E residue 87 SER Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 115 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 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: 8.9990 chunk 58 optimal weight: 0.9980 chunk 94 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 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 ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12906 Z= 0.246 Angle : 0.661 9.314 18692 Z= 0.372 Chirality : 0.036 0.152 2130 Planarity : 0.005 0.053 1345 Dihedral : 31.645 177.937 4063 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.23 % Allowed : 25.24 % Favored : 70.53 % 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: 1.06 (0.31), residues: 746 helix: 1.57 (0.22), residues: 529 sheet: None (None), residues: 0 loop : -1.52 (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 0.051 0.002 TYR D 80 ARG 0.003 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 176 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 149 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: A 87 SER cc_start: 0.8312 (p) cc_final: 0.7911 (p) REVERT: A 123 ASP cc_start: 0.7913 (m-30) cc_final: 0.7013 (m-30) REVERT: C 33 LEU cc_start: 0.8512 (mt) cc_final: 0.8121 (tp) REVERT: C 64 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7623 (tm-30) REVERT: D 31 LYS cc_start: 0.7580 (mttt) cc_final: 0.7268 (pttt) REVERT: D 59 MET cc_start: 0.8409 (tpp) cc_final: 0.7597 (tpp) REVERT: D 90 GLU cc_start: 0.8092 (mp0) cc_final: 0.7889 (pm20) REVERT: D 110 GLU cc_start: 0.8046 (tp30) cc_final: 0.7823 (tt0) REVERT: D 117 LYS cc_start: 0.8298 (tttt) cc_final: 0.7767 (tptt) REVERT: E 79 LYS cc_start: 0.7881 (ttpp) cc_final: 0.7602 (ptmm) REVERT: E 123 ASP cc_start: 0.7883 (m-30) cc_final: 0.7443 (m-30) REVERT: G 64 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7660 (tm-30) REVERT: G 68 ASN cc_start: 0.8626 (t0) cc_final: 0.7829 (t0) REVERT: H 31 LYS cc_start: 0.8337 (tptp) cc_final: 0.7849 (ttpt) REVERT: H 34 TYR cc_start: 0.8364 (m-80) cc_final: 0.7885 (m-10) REVERT: H 48 ASP cc_start: 0.7815 (p0) cc_final: 0.7240 (p0) REVERT: H 110 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7664 (mm-30) REVERT: H 117 LYS cc_start: 0.8678 (ttpt) cc_final: 0.8219 (ttpt) outliers start: 27 outliers final: 26 residues processed: 171 average time/residue: 0.2141 time to fit residues: 54.7148 Evaluate side-chains 167 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 141 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 18 SER 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 E residue 87 SER Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 70 ILE 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: 6.9990 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** F 75 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: 0.7252 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12906 Z= 0.207 Angle : 0.649 9.610 18692 Z= 0.364 Chirality : 0.035 0.154 2130 Planarity : 0.005 0.055 1345 Dihedral : 31.588 177.852 4063 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.29 % Allowed : 26.96 % Favored : 69.75 % 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: 1.26 (0.31), residues: 746 helix: 1.74 (0.22), residues: 523 sheet: None (None), residues: 0 loop : -1.42 (0.44), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.007 0.001 PHE H 67 TYR 0.047 0.002 TYR D 80 ARG 0.004 0.000 ARG C 77 ********************** 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 172 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 151 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.8138 (p) cc_final: 0.7812 (p) REVERT: A 108 ASN cc_start: 0.8491 (t0) cc_final: 0.8158 (t0) REVERT: A 123 ASP cc_start: 0.7948 (m-30) cc_final: 0.7130 (m-30) REVERT: C 33 LEU cc_start: 0.8444 (mt) cc_final: 0.8073 (tp) REVERT: C 64 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7600 (tm-30) REVERT: D 31 LYS cc_start: 0.7547 (mttt) cc_final: 0.7234 (pttt) REVERT: D 59 MET cc_start: 0.8326 (tpp) cc_final: 0.7542 (tpp) REVERT: D 90 GLU cc_start: 0.8124 (mp0) cc_final: 0.7896 (pm20) REVERT: D 110 GLU cc_start: 0.8207 (tp30) cc_final: 0.7874 (tt0) REVERT: D 117 LYS cc_start: 0.8283 (tttt) cc_final: 0.7783 (tptt) REVERT: E 82 LEU cc_start: 0.8363 (mm) cc_final: 0.8013 (mt) REVERT: E 123 ASP cc_start: 0.7859 (m-30) cc_final: 0.7361 (m-30) REVERT: G 64 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7638 (tm-30) REVERT: G 68 ASN cc_start: 0.8617 (t0) cc_final: 0.7836 (t0) REVERT: H 31 LYS cc_start: 0.8297 (tptp) cc_final: 0.7764 (ttpt) REVERT: H 48 ASP cc_start: 0.7735 (p0) cc_final: 0.7170 (p0) REVERT: H 58 ILE cc_start: 0.9111 (tt) cc_final: 0.8884 (tt) REVERT: H 59 MET cc_start: 0.8627 (tpp) cc_final: 0.8023 (tpp) REVERT: H 110 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7655 (mm-30) REVERT: H 117 LYS cc_start: 0.8658 (ttpt) cc_final: 0.8208 (ttpt) outliers start: 21 outliers final: 20 residues processed: 168 average time/residue: 0.2222 time to fit residues: 54.3898 Evaluate side-chains 166 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 146 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 18 SER 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 86 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 100 VAL 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 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 73 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 69 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** 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 = 0.3768 r_free = 0.3768 target = 0.096798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.080530 restraints weight = 43019.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.082240 restraints weight = 22602.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.083367 restraints weight = 15070.021| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12906 Z= 0.207 Angle : 0.647 9.669 18692 Z= 0.363 Chirality : 0.035 0.153 2130 Planarity : 0.005 0.055 1345 Dihedral : 31.545 177.869 4063 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.29 % Allowed : 27.43 % Favored : 69.28 % 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: 1.32 (0.31), residues: 746 helix: 1.79 (0.22), residues: 523 sheet: None (None), residues: 0 loop : -1.40 (0.43), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.007 0.001 PHE H 67 TYR 0.041 0.002 TYR D 80 ARG 0.004 0.000 ARG E 116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1985.82 seconds wall clock time: 36 minutes 50.53 seconds (2210.53 seconds total)