Starting phenix.real_space_refine on Mon Apr 8 02:21:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox0_17251/04_2024/8ox0_17251.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox0_17251/04_2024/8ox0_17251.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox0_17251/04_2024/8ox0_17251.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox0_17251/04_2024/8ox0_17251.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox0_17251/04_2024/8ox0_17251.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox0_17251/04_2024/8ox0_17251.pdb" } resolution = 2.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 290 5.49 5 S 14 5.16 5 C 6773 2.51 5 N 2308 2.21 5 O 2886 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 12271 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 708 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "C" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 847 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 774 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "E" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 694 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "G" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 847 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "H" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 774 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "J" Number of atoms: 3064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 3064 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "I" Number of atoms: 2881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2881 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "E" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "G" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "H" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "J" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 6.36, per 1000 atoms: 0.52 Number of scatterers: 12271 At special positions: 0 Unit cell: (92.71, 118.99, 125.56, 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 14 16.00 P 290 15.00 O 2886 8.00 N 2308 7.00 C 6773 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: 5.33 Conformation dependent library (CDL) restraints added in 971.9 milliseconds 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1470 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 70.8% alpha, 3.0% beta 143 base pairs and 278 stacking pairs defined. Time for finding SS restraints: 5.24 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.712A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.519A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.490A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.530A 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 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.524A pdb=" N SER D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.624A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 4.009A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.852A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.802A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.512A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.899A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.567A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.089A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.657A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.836A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.113A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 409 hydrogen bonds defined for protein. 1203 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 355 hydrogen bonds 706 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 278 stacking parallelities Total time for adding SS restraints: 4.91 Time building geometry restraints manager: 5.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1694 1.33 - 1.45: 4763 1.45 - 1.57: 5960 1.57 - 1.69: 578 1.69 - 1.81: 24 Bond restraints: 13019 Sorted by residual: bond pdb=" C ARG F 95 " pdb=" O ARG F 95 " ideal model delta sigma weight residual 1.233 1.203 0.030 1.15e-02 7.56e+03 7.02e+00 bond pdb=" CA GLU E 105 " pdb=" C GLU E 105 " ideal model delta sigma weight residual 1.524 1.557 -0.033 1.27e-02 6.20e+03 6.83e+00 bond pdb=" CA LYS F 31 " pdb=" C LYS F 31 " ideal model delta sigma weight residual 1.520 1.550 -0.029 1.23e-02 6.61e+03 5.75e+00 bond pdb=" C PRO G 26 " pdb=" O PRO G 26 " ideal model delta sigma weight residual 1.235 1.217 0.018 7.90e-03 1.60e+04 4.96e+00 bond pdb=" CA GLU A 105 " pdb=" C GLU A 105 " ideal model delta sigma weight residual 1.524 1.551 -0.028 1.27e-02 6.20e+03 4.74e+00 ... (remaining 13014 not shown) Histogram of bond angle deviations from ideal: 98.52 - 105.29: 1318 105.29 - 112.05: 6849 112.05 - 118.82: 3616 118.82 - 125.58: 6003 125.58 - 132.35: 1018 Bond angle restraints: 18804 Sorted by residual: angle pdb=" O3' DA I 14 " pdb=" C3' DA I 14 " pdb=" C2' DA I 14 " ideal model delta sigma weight residual 111.50 106.11 5.39 1.50e+00 4.44e-01 1.29e+01 angle pdb=" O3' DT J -26 " pdb=" C3' DT J -26 " pdb=" C2' DT J -26 " ideal model delta sigma weight residual 111.50 106.16 5.34 1.50e+00 4.44e-01 1.27e+01 angle pdb=" C4' DT I -18 " pdb=" C3' DT I -18 " pdb=" O3' DT I -18 " ideal model delta sigma weight residual 110.00 114.63 -4.63 1.50e+00 4.44e-01 9.51e+00 angle pdb=" O3' DA I 44 " pdb=" C3' DA I 44 " pdb=" C2' DA I 44 " ideal model delta sigma weight residual 111.50 107.05 4.45 1.50e+00 4.44e-01 8.78e+00 angle pdb=" C2' DT J -26 " pdb=" C1' DT J -26 " pdb=" N1 DT J -26 " ideal model delta sigma weight residual 113.50 117.90 -4.40 1.50e+00 4.44e-01 8.61e+00 ... (remaining 18799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 5747 35.46 - 70.92: 1401 70.92 - 106.38: 4 106.38 - 141.83: 0 141.83 - 177.29: 3 Dihedral angle restraints: 7155 sinusoidal: 4876 harmonic: 2279 Sorted by residual: dihedral pdb=" C4' DT I -18 " pdb=" C3' DT I -18 " pdb=" O3' DT I -18 " pdb=" P DA I -17 " ideal model delta sinusoidal sigma weight residual 220.00 42.71 177.29 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DA J -71 " pdb=" C3' DA J -71 " pdb=" O3' DA J -71 " pdb=" P DT J -70 " ideal model delta sinusoidal sigma weight residual 220.00 43.55 176.45 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC I 22 " pdb=" C3' DC I 22 " pdb=" O3' DC I 22 " pdb=" P DC I 23 " ideal model delta sinusoidal sigma weight residual 220.00 64.11 155.89 1 3.50e+01 8.16e-04 1.50e+01 ... (remaining 7152 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1307 0.048 - 0.096: 634 0.096 - 0.144: 144 0.144 - 0.193: 36 0.193 - 0.241: 8 Chirality restraints: 2129 Sorted by residual: chirality pdb=" C3' DC I 22 " pdb=" C4' DC I 22 " pdb=" O3' DC I 22 " pdb=" C2' DC I 22 " both_signs ideal model delta sigma weight residual False -2.66 -2.42 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C3' DA J -71 " pdb=" C4' DA J -71 " pdb=" O3' DA J -71 " pdb=" C2' DA J -71 " both_signs ideal model delta sigma weight residual False -2.66 -2.43 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA ARG C 88 " pdb=" N ARG C 88 " pdb=" C ARG C 88 " pdb=" CB ARG C 88 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 2126 not shown) Planarity restraints: 1375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG J -35 " -0.034 2.00e-02 2.50e+03 1.43e-02 6.12e+00 pdb=" N9 DG J -35 " 0.032 2.00e-02 2.50e+03 pdb=" C8 DG J -35 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DG J -35 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DG J -35 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DG J -35 " -0.005 2.00e-02 2.50e+03 pdb=" O6 DG J -35 " -0.011 2.00e-02 2.50e+03 pdb=" N1 DG J -35 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DG J -35 " 0.003 2.00e-02 2.50e+03 pdb=" N2 DG J -35 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DG J -35 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DG J -35 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J 15 " -0.033 2.00e-02 2.50e+03 1.38e-02 5.74e+00 pdb=" N9 DG J 15 " 0.028 2.00e-02 2.50e+03 pdb=" C8 DG J 15 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DG J 15 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DG J 15 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DG J 15 " -0.006 2.00e-02 2.50e+03 pdb=" O6 DG J 15 " -0.015 2.00e-02 2.50e+03 pdb=" N1 DG J 15 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG J 15 " 0.007 2.00e-02 2.50e+03 pdb=" N2 DG J 15 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DG J 15 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DG J 15 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 64 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.17e+00 pdb=" C ASN B 64 " 0.039 2.00e-02 2.50e+03 pdb=" O ASN B 64 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL B 65 " -0.013 2.00e-02 2.50e+03 ... (remaining 1372 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 424 2.70 - 3.25: 10392 3.25 - 3.80: 22837 3.80 - 4.35: 29973 4.35 - 4.90: 41615 Nonbonded interactions: 105241 Sorted by model distance: nonbonded pdb=" O ARG F 23 " pdb=" OD1 ASP F 24 " model vdw 2.156 3.040 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.289 2.440 nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.316 2.440 nonbonded pdb=" NH2 ARG B 35 " pdb=" OP2 DG J 8 " model vdw 2.336 2.520 nonbonded pdb=" N2 DG J 21 " pdb=" O2 DC I -21 " model vdw 2.340 2.496 ... (remaining 105236 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 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 17 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 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: 6.340 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 37.330 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.080 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:12.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 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 : 0.007 0.035 13019 Z= 0.405 Angle : 0.876 6.490 18804 Z= 0.568 Chirality : 0.058 0.241 2129 Planarity : 0.005 0.042 1375 Dihedral : 27.178 177.293 5685 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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: 1.78 (0.28), residues: 771 helix: 1.92 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.55 (0.32), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS F 75 PHE 0.019 0.004 PHE H 67 TYR 0.018 0.004 TYR B 51 ARG 0.011 0.001 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8164 (ttt180) cc_final: 0.7737 (ttp-110) REVERT: A 64 LYS cc_start: 0.7812 (mttt) cc_final: 0.7605 (mttp) REVERT: B 91 LYS cc_start: 0.7694 (tttp) cc_final: 0.7174 (ttpt) REVERT: C 90 ASP cc_start: 0.7168 (t0) cc_final: 0.6927 (t70) REVERT: C 91 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7506 (mp0) REVERT: D 48 ASP cc_start: 0.8654 (m-30) cc_final: 0.8277 (OUTLIER) REVERT: D 96 ARG cc_start: 0.7629 (mtm180) cc_final: 0.7230 (mtt90) REVERT: E 68 GLN cc_start: 0.7502 (tt0) cc_final: 0.7122 (tt0) REVERT: F 93 GLN cc_start: 0.7487 (mm-40) cc_final: 0.7141 (mp10) REVERT: G 15 LYS cc_start: 0.7822 (mtmm) cc_final: 0.7282 (mtpt) REVERT: G 73 ASN cc_start: 0.7834 (m110) cc_final: 0.7588 (m110) REVERT: G 75 LYS cc_start: 0.8046 (mttt) cc_final: 0.7783 (mtpp) REVERT: G 90 ASP cc_start: 0.7528 (t0) cc_final: 0.7269 (t0) REVERT: G 95 LYS cc_start: 0.8030 (tttt) cc_final: 0.7660 (tppt) REVERT: G 99 ARG cc_start: 0.7726 (mmm160) cc_final: 0.7242 (mpt180) REVERT: H 31 LYS cc_start: 0.8126 (mtpp) cc_final: 0.7752 (mttp) REVERT: H 105 LYS cc_start: 0.7467 (ttpt) cc_final: 0.7063 (mmtm) outliers start: 0 outliers final: 1 residues processed: 148 average time/residue: 2.0955 time to fit residues: 326.2615 Evaluate side-chains 129 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 92 optimal weight: 8.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.0681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13019 Z= 0.201 Angle : 0.625 7.395 18804 Z= 0.376 Chirality : 0.036 0.166 2129 Planarity : 0.004 0.043 1375 Dihedral : 30.943 179.903 4095 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.37 % Allowed : 8.85 % Favored : 89.77 % 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: 2.30 (0.29), residues: 771 helix: 2.30 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -0.49 (0.33), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 31 PHE 0.013 0.002 PHE A 67 TYR 0.012 0.001 TYR H 37 ARG 0.008 0.000 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 132 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: A 53 ARG cc_start: 0.7823 (ttt180) cc_final: 0.7472 (ttp-110) REVERT: A 64 LYS cc_start: 0.7787 (mttt) cc_final: 0.7582 (mttm) REVERT: B 91 LYS cc_start: 0.7656 (tttp) cc_final: 0.7128 (ttpt) REVERT: C 90 ASP cc_start: 0.7129 (t0) cc_final: 0.6915 (t70) REVERT: C 91 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7375 (mp0) REVERT: D 48 ASP cc_start: 0.8645 (m-30) cc_final: 0.8270 (p0) REVERT: D 96 ARG cc_start: 0.7560 (mtm180) cc_final: 0.7286 (mtm-85) REVERT: E 68 GLN cc_start: 0.7474 (tt0) cc_final: 0.7136 (tt0) REVERT: E 133 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7116 (mt-10) REVERT: F 93 GLN cc_start: 0.7443 (mm-40) cc_final: 0.7066 (mp10) REVERT: G 15 LYS cc_start: 0.7802 (mtmm) cc_final: 0.7275 (mtpt) REVERT: G 73 ASN cc_start: 0.7438 (m110) cc_final: 0.7183 (m110) REVERT: G 95 LYS cc_start: 0.8026 (tttt) cc_final: 0.7667 (tppt) REVERT: G 99 ARG cc_start: 0.7676 (mmm160) cc_final: 0.7174 (mpt180) REVERT: H 31 LYS cc_start: 0.8089 (mtpp) cc_final: 0.7732 (mttp) REVERT: H 105 LYS cc_start: 0.7410 (ttpt) cc_final: 0.7018 (mmmm) outliers start: 9 outliers final: 5 residues processed: 135 average time/residue: 2.0910 time to fit residues: 296.5716 Evaluate side-chains 135 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 129 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain H residue 36 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 3.9990 chunk 28 optimal weight: 20.0000 chunk 77 optimal weight: 8.9990 chunk 63 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 13019 Z= 0.419 Angle : 0.649 8.155 18804 Z= 0.388 Chirality : 0.040 0.162 2129 Planarity : 0.005 0.038 1375 Dihedral : 30.935 178.494 4095 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.98 % Allowed : 9.31 % Favored : 88.70 % 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: 2.39 (0.29), residues: 771 helix: 2.41 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.58 (0.33), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 46 PHE 0.015 0.002 PHE A 104 TYR 0.013 0.002 TYR E 54 ARG 0.003 0.001 ARG F 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: A 53 ARG cc_start: 0.7816 (ttt180) cc_final: 0.7422 (ttp-110) REVERT: B 91 LYS cc_start: 0.7717 (tttp) cc_final: 0.7200 (ttpt) REVERT: C 90 ASP cc_start: 0.7239 (t0) cc_final: 0.7012 (t70) REVERT: C 91 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7413 (mp0) REVERT: D 48 ASP cc_start: 0.8615 (m-30) cc_final: 0.8252 (OUTLIER) REVERT: D 96 ARG cc_start: 0.7561 (mtm180) cc_final: 0.7298 (mtm-85) REVERT: E 133 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7041 (mt-10) REVERT: F 93 GLN cc_start: 0.7428 (mm-40) cc_final: 0.7086 (mp10) REVERT: G 15 LYS cc_start: 0.7777 (mtmm) cc_final: 0.7278 (mtpt) REVERT: G 90 ASP cc_start: 0.7015 (t0) cc_final: 0.6701 (t0) REVERT: G 95 LYS cc_start: 0.8038 (tttt) cc_final: 0.7689 (tppt) REVERT: G 99 ARG cc_start: 0.7600 (mmm160) cc_final: 0.7150 (mpt180) REVERT: H 31 LYS cc_start: 0.8115 (mtpp) cc_final: 0.7752 (mttp) REVERT: H 105 LYS cc_start: 0.7448 (ttpt) cc_final: 0.7033 (mmtm) outliers start: 13 outliers final: 8 residues processed: 127 average time/residue: 2.1435 time to fit residues: 286.1258 Evaluate side-chains 128 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 120 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 112 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 chunk 55 optimal weight: 0.0470 overall best weight: 1.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13019 Z= 0.228 Angle : 0.600 7.221 18804 Z= 0.365 Chirality : 0.036 0.145 2129 Planarity : 0.004 0.039 1375 Dihedral : 30.997 179.412 4095 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.98 % Allowed : 10.84 % Favored : 87.18 % 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: 2.58 (0.29), residues: 771 helix: 2.55 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.49 (0.33), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.010 0.002 PHE A 67 TYR 0.012 0.002 TYR H 37 ARG 0.004 0.000 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 129 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: A 53 ARG cc_start: 0.7814 (ttt180) cc_final: 0.7436 (ttp-110) REVERT: B 91 LYS cc_start: 0.7677 (tttp) cc_final: 0.7170 (ttpt) REVERT: C 90 ASP cc_start: 0.7245 (t0) cc_final: 0.7010 (t70) REVERT: C 91 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7408 (mp0) REVERT: D 48 ASP cc_start: 0.8604 (m-30) cc_final: 0.8263 (p0) REVERT: D 96 ARG cc_start: 0.7538 (mtm180) cc_final: 0.7284 (mtm-85) REVERT: E 68 GLN cc_start: 0.7462 (tt0) cc_final: 0.7096 (tt0) REVERT: E 133 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7039 (mt-10) REVERT: F 93 GLN cc_start: 0.7419 (mm-40) cc_final: 0.7068 (mp10) REVERT: G 15 LYS cc_start: 0.7770 (mtmm) cc_final: 0.7298 (mtpt) REVERT: G 95 LYS cc_start: 0.8028 (tttt) cc_final: 0.7665 (tppt) REVERT: G 99 ARG cc_start: 0.7587 (mmm160) cc_final: 0.7135 (mpt180) REVERT: H 31 LYS cc_start: 0.8102 (mtpp) cc_final: 0.7713 (mttp) REVERT: H 32 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7904 (pt0) REVERT: H 105 LYS cc_start: 0.7403 (ttpt) cc_final: 0.6995 (mmtm) outliers start: 13 outliers final: 8 residues processed: 131 average time/residue: 2.0272 time to fit residues: 279.5032 Evaluate side-chains 136 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 126 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 36 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13019 Z= 0.292 Angle : 0.598 7.129 18804 Z= 0.362 Chirality : 0.037 0.161 2129 Planarity : 0.004 0.037 1375 Dihedral : 30.979 178.728 4095 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.14 % Allowed : 10.69 % Favored : 87.18 % 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: 2.69 (0.29), residues: 771 helix: 2.64 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.47 (0.34), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.010 0.002 PHE A 67 TYR 0.011 0.002 TYR E 54 ARG 0.008 0.000 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 127 time to evaluate : 1.017 Fit side-chains revert: symmetry clash REVERT: A 53 ARG cc_start: 0.7856 (ttt180) cc_final: 0.7475 (ttp-110) REVERT: B 91 LYS cc_start: 0.7717 (tttp) cc_final: 0.7207 (ttpt) REVERT: C 90 ASP cc_start: 0.7264 (t0) cc_final: 0.7032 (t70) REVERT: C 91 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7420 (mp0) REVERT: D 48 ASP cc_start: 0.8606 (m-30) cc_final: 0.8259 (OUTLIER) REVERT: D 96 ARG cc_start: 0.7535 (mtm180) cc_final: 0.7288 (mtm-85) REVERT: E 133 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.7020 (mt-10) REVERT: F 93 GLN cc_start: 0.7432 (mm-40) cc_final: 0.7072 (mp10) REVERT: G 15 LYS cc_start: 0.7763 (mtmm) cc_final: 0.7298 (mtpt) REVERT: G 95 LYS cc_start: 0.8034 (tttt) cc_final: 0.7669 (tppt) REVERT: G 99 ARG cc_start: 0.7584 (mmm160) cc_final: 0.7138 (mpt180) REVERT: H 31 LYS cc_start: 0.8116 (mtpp) cc_final: 0.7730 (mttp) REVERT: H 32 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7925 (pt0) REVERT: H 105 LYS cc_start: 0.7409 (ttpt) cc_final: 0.6993 (mmtm) outliers start: 14 outliers final: 9 residues processed: 129 average time/residue: 2.0573 time to fit residues: 279.4650 Evaluate side-chains 136 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 126 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13019 Z= 0.190 Angle : 0.580 7.109 18804 Z= 0.355 Chirality : 0.034 0.150 2129 Planarity : 0.004 0.036 1375 Dihedral : 30.983 179.019 4095 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.83 % Allowed : 11.15 % Favored : 87.02 % 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: 2.76 (0.29), residues: 771 helix: 2.69 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.44 (0.34), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.010 0.001 PHE A 67 TYR 0.011 0.001 TYR H 37 ARG 0.013 0.000 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 125 time to evaluate : 1.064 Fit side-chains revert: symmetry clash REVERT: A 53 ARG cc_start: 0.7849 (ttt180) cc_final: 0.7474 (ttp-110) REVERT: B 91 LYS cc_start: 0.7671 (tttp) cc_final: 0.7454 (ttmm) REVERT: C 90 ASP cc_start: 0.7269 (t0) cc_final: 0.7037 (t70) REVERT: C 91 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7415 (mp0) REVERT: D 48 ASP cc_start: 0.8604 (m-30) cc_final: 0.8260 (p0) REVERT: D 96 ARG cc_start: 0.7528 (mtm180) cc_final: 0.7278 (mtm-85) REVERT: E 68 GLN cc_start: 0.7479 (tt0) cc_final: 0.7110 (tt0) REVERT: E 133 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.7000 (mt-10) REVERT: F 93 GLN cc_start: 0.7412 (mm-40) cc_final: 0.7052 (mp10) REVERT: G 15 LYS cc_start: 0.7752 (mtmm) cc_final: 0.7296 (mtpt) REVERT: G 90 ASP cc_start: 0.6865 (t70) cc_final: 0.6445 (t0) REVERT: G 95 LYS cc_start: 0.8027 (tttt) cc_final: 0.7663 (tppt) REVERT: G 99 ARG cc_start: 0.7603 (mmm160) cc_final: 0.7159 (mpt180) REVERT: H 31 LYS cc_start: 0.8107 (mtpp) cc_final: 0.7721 (mttp) REVERT: H 32 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7912 (pt0) REVERT: H 105 LYS cc_start: 0.7391 (ttpt) cc_final: 0.6983 (mmtm) outliers start: 12 outliers final: 7 residues processed: 126 average time/residue: 2.0558 time to fit residues: 272.5459 Evaluate side-chains 133 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 124 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 36 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 98 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13019 Z= 0.201 Angle : 0.575 6.950 18804 Z= 0.352 Chirality : 0.035 0.151 2129 Planarity : 0.004 0.036 1375 Dihedral : 30.972 178.951 4095 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.83 % Allowed : 11.30 % Favored : 86.87 % 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: 2.78 (0.29), residues: 771 helix: 2.71 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.44 (0.34), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 75 PHE 0.009 0.001 PHE A 67 TYR 0.010 0.001 TYR H 37 ARG 0.011 0.000 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 126 time to evaluate : 0.954 Fit side-chains REVERT: A 53 ARG cc_start: 0.7847 (ttt180) cc_final: 0.7476 (ttp-110) REVERT: B 91 LYS cc_start: 0.7676 (tttp) cc_final: 0.7185 (ttpt) REVERT: C 73 ASN cc_start: 0.6729 (m-40) cc_final: 0.6395 (t0) REVERT: C 90 ASP cc_start: 0.7275 (t0) cc_final: 0.7042 (t70) REVERT: C 91 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7415 (mp0) REVERT: D 48 ASP cc_start: 0.8599 (m-30) cc_final: 0.8257 (p0) REVERT: D 96 ARG cc_start: 0.7528 (mtm180) cc_final: 0.7278 (mtm-85) REVERT: E 68 GLN cc_start: 0.7474 (tt0) cc_final: 0.7104 (tt0) REVERT: E 133 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.7013 (mt-10) REVERT: F 93 GLN cc_start: 0.7410 (mm-40) cc_final: 0.7044 (mp10) REVERT: G 15 LYS cc_start: 0.7754 (mtmm) cc_final: 0.7299 (mtpt) REVERT: G 95 LYS cc_start: 0.8027 (tttt) cc_final: 0.7664 (tppt) REVERT: G 99 ARG cc_start: 0.7578 (mmm160) cc_final: 0.7131 (mpt180) REVERT: H 31 LYS cc_start: 0.8105 (mtpp) cc_final: 0.7718 (mttp) REVERT: H 32 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7909 (pt0) REVERT: H 105 LYS cc_start: 0.7392 (ttpt) cc_final: 0.6985 (mmtm) outliers start: 12 outliers final: 8 residues processed: 128 average time/residue: 2.0734 time to fit residues: 279.1887 Evaluate side-chains 135 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 125 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 36 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 77 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13019 Z= 0.305 Angle : 0.592 6.512 18804 Z= 0.359 Chirality : 0.037 0.155 2129 Planarity : 0.004 0.034 1375 Dihedral : 30.960 178.677 4095 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.83 % Allowed : 11.60 % Favored : 86.56 % 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: 2.71 (0.29), residues: 771 helix: 2.67 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.52 (0.34), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.009 0.002 PHE A 67 TYR 0.010 0.002 TYR H 37 ARG 0.008 0.000 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 0.986 Fit side-chains REVERT: A 53 ARG cc_start: 0.7860 (ttt180) cc_final: 0.7480 (ttp-110) REVERT: B 91 LYS cc_start: 0.7670 (tttp) cc_final: 0.7172 (ttpt) REVERT: C 73 ASN cc_start: 0.6682 (m-40) cc_final: 0.6359 (t0) REVERT: C 90 ASP cc_start: 0.7284 (t0) cc_final: 0.7048 (t70) REVERT: C 91 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7423 (mp0) REVERT: D 48 ASP cc_start: 0.8603 (m-30) cc_final: 0.8260 (OUTLIER) REVERT: D 96 ARG cc_start: 0.7511 (mtm180) cc_final: 0.7258 (mtm-85) REVERT: E 68 GLN cc_start: 0.7494 (tt0) cc_final: 0.7212 (tt0) REVERT: E 133 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6884 (mt-10) REVERT: F 93 GLN cc_start: 0.7390 (mm-40) cc_final: 0.7024 (mp10) REVERT: G 15 LYS cc_start: 0.7768 (mtmm) cc_final: 0.7333 (mtpt) REVERT: G 95 LYS cc_start: 0.8025 (tttt) cc_final: 0.7662 (tppt) REVERT: G 99 ARG cc_start: 0.7562 (mmm160) cc_final: 0.7137 (mpt180) REVERT: H 31 LYS cc_start: 0.8151 (mtpp) cc_final: 0.7729 (mttp) REVERT: H 32 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7882 (pt0) REVERT: H 105 LYS cc_start: 0.7373 (ttpt) cc_final: 0.6950 (mmtm) outliers start: 12 outliers final: 8 residues processed: 126 average time/residue: 2.0074 time to fit residues: 266.4347 Evaluate side-chains 132 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 123 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 36 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 45 optimal weight: 0.0570 chunk 67 optimal weight: 0.1980 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13019 Z= 0.188 Angle : 0.580 6.576 18804 Z= 0.353 Chirality : 0.033 0.147 2129 Planarity : 0.004 0.036 1375 Dihedral : 30.970 178.944 4095 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.68 % Allowed : 12.21 % Favored : 86.11 % 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: 2.83 (0.29), residues: 771 helix: 2.75 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.47 (0.34), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.010 0.002 PHE A 67 TYR 0.012 0.002 TYR H 37 ARG 0.009 0.001 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 124 time to evaluate : 1.003 Fit side-chains REVERT: A 53 ARG cc_start: 0.7852 (ttt180) cc_final: 0.7479 (ttp-110) REVERT: B 91 LYS cc_start: 0.7629 (tttp) cc_final: 0.7407 (ttmm) REVERT: C 73 ASN cc_start: 0.6653 (m-40) cc_final: 0.6334 (t0) REVERT: C 90 ASP cc_start: 0.7292 (t0) cc_final: 0.7051 (t70) REVERT: C 91 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7425 (mp0) REVERT: D 48 ASP cc_start: 0.8603 (m-30) cc_final: 0.8261 (OUTLIER) REVERT: D 96 ARG cc_start: 0.7489 (mtm180) cc_final: 0.7232 (mtm-85) REVERT: E 68 GLN cc_start: 0.7493 (tt0) cc_final: 0.7122 (tt0) REVERT: E 133 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6917 (mt-10) REVERT: F 93 GLN cc_start: 0.7412 (mm-40) cc_final: 0.7055 (mp10) REVERT: G 15 LYS cc_start: 0.7766 (mtmm) cc_final: 0.7303 (mtpt) REVERT: G 95 LYS cc_start: 0.7981 (tttt) cc_final: 0.7589 (tppt) REVERT: G 99 ARG cc_start: 0.7544 (mmm160) cc_final: 0.7118 (mpt180) REVERT: H 31 LYS cc_start: 0.8129 (mtpp) cc_final: 0.7709 (mttp) REVERT: H 32 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7872 (pt0) REVERT: H 105 LYS cc_start: 0.7379 (ttpt) cc_final: 0.6965 (mmtm) outliers start: 11 outliers final: 8 residues processed: 127 average time/residue: 1.9716 time to fit residues: 263.8162 Evaluate side-chains 132 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 123 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 80 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 13019 Z= 0.412 Angle : 0.632 6.836 18804 Z= 0.379 Chirality : 0.040 0.153 2129 Planarity : 0.005 0.036 1375 Dihedral : 31.109 178.712 4095 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.37 % Allowed : 12.37 % Favored : 86.26 % 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: 2.53 (0.29), residues: 771 helix: 2.55 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.61 (0.34), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 18 PHE 0.010 0.002 PHE A 104 TYR 0.013 0.002 TYR E 54 ARG 0.008 0.001 ARG D 30 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 124 time to evaluate : 0.841 Fit side-chains REVERT: A 53 ARG cc_start: 0.7890 (ttt180) cc_final: 0.7491 (ttp-110) REVERT: B 91 LYS cc_start: 0.7666 (tttp) cc_final: 0.7450 (ttmm) REVERT: C 73 ASN cc_start: 0.6757 (m-40) cc_final: 0.6407 (t0) REVERT: C 90 ASP cc_start: 0.7306 (t0) cc_final: 0.7063 (t70) REVERT: C 91 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7419 (mp0) REVERT: D 48 ASP cc_start: 0.8622 (m-30) cc_final: 0.8283 (OUTLIER) REVERT: D 96 ARG cc_start: 0.7563 (mtm180) cc_final: 0.7280 (mtm-85) REVERT: E 133 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6864 (mt-10) REVERT: F 93 GLN cc_start: 0.7403 (mm-40) cc_final: 0.7037 (mp10) REVERT: G 15 LYS cc_start: 0.7788 (mtmm) cc_final: 0.7287 (mtpt) REVERT: G 95 LYS cc_start: 0.8001 (tttt) cc_final: 0.7633 (tppt) REVERT: G 99 ARG cc_start: 0.7550 (mmm160) cc_final: 0.7141 (mpt180) REVERT: H 31 LYS cc_start: 0.8283 (mtpp) cc_final: 0.7882 (mttp) REVERT: H 32 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7849 (pt0) REVERT: H 105 LYS cc_start: 0.7439 (ttpt) cc_final: 0.7011 (mmtm) outliers start: 9 outliers final: 7 residues processed: 126 average time/residue: 2.1434 time to fit residues: 284.0586 Evaluate side-chains 131 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 123 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 36 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 92 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.090450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.071672 restraints weight = 22144.049| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.26 r_work: 0.3021 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13019 Z= 0.184 Angle : 0.597 6.873 18804 Z= 0.363 Chirality : 0.035 0.138 2129 Planarity : 0.004 0.037 1375 Dihedral : 31.135 179.396 4095 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.37 % Allowed : 12.67 % Favored : 85.95 % 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: 2.70 (0.29), residues: 771 helix: 2.67 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.54 (0.34), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.010 0.002 PHE A 67 TYR 0.013 0.002 TYR H 37 ARG 0.008 0.001 ARG D 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4713.73 seconds wall clock time: 87 minutes 15.65 seconds (5235.65 seconds total)