Starting phenix.real_space_refine on Fri Nov 15 20:48:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi1_40059/11_2024/8gi1_40059.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi1_40059/11_2024/8gi1_40059.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi1_40059/11_2024/8gi1_40059.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi1_40059/11_2024/8gi1_40059.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi1_40059/11_2024/8gi1_40059.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi1_40059/11_2024/8gi1_40059.cif" } resolution = 3.65 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= 0.005 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: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 6232 2.51 5 N 1664 2.21 5 O 1776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 9704 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1213 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 1, 'TRANS': 142} Chain breaks: 1 Chain: "B" Number of atoms: 1213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1213 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 1, 'TRANS': 142} Chain breaks: 1 Chain: "C" Number of atoms: 1213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1213 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 1, 'TRANS': 142} Chain breaks: 1 Chain: "D" Number of atoms: 1213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1213 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 1, 'TRANS': 142} Chain breaks: 1 Chain: "E" Number of atoms: 1213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1213 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 1, 'TRANS': 142} Chain breaks: 1 Chain: "F" Number of atoms: 1213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1213 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 1, 'TRANS': 142} Chain breaks: 1 Chain: "G" Number of atoms: 1213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1213 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 1, 'TRANS': 142} Chain breaks: 1 Chain: "H" Number of atoms: 1213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1213 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 1, 'TRANS': 142} Chain breaks: 1 Time building chain proxies: 6.06, per 1000 atoms: 0.62 Number of scatterers: 9704 At special positions: 0 Unit cell: (121.03, 121.03, 91.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 1776 8.00 N 1664 7.00 C 6232 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.2 seconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2256 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 8 sheets defined 75.8% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 19 through 56 removed outlier: 3.597A pdb=" N HIS A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS A 56 " --> pdb=" O LYS A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 62 Processing helix chain 'A' and resid 91 through 104 Processing helix chain 'A' and resid 107 through 111 Processing helix chain 'A' and resid 113 through 135 Processing helix chain 'A' and resid 146 through 166 removed outlier: 4.065A pdb=" N VAL A 150 " --> pdb=" O ASN A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 169 No H-bonds generated for 'chain 'A' and resid 167 through 169' Processing helix chain 'B' and resid 20 through 56 removed outlier: 3.691A pdb=" N TYR B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR B 25 " --> pdb=" O TYR B 21 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL B 36 " --> pdb=" O HIS B 32 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS B 56 " --> pdb=" O LYS B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 91 through 104 Processing helix chain 'B' and resid 107 through 111 Processing helix chain 'B' and resid 113 through 135 Processing helix chain 'B' and resid 146 through 166 removed outlier: 4.065A pdb=" N VAL B 150 " --> pdb=" O ASN B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 169 No H-bonds generated for 'chain 'B' and resid 167 through 169' Processing helix chain 'C' and resid 20 through 56 removed outlier: 3.597A pdb=" N HIS C 32 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL C 36 " --> pdb=" O HIS C 32 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TYR C 41 " --> pdb=" O GLU C 37 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS C 56 " --> pdb=" O LYS C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 91 through 104 Processing helix chain 'C' and resid 107 through 111 Processing helix chain 'C' and resid 113 through 135 Processing helix chain 'C' and resid 146 through 166 removed outlier: 4.065A pdb=" N VAL C 150 " --> pdb=" O ASN C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 169 No H-bonds generated for 'chain 'C' and resid 167 through 169' Processing helix chain 'D' and resid 20 through 56 removed outlier: 3.591A pdb=" N HIS D 32 " --> pdb=" O ILE D 28 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN D 38 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR D 41 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS D 56 " --> pdb=" O LYS D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 62 Processing helix chain 'D' and resid 91 through 104 Processing helix chain 'D' and resid 107 through 111 Processing helix chain 'D' and resid 113 through 135 Processing helix chain 'D' and resid 146 through 166 removed outlier: 4.065A pdb=" N VAL D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 169 No H-bonds generated for 'chain 'D' and resid 167 through 169' Processing helix chain 'E' and resid 20 through 56 removed outlier: 3.531A pdb=" N SER E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL E 36 " --> pdb=" O HIS E 32 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR E 41 " --> pdb=" O GLU E 37 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA E 42 " --> pdb=" O ASN E 38 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS E 56 " --> pdb=" O LYS E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 62 Processing helix chain 'E' and resid 91 through 104 Processing helix chain 'E' and resid 107 through 111 Processing helix chain 'E' and resid 113 through 135 Processing helix chain 'E' and resid 146 through 166 removed outlier: 4.066A pdb=" N VAL E 150 " --> pdb=" O ASN E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 169 No H-bonds generated for 'chain 'E' and resid 167 through 169' Processing helix chain 'F' and resid 20 through 56 removed outlier: 3.636A pdb=" N TYR F 41 " --> pdb=" O GLU F 37 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA F 42 " --> pdb=" O ASN F 38 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS F 56 " --> pdb=" O LYS F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 62 Processing helix chain 'F' and resid 91 through 104 Processing helix chain 'F' and resid 107 through 111 Processing helix chain 'F' and resid 113 through 135 Processing helix chain 'F' and resid 146 through 166 removed outlier: 4.065A pdb=" N VAL F 150 " --> pdb=" O ASN F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 169 No H-bonds generated for 'chain 'F' and resid 167 through 169' Processing helix chain 'G' and resid 20 through 56 removed outlier: 3.594A pdb=" N HIS G 32 " --> pdb=" O ILE G 28 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER G 35 " --> pdb=" O LEU G 31 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL G 36 " --> pdb=" O HIS G 32 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR G 41 " --> pdb=" O GLU G 37 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS G 56 " --> pdb=" O LYS G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 62 Processing helix chain 'G' and resid 91 through 104 Processing helix chain 'G' and resid 107 through 111 Processing helix chain 'G' and resid 113 through 135 Processing helix chain 'G' and resid 146 through 166 removed outlier: 4.065A pdb=" N VAL G 150 " --> pdb=" O ASN G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 169 No H-bonds generated for 'chain 'G' and resid 167 through 169' Processing helix chain 'H' and resid 20 through 56 removed outlier: 3.769A pdb=" N ILE H 39 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA H 42 " --> pdb=" O ASN H 38 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS H 56 " --> pdb=" O LYS H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 62 Processing helix chain 'H' and resid 91 through 104 Processing helix chain 'H' and resid 107 through 111 Processing helix chain 'H' and resid 113 through 135 Processing helix chain 'H' and resid 146 through 166 removed outlier: 4.065A pdb=" N VAL H 150 " --> pdb=" O ASN H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 169 No H-bonds generated for 'chain 'H' and resid 167 through 169' Processing sheet with id=AA1, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA2, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA3, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AA5, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AA6, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AA7, first strand: chain 'G' and resid 71 through 72 Processing sheet with id=AA8, first strand: chain 'H' and resid 71 through 72 650 hydrogen bonds defined for protein. 1806 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 2.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1708 1.31 - 1.43: 2573 1.43 - 1.55: 5427 1.55 - 1.68: 108 1.68 - 1.80: 56 Bond restraints: 9872 Sorted by residual: bond pdb=" CA SER E 35 " pdb=" C SER E 35 " ideal model delta sigma weight residual 1.523 1.460 0.063 1.30e-02 5.92e+03 2.38e+01 bond pdb=" C GLN H 33 " pdb=" O GLN H 33 " ideal model delta sigma weight residual 1.237 1.190 0.047 1.17e-02 7.31e+03 1.58e+01 bond pdb=" C VAL E 36 " pdb=" O VAL E 36 " ideal model delta sigma weight residual 1.237 1.192 0.045 1.17e-02 7.31e+03 1.46e+01 bond pdb=" CA HIS C 32 " pdb=" C HIS C 32 " ideal model delta sigma weight residual 1.524 1.474 0.049 1.32e-02 5.74e+03 1.40e+01 bond pdb=" CB ILE F 110 " pdb=" CG1 ILE F 110 " ideal model delta sigma weight residual 1.530 1.455 0.075 2.00e-02 2.50e+03 1.40e+01 ... (remaining 9867 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 11152 1.92 - 3.84: 1824 3.84 - 5.76: 223 5.76 - 7.68: 32 7.68 - 9.60: 9 Bond angle restraints: 13240 Sorted by residual: angle pdb=" N ASN H 38 " pdb=" CA ASN H 38 " pdb=" C ASN H 38 " ideal model delta sigma weight residual 112.54 122.14 -9.60 1.22e+00 6.72e-01 6.19e+01 angle pdb=" N ASN E 38 " pdb=" CA ASN E 38 " pdb=" C ASN E 38 " ideal model delta sigma weight residual 111.36 119.30 -7.94 1.09e+00 8.42e-01 5.30e+01 angle pdb=" N ASN F 38 " pdb=" CA ASN F 38 " pdb=" C ASN F 38 " ideal model delta sigma weight residual 112.89 120.48 -7.59 1.24e+00 6.50e-01 3.75e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.14 117.53 -6.39 1.08e+00 8.57e-01 3.50e+01 angle pdb=" N GLN F 33 " pdb=" CA GLN F 33 " pdb=" C GLN F 33 " ideal model delta sigma weight residual 112.54 106.19 6.35 1.22e+00 6.72e-01 2.71e+01 ... (remaining 13235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 5725 16.00 - 31.99: 172 31.99 - 47.99: 102 47.99 - 63.99: 47 63.99 - 79.99: 2 Dihedral angle restraints: 6048 sinusoidal: 2560 harmonic: 3488 Sorted by residual: dihedral pdb=" N ASN H 38 " pdb=" C ASN H 38 " pdb=" CA ASN H 38 " pdb=" CB ASN H 38 " ideal model delta harmonic sigma weight residual 122.80 137.41 -14.61 0 2.50e+00 1.60e-01 3.41e+01 dihedral pdb=" C ASN H 38 " pdb=" N ASN H 38 " pdb=" CA ASN H 38 " pdb=" CB ASN H 38 " ideal model delta harmonic sigma weight residual -122.60 -137.10 14.50 0 2.50e+00 1.60e-01 3.36e+01 dihedral pdb=" N ASN F 38 " pdb=" C ASN F 38 " pdb=" CA ASN F 38 " pdb=" CB ASN F 38 " ideal model delta harmonic sigma weight residual 122.80 134.67 -11.87 0 2.50e+00 1.60e-01 2.26e+01 ... (remaining 6045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 1201 0.129 - 0.257: 215 0.257 - 0.385: 11 0.385 - 0.514: 3 0.514 - 0.642: 2 Chirality restraints: 1432 Sorted by residual: chirality pdb=" CA ASN H 38 " pdb=" N ASN H 38 " pdb=" C ASN H 38 " pdb=" CB ASN H 38 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" CA ASN F 38 " pdb=" N ASN F 38 " pdb=" C ASN F 38 " pdb=" CB ASN F 38 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.28e+00 chirality pdb=" CA ASN E 38 " pdb=" N ASN E 38 " pdb=" C ASN E 38 " pdb=" CB ASN E 38 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.45e+00 ... (remaining 1429 not shown) Planarity restraints: 1656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS F 32 " -0.020 2.00e-02 2.50e+03 4.26e-02 1.82e+01 pdb=" C HIS F 32 " 0.074 2.00e-02 2.50e+03 pdb=" O HIS F 32 " -0.029 2.00e-02 2.50e+03 pdb=" N GLN F 33 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 33 " 0.020 2.00e-02 2.50e+03 3.95e-02 1.56e+01 pdb=" C GLN A 33 " -0.068 2.00e-02 2.50e+03 pdb=" O GLN A 33 " 0.025 2.00e-02 2.50e+03 pdb=" N LYS A 34 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 36 " -0.016 2.00e-02 2.50e+03 3.31e-02 1.10e+01 pdb=" C VAL E 36 " 0.057 2.00e-02 2.50e+03 pdb=" O VAL E 36 " -0.021 2.00e-02 2.50e+03 pdb=" N GLU E 37 " -0.020 2.00e-02 2.50e+03 ... (remaining 1653 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 15 2.02 - 2.74: 1375 2.74 - 3.46: 13854 3.46 - 4.18: 21954 4.18 - 4.90: 38622 Nonbonded interactions: 75820 Sorted by model distance: nonbonded pdb=" CB ALA A 27 " pdb=" OH TYR H 26 " model vdw 1.301 3.460 nonbonded pdb=" OH TYR F 26 " pdb=" CB ALA G 27 " model vdw 1.346 3.460 nonbonded pdb=" OH TYR C 26 " pdb=" CB ALA D 27 " model vdw 1.515 3.460 nonbonded pdb=" CE2 TYR B 26 " pdb=" NE2 GLN B 30 " model vdw 1.563 3.420 nonbonded pdb=" OH TYR B 26 " pdb=" CB ALA C 27 " model vdw 1.598 3.460 ... (remaining 75815 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 24.480 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 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 : 0.017 0.081 9872 Z= 1.091 Angle : 1.445 9.600 13240 Z= 0.965 Chirality : 0.096 0.642 1432 Planarity : 0.007 0.043 1656 Dihedral : 11.694 79.986 3792 Min Nonbonded Distance : 1.301 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.86 % Allowed : 3.72 % Favored : 95.42 % Cbeta Deviations : 1.06 % 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: 1.00 (0.24), residues: 1120 helix: 0.91 (0.17), residues: 744 sheet: None (None), residues: 0 loop : 0.42 (0.35), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.004 TRP E 73 HIS 0.007 0.002 HIS E 51 PHE 0.032 0.006 PHE G 87 TYR 0.015 0.003 TYR E 44 ARG 0.007 0.001 ARG D 93 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 268 time to evaluate : 1.152 Fit side-chains REVERT: B 112 MET cc_start: 0.8371 (ptm) cc_final: 0.8033 (ptm) REVERT: C 56 LYS cc_start: 0.8538 (pttt) cc_final: 0.8319 (pttp) REVERT: D 53 SER cc_start: 0.8369 (m) cc_final: 0.8022 (p) REVERT: D 112 MET cc_start: 0.8362 (ptm) cc_final: 0.8010 (ptm) REVERT: E 56 LYS cc_start: 0.8546 (pttt) cc_final: 0.8314 (pttp) REVERT: F 112 MET cc_start: 0.8400 (ptm) cc_final: 0.8024 (ptm) REVERT: G 56 LYS cc_start: 0.8562 (pttt) cc_final: 0.8251 (pttp) REVERT: H 53 SER cc_start: 0.8361 (m) cc_final: 0.8036 (p) REVERT: H 112 MET cc_start: 0.8340 (ptm) cc_final: 0.8029 (ptm) outliers start: 9 outliers final: 8 residues processed: 277 average time/residue: 0.2438 time to fit residues: 90.7627 Evaluate side-chains 126 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain C residue 85 TYR Chi-restraints excluded: chain D residue 85 TYR Chi-restraints excluded: chain E residue 85 TYR Chi-restraints excluded: chain F residue 85 TYR Chi-restraints excluded: chain G residue 85 TYR Chi-restraints excluded: chain H residue 85 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 GLN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9872 Z= 0.250 Angle : 0.620 10.527 13240 Z= 0.345 Chirality : 0.039 0.171 1432 Planarity : 0.004 0.022 1656 Dihedral : 4.897 41.067 1312 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.77 % Allowed : 13.45 % Favored : 83.78 % 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: 3.31 (0.26), residues: 1120 helix: 2.95 (0.18), residues: 720 sheet: None (None), residues: 0 loop : 0.85 (0.36), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 73 HIS 0.003 0.001 HIS A 32 PHE 0.011 0.002 PHE H 130 TYR 0.022 0.002 TYR A 24 ARG 0.004 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 1.159 Fit side-chains revert: symmetry clash REVERT: A 102 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7349 (mt-10) REVERT: A 124 ARG cc_start: 0.7651 (ttt-90) cc_final: 0.7355 (tmt170) REVERT: B 90 GLU cc_start: 0.6422 (mm-30) cc_final: 0.5702 (pp20) REVERT: C 40 GLU cc_start: 0.7305 (tm-30) cc_final: 0.7040 (tm-30) REVERT: C 56 LYS cc_start: 0.8862 (pttt) cc_final: 0.8503 (pttp) REVERT: C 90 GLU cc_start: 0.6811 (mm-30) cc_final: 0.5955 (pp20) REVERT: C 102 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7347 (mt-10) REVERT: C 124 ARG cc_start: 0.7492 (ttt-90) cc_final: 0.7283 (tmt170) REVERT: D 90 GLU cc_start: 0.6499 (mm-30) cc_final: 0.5696 (pp20) REVERT: E 56 LYS cc_start: 0.8865 (pttt) cc_final: 0.8574 (pttp) REVERT: E 90 GLU cc_start: 0.6937 (mm-30) cc_final: 0.5625 (pp20) REVERT: E 124 ARG cc_start: 0.7464 (ttt-90) cc_final: 0.7226 (tmt170) REVERT: F 90 GLU cc_start: 0.6494 (mm-30) cc_final: 0.5659 (pp20) REVERT: G 56 LYS cc_start: 0.8871 (pttt) cc_final: 0.8496 (pttp) REVERT: G 90 GLU cc_start: 0.6774 (mm-30) cc_final: 0.5905 (pp20) REVERT: G 102 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7331 (mt-10) REVERT: G 124 ARG cc_start: 0.7579 (ttt-90) cc_final: 0.7347 (tmt170) REVERT: H 90 GLU cc_start: 0.6517 (mm-30) cc_final: 0.5686 (pp20) outliers start: 29 outliers final: 15 residues processed: 176 average time/residue: 0.2675 time to fit residues: 63.7060 Evaluate side-chains 129 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 85 TYR Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 85 TYR Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 85 TYR Chi-restraints excluded: chain G residue 91 ASN Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain H residue 72 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 30.0000 chunk 31 optimal weight: 1.9990 chunk 84 optimal weight: 30.0000 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 40.0000 chunk 101 optimal weight: 0.5980 chunk 110 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 GLN ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.4370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9872 Z= 0.259 Angle : 0.588 7.442 13240 Z= 0.325 Chirality : 0.039 0.168 1432 Planarity : 0.003 0.024 1656 Dihedral : 4.225 37.552 1304 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.44 % Allowed : 13.36 % Favored : 83.21 % 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: 2.65 (0.26), residues: 1120 helix: 2.97 (0.20), residues: 632 sheet: None (None), residues: 0 loop : 0.14 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 73 HIS 0.003 0.001 HIS B 32 PHE 0.008 0.002 PHE F 130 TYR 0.017 0.002 TYR F 26 ARG 0.004 0.000 ARG D 143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 0.975 Fit side-chains REVERT: A 63 ASN cc_start: 0.6916 (p0) cc_final: 0.6620 (p0) REVERT: A 124 ARG cc_start: 0.7425 (ttt-90) cc_final: 0.7194 (tmt170) REVERT: A 135 GLN cc_start: 0.5770 (tp40) cc_final: 0.5332 (pp30) REVERT: C 56 LYS cc_start: 0.8985 (pttt) cc_final: 0.8537 (pttp) REVERT: C 63 ASN cc_start: 0.7070 (p0) cc_final: 0.6779 (p0) REVERT: C 102 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7635 (mt-10) REVERT: C 124 ARG cc_start: 0.7381 (ttt-90) cc_final: 0.7148 (ttt180) REVERT: C 135 GLN cc_start: 0.5720 (tp40) cc_final: 0.5276 (pp30) REVERT: C 143 ARG cc_start: 0.7540 (ttm110) cc_final: 0.7257 (ttp-110) REVERT: E 56 LYS cc_start: 0.8975 (pttt) cc_final: 0.8703 (pttp) REVERT: E 63 ASN cc_start: 0.7076 (p0) cc_final: 0.6787 (p0) REVERT: E 124 ARG cc_start: 0.7289 (ttt-90) cc_final: 0.7027 (tmt170) REVERT: E 135 GLN cc_start: 0.5745 (tp40) cc_final: 0.5270 (pp30) REVERT: E 169 ASN cc_start: 0.7577 (t0) cc_final: 0.7336 (t0) REVERT: G 56 LYS cc_start: 0.8988 (pttt) cc_final: 0.8535 (pttp) REVERT: G 63 ASN cc_start: 0.7103 (p0) cc_final: 0.6808 (p0) REVERT: G 102 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7645 (mt-10) REVERT: G 124 ARG cc_start: 0.7383 (ttt-90) cc_final: 0.7090 (ttt180) REVERT: G 135 GLN cc_start: 0.5822 (tp40) cc_final: 0.5261 (pp30) REVERT: G 143 ARG cc_start: 0.7570 (ttm110) cc_final: 0.7267 (ttp-110) outliers start: 36 outliers final: 19 residues processed: 168 average time/residue: 0.2553 time to fit residues: 58.0185 Evaluate side-chains 124 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 85 TYR Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 85 TYR Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 85 TYR Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 164 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 108 optimal weight: 0.0980 chunk 53 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 32 HIS E 51 HIS ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9872 Z= 0.183 Angle : 0.503 5.372 13240 Z= 0.283 Chirality : 0.035 0.142 1432 Planarity : 0.003 0.025 1656 Dihedral : 4.148 38.029 1304 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.67 % Allowed : 15.65 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.25), residues: 1120 helix: 3.05 (0.19), residues: 632 sheet: None (None), residues: 0 loop : -0.07 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP G 73 HIS 0.002 0.001 HIS E 32 PHE 0.005 0.001 PHE G 87 TYR 0.017 0.001 TYR F 26 ARG 0.006 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 1.313 Fit side-chains revert: symmetry clash REVERT: A 40 GLU cc_start: 0.7105 (tm-30) cc_final: 0.6733 (tm-30) REVERT: A 63 ASN cc_start: 0.7053 (p0) cc_final: 0.6766 (p0) REVERT: A 143 ARG cc_start: 0.7822 (ttm110) cc_final: 0.7462 (ttp-110) REVERT: B 90 GLU cc_start: 0.7180 (mm-30) cc_final: 0.5890 (pp20) REVERT: C 56 LYS cc_start: 0.8985 (pttt) cc_final: 0.8646 (pttp) REVERT: C 63 ASN cc_start: 0.7192 (p0) cc_final: 0.6932 (p0) REVERT: C 102 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7390 (mt-10) REVERT: C 135 GLN cc_start: 0.5922 (tp40) cc_final: 0.5507 (pp30) REVERT: E 56 LYS cc_start: 0.8918 (pttt) cc_final: 0.8535 (pttp) REVERT: E 63 ASN cc_start: 0.7204 (p0) cc_final: 0.6916 (p0) REVERT: E 102 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7524 (mt-10) REVERT: E 124 ARG cc_start: 0.7514 (ttt-90) cc_final: 0.7251 (tmt170) REVERT: E 135 GLN cc_start: 0.5849 (tp40) cc_final: 0.5396 (pp30) REVERT: E 143 ARG cc_start: 0.7836 (ttm110) cc_final: 0.7459 (ttp-110) REVERT: G 56 LYS cc_start: 0.8977 (pttt) cc_final: 0.8640 (pttp) REVERT: G 63 ASN cc_start: 0.7105 (p0) cc_final: 0.6884 (p0) REVERT: G 102 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7444 (mt-10) REVERT: G 124 ARG cc_start: 0.7595 (ttt-90) cc_final: 0.7327 (tmt170) outliers start: 28 outliers final: 16 residues processed: 162 average time/residue: 0.2675 time to fit residues: 58.4952 Evaluate side-chains 131 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 85 TYR Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 85 TYR Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 85 TYR Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 164 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 80 optimal weight: 0.3980 chunk 44 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 50.0000 chunk 55 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS A 51 HIS B 51 HIS D 51 HIS ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.5091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9872 Z= 0.240 Angle : 0.544 5.947 13240 Z= 0.303 Chirality : 0.037 0.130 1432 Planarity : 0.003 0.025 1656 Dihedral : 4.081 33.669 1304 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.77 % Allowed : 16.89 % Favored : 80.34 % 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 (0.25), residues: 1120 helix: 3.05 (0.20), residues: 632 sheet: None (None), residues: 0 loop : -0.29 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP C 73 HIS 0.002 0.001 HIS E 51 PHE 0.007 0.001 PHE G 95 TYR 0.016 0.001 TYR E 26 ARG 0.007 0.000 ARG F 143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 1.152 Fit side-chains REVERT: A 63 ASN cc_start: 0.7109 (p0) cc_final: 0.6876 (p0) REVERT: A 169 ASN cc_start: 0.7701 (t0) cc_final: 0.7443 (t0) REVERT: C 56 LYS cc_start: 0.9029 (pttt) cc_final: 0.8754 (pttp) REVERT: C 63 ASN cc_start: 0.7205 (p0) cc_final: 0.6952 (p0) REVERT: C 169 ASN cc_start: 0.7577 (t0) cc_final: 0.7209 (t0) REVERT: E 56 LYS cc_start: 0.9002 (pttt) cc_final: 0.8755 (pttp) REVERT: E 63 ASN cc_start: 0.7239 (p0) cc_final: 0.7018 (p0) REVERT: E 124 ARG cc_start: 0.7478 (ttt-90) cc_final: 0.7226 (tmt170) REVERT: E 169 ASN cc_start: 0.7701 (t0) cc_final: 0.7356 (t0) REVERT: G 56 LYS cc_start: 0.8989 (pttt) cc_final: 0.8717 (pttp) REVERT: G 63 ASN cc_start: 0.7269 (p0) cc_final: 0.7030 (p0) outliers start: 29 outliers final: 20 residues processed: 136 average time/residue: 0.2663 time to fit residues: 49.2608 Evaluate side-chains 130 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 85 TYR Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 164 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 3.9990 chunk 21 optimal weight: 0.0050 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 30.0000 chunk 104 optimal weight: 0.8980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN C 51 HIS ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.5312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9872 Z= 0.180 Angle : 0.488 8.524 13240 Z= 0.274 Chirality : 0.035 0.123 1432 Planarity : 0.003 0.027 1656 Dihedral : 3.679 33.167 1298 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.34 % Allowed : 17.18 % Favored : 79.48 % 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: 2.50 (0.25), residues: 1120 helix: 3.13 (0.19), residues: 632 sheet: None (None), residues: 0 loop : -0.40 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP C 73 HIS 0.002 0.001 HIS E 51 PHE 0.005 0.001 PHE G 95 TYR 0.016 0.001 TYR E 26 ARG 0.005 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 121 time to evaluate : 1.085 Fit side-chains revert: symmetry clash REVERT: A 63 ASN cc_start: 0.7075 (p0) cc_final: 0.6841 (p0) REVERT: A 169 ASN cc_start: 0.7639 (t0) cc_final: 0.7339 (t0) REVERT: B 102 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7777 (mm-30) REVERT: C 56 LYS cc_start: 0.9005 (pttt) cc_final: 0.8751 (pttp) REVERT: E 56 LYS cc_start: 0.8989 (pttt) cc_final: 0.8719 (pttp) REVERT: E 63 ASN cc_start: 0.7209 (p0) cc_final: 0.6997 (p0) REVERT: E 169 ASN cc_start: 0.7396 (t0) cc_final: 0.7139 (t0) REVERT: G 56 LYS cc_start: 0.8995 (pttt) cc_final: 0.8727 (pttp) REVERT: G 63 ASN cc_start: 0.7237 (p0) cc_final: 0.7008 (p0) REVERT: H 102 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7788 (mm-30) outliers start: 35 outliers final: 23 residues processed: 148 average time/residue: 0.2471 time to fit residues: 49.7788 Evaluate side-chains 134 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 85 TYR Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 85 TYR Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 164 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 0.0000 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 32 HIS ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.5443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9872 Z= 0.196 Angle : 0.504 7.394 13240 Z= 0.280 Chirality : 0.036 0.123 1432 Planarity : 0.003 0.032 1656 Dihedral : 3.690 30.869 1298 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.05 % Allowed : 17.75 % Favored : 79.20 % 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: 2.46 (0.25), residues: 1120 helix: 3.17 (0.19), residues: 632 sheet: None (None), residues: 0 loop : -0.53 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP C 73 HIS 0.002 0.001 HIS G 51 PHE 0.006 0.001 PHE G 95 TYR 0.015 0.001 TYR F 26 ARG 0.006 0.000 ARG D 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 1.276 Fit side-chains REVERT: A 63 ASN cc_start: 0.6988 (p0) cc_final: 0.6783 (p0) REVERT: A 169 ASN cc_start: 0.7632 (t0) cc_final: 0.7331 (t0) REVERT: C 56 LYS cc_start: 0.8984 (pttt) cc_final: 0.8722 (pttp) REVERT: E 56 LYS cc_start: 0.8981 (pttt) cc_final: 0.8713 (pttp) REVERT: E 169 ASN cc_start: 0.7458 (t0) cc_final: 0.7181 (t0) REVERT: G 56 LYS cc_start: 0.9001 (pttt) cc_final: 0.8714 (pttp) outliers start: 32 outliers final: 24 residues processed: 146 average time/residue: 0.2405 time to fit residues: 48.0826 Evaluate side-chains 136 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 85 TYR Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 164 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 0.1980 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 84 optimal weight: 50.0000 chunk 98 optimal weight: 20.0000 chunk 103 optimal weight: 4.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 51 HIS ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.5540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9872 Z= 0.271 Angle : 0.574 7.048 13240 Z= 0.316 Chirality : 0.038 0.133 1432 Planarity : 0.003 0.025 1656 Dihedral : 3.832 16.494 1296 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.15 % Allowed : 17.75 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.25), residues: 1120 helix: 2.99 (0.19), residues: 632 sheet: None (None), residues: 0 loop : -0.78 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP C 73 HIS 0.003 0.001 HIS C 51 PHE 0.006 0.001 PHE B 95 TYR 0.015 0.001 TYR E 86 ARG 0.007 0.001 ARG D 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 1.172 Fit side-chains REVERT: A 63 ASN cc_start: 0.7015 (p0) cc_final: 0.6801 (p0) outliers start: 33 outliers final: 23 residues processed: 151 average time/residue: 0.2745 time to fit residues: 54.9164 Evaluate side-chains 134 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 TYR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 85 TYR Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 164 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.5679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9872 Z= 0.201 Angle : 0.523 6.729 13240 Z= 0.291 Chirality : 0.036 0.124 1432 Planarity : 0.003 0.031 1656 Dihedral : 3.689 16.177 1296 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.86 % Allowed : 18.51 % Favored : 78.63 % 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: 2.17 (0.25), residues: 1120 helix: 3.09 (0.19), residues: 632 sheet: None (None), residues: 0 loop : -0.91 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP C 73 HIS 0.002 0.001 HIS C 51 PHE 0.006 0.001 PHE G 95 TYR 0.014 0.001 TYR F 26 ARG 0.008 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 1.130 Fit side-chains REVERT: A 63 ASN cc_start: 0.7095 (p0) cc_final: 0.6856 (p0) REVERT: G 143 ARG cc_start: 0.7804 (ttm110) cc_final: 0.7584 (ttm110) outliers start: 30 outliers final: 25 residues processed: 133 average time/residue: 0.2623 time to fit residues: 49.0786 Evaluate side-chains 127 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 85 TYR Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 85 TYR Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 164 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 70 optimal weight: 50.0000 chunk 94 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 169 ASN ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.5731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9872 Z= 0.196 Angle : 0.519 6.594 13240 Z= 0.289 Chirality : 0.036 0.124 1432 Planarity : 0.003 0.029 1656 Dihedral : 3.680 16.040 1296 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.67 % Allowed : 18.03 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.25), residues: 1120 helix: 3.06 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -1.03 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP C 73 HIS 0.002 0.001 HIS C 51 PHE 0.006 0.001 PHE G 95 TYR 0.037 0.001 TYR A 24 ARG 0.008 0.000 ARG B 143 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 1.128 Fit side-chains REVERT: A 63 ASN cc_start: 0.7064 (p0) cc_final: 0.6839 (p0) outliers start: 28 outliers final: 24 residues processed: 132 average time/residue: 0.2404 time to fit residues: 43.3684 Evaluate side-chains 126 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 85 TYR Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 85 TYR Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 164 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 169 ASN ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.173545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.124587 restraints weight = 10547.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.122898 restraints weight = 9431.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.122686 restraints weight = 9353.410| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.5757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9872 Z= 0.247 Angle : 0.563 6.574 13240 Z= 0.311 Chirality : 0.038 0.130 1432 Planarity : 0.003 0.038 1656 Dihedral : 3.810 16.400 1296 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.96 % Allowed : 18.03 % Favored : 79.01 % 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: 2.07 (0.25), residues: 1120 helix: 2.95 (0.19), residues: 664 sheet: None (None), residues: 0 loop : -1.15 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 73 HIS 0.003 0.001 HIS C 51 PHE 0.005 0.001 PHE B 95 TYR 0.031 0.001 TYR A 24 ARG 0.009 0.001 ARG B 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1912.20 seconds wall clock time: 36 minutes 8.70 seconds (2168.70 seconds total)