Starting phenix.real_space_refine on Sat Dec 9 20:22:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox0_17251/12_2023/8ox0_17251.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox0_17251/12_2023/8ox0_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_17251/12_2023/8ox0_17251.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox0_17251/12_2023/8ox0_17251.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox0_17251/12_2023/8ox0_17251.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox0_17251/12_2023/8ox0_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-1.21rc1-5172/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: 6.89, per 1000 atoms: 0.56 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: 6.44 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 6.12 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: 4.83 Time building geometry restraints manager: 6.62 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: 1.540 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: 6.310 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 40.840 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.420 ------------------------------------------------------------------------------- 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 : 1.071 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 148 average time/residue: 1.9566 time to fit residues: 305.0421 Evaluate side-chains 127 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 126 time to evaluate : 0.984 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2411 time to fit residues: 1.4939 ------------------------------------------------------------------------------- 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: 2.9990 chunk 26 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 92 optimal weight: 8.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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: 0.0782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13019 Z= 0.235 Angle : 0.623 7.158 18804 Z= 0.375 Chirality : 0.036 0.150 2129 Planarity : 0.004 0.043 1375 Dihedral : 30.956 179.795 4095 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.53 % Allowed : 10.69 % Favored : 87.79 % 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: 2.31 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.50 (0.33), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 75 PHE 0.012 0.002 PHE A 67 TYR 0.012 0.002 TYR H 37 ARG 0.007 0.001 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 138 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 128 time to evaluate : 1.012 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 131 average time/residue: 1.9907 time to fit residues: 275.4988 Evaluate side-chains 132 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 126 time to evaluate : 2.181 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 3 residues processed: 4 average time/residue: 0.8172 time to fit residues: 6.2219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 25 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- 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: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 13019 Z= 0.447 Angle : 0.662 8.257 18804 Z= 0.393 Chirality : 0.041 0.164 2129 Planarity : 0.005 0.039 1375 Dihedral : 30.964 178.756 4095 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.60 % Allowed : 10.23 % 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: 2.26 (0.29), residues: 771 helix: 2.31 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.62 (0.32), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 46 PHE 0.015 0.002 PHE A 104 TYR 0.014 0.002 TYR E 54 ARG 0.003 0.001 ARG C 20 *********************** 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 137 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 120 time to evaluate : 1.014 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 124 average time/residue: 1.9228 time to fit residues: 251.7372 Evaluate side-chains 128 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 119 time to evaluate : 1.091 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 3 residues processed: 6 average time/residue: 0.9280 time to fit residues: 7.5443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 overall best weight: 2.1184 ------------------------------------------------------------------------------- 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: 0.1055 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= 0.239 Angle : 0.603 7.508 18804 Z= 0.367 Chirality : 0.036 0.146 2129 Planarity : 0.004 0.040 1375 Dihedral : 31.030 179.485 4095 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.98 % Allowed : 12.21 % Favored : 85.80 % 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: 2.48 (0.29), residues: 771 helix: 2.48 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.55 (0.33), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.009 0.001 PHE A 67 TYR 0.012 0.002 TYR H 37 ARG 0.006 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 139 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 126 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 130 average time/residue: 1.8874 time to fit residues: 259.2359 Evaluate side-chains 131 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 124 time to evaluate : 1.051 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 3 residues processed: 4 average time/residue: 0.8286 time to fit residues: 4.8576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 40 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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: 0.7723 moved from start: 0.1085 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= 0.203 Angle : 0.591 7.508 18804 Z= 0.361 Chirality : 0.035 0.147 2129 Planarity : 0.004 0.038 1375 Dihedral : 31.006 179.170 4095 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.37 % Allowed : 12.98 % Favored : 85.65 % 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: 2.56 (0.29), residues: 771 helix: 2.53 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.52 (0.33), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.010 0.001 PHE A 67 TYR 0.011 0.001 TYR H 37 ARG 0.015 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 133 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 124 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 127 average time/residue: 1.8946 time to fit residues: 254.3049 Evaluate side-chains 129 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 123 time to evaluate : 1.100 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 3 residues processed: 3 average time/residue: 0.6428 time to fit residues: 3.5309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 98 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 45 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 95 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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: 0.7722 moved from start: 0.1114 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= 0.229 Angle : 0.587 7.304 18804 Z= 0.358 Chirality : 0.036 0.149 2129 Planarity : 0.004 0.038 1375 Dihedral : 30.996 179.072 4095 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.22 % Allowed : 13.59 % Favored : 85.19 % 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: 2.62 (0.29), residues: 771 helix: 2.58 (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 0.002 0.001 HIS F 75 PHE 0.009 0.001 PHE A 78 TYR 0.010 0.001 TYR H 37 ARG 0.012 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 131 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 123 time to evaluate : 1.055 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 126 average time/residue: 1.9179 time to fit residues: 255.1816 Evaluate side-chains 129 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 122 time to evaluate : 0.959 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 3 residues processed: 4 average time/residue: 0.8035 time to fit residues: 4.6787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 61 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 60 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13019 Z= 0.178 Angle : 0.580 7.758 18804 Z= 0.355 Chirality : 0.034 0.148 2129 Planarity : 0.004 0.037 1375 Dihedral : 30.983 179.121 4095 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.22 % Allowed : 13.89 % Favored : 84.89 % 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: 2.64 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.46 (0.34), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.010 0.001 PHE A 67 TYR 0.010 0.001 TYR H 37 ARG 0.014 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 130 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 122 time to evaluate : 1.099 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 125 average time/residue: 1.9464 time to fit residues: 256.9738 Evaluate side-chains 123 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 120 time to evaluate : 0.965 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.1017 time to fit residues: 1.2485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 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: 0.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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: 0.7717 moved from start: 0.1293 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= 0.267 Angle : 0.583 6.641 18804 Z= 0.355 Chirality : 0.036 0.157 2129 Planarity : 0.004 0.039 1375 Dihedral : 30.901 178.698 4095 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.53 % Allowed : 13.28 % Favored : 85.19 % 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: 2.74 (0.29), residues: 771 helix: 2.69 (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 0.002 0.001 HIS F 75 PHE 0.009 0.001 PHE A 67 TYR 0.010 0.001 TYR H 37 ARG 0.009 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 131 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 121 time to evaluate : 1.060 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 123 average time/residue: 2.0002 time to fit residues: 259.7439 Evaluate side-chains 126 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 121 time to evaluate : 1.064 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 3 average time/residue: 0.5737 time to fit residues: 3.1633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 28 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 chunk 60 optimal weight: 0.3980 chunk 96 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 13019 Z= 0.191 Angle : 0.578 6.785 18804 Z= 0.354 Chirality : 0.034 0.153 2129 Planarity : 0.004 0.035 1375 Dihedral : 30.905 178.862 4095 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.76 % Allowed : 14.96 % Favored : 84.27 % 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: 2.76 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.48 (0.34), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.010 0.001 PHE A 67 TYR 0.012 0.001 TYR H 37 ARG 0.010 0.000 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 127 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 122 time to evaluate : 1.013 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 124 average time/residue: 1.9592 time to fit residues: 256.2430 Evaluate side-chains 125 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 121 time to evaluate : 0.998 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.7984 time to fit residues: 2.9358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 8 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 49 optimal weight: 7.9990 chunk 64 optimal weight: 0.0070 chunk 86 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13019 Z= 0.236 Angle : 0.571 6.682 18804 Z= 0.349 Chirality : 0.035 0.156 2129 Planarity : 0.004 0.035 1375 Dihedral : 30.891 178.580 4095 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.76 % Allowed : 14.66 % Favored : 84.58 % 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: 2.82 (0.29), residues: 771 helix: 2.76 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.48 (0.34), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.009 0.001 PHE A 67 TYR 0.010 0.001 TYR H 37 ARG 0.009 0.000 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 124 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 119 time to evaluate : 0.948 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 121 average time/residue: 1.9405 time to fit residues: 247.7292 Evaluate side-chains 123 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 119 time to evaluate : 0.930 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.7413 time to fit residues: 2.7372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 92 optimal weight: 8.9990 chunk 54 optimal weight: 0.6980 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 = 0.3557 r_free = 0.3557 target = 0.091104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.072221 restraints weight = 22167.182| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.27 r_work: 0.3038 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13019 Z= 0.197 Angle : 0.569 6.711 18804 Z= 0.349 Chirality : 0.034 0.155 2129 Planarity : 0.004 0.035 1375 Dihedral : 30.890 178.641 4095 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.76 % Allowed : 14.96 % Favored : 84.27 % 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: 2.87 (0.29), residues: 771 helix: 2.79 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.46 (0.34), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.009 0.001 PHE A 67 TYR 0.011 0.001 TYR H 37 ARG 0.009 0.000 ARG D 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4560.07 seconds wall clock time: 81 minutes 23.32 seconds (4883.32 seconds total)