Starting phenix.real_space_refine on Sat Sep 28 10:23:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbu_13303/09_2024/7pbu_13303_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbu_13303/09_2024/7pbu_13303.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbu_13303/09_2024/7pbu_13303.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbu_13303/09_2024/7pbu_13303.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbu_13303/09_2024/7pbu_13303_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbu_13303/09_2024/7pbu_13303_neut.cif" } resolution = 3.3 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= 0.002 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: 6 Type Number sf(0) Gaussians P 68 5.49 5 S 40 5.16 5 C 6060 2.51 5 N 1666 2.21 5 O 1902 1.98 5 H 9507 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 19243 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2137 Classifications: {'peptide': 133} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 126} Chain: "B" Number of atoms: 2137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2137 Classifications: {'peptide': 133} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 126} Chain: "C" Number of atoms: 2137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2137 Classifications: {'peptide': 133} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 126} Chain: "D" Number of atoms: 2137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2137 Classifications: {'peptide': 133} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 126} Chain: "E" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 544 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "F" Number of atoms: 2137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2137 Classifications: {'peptide': 133} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 126} Chain: "G" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 544 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "H" Number of atoms: 2114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2114 Classifications: {'peptide': 132} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 125} Chain: "I" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 541 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "J" Number of atoms: 2137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2137 Classifications: {'peptide': 133} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 126} Chain: "K" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 541 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "L" Number of atoms: 2137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2137 Classifications: {'peptide': 133} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 126} Time building chain proxies: 10.05, per 1000 atoms: 0.52 Number of scatterers: 19243 At special positions: 0 Unit cell: (88.29, 104.64, 101.37, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 40 16.00 P 68 15.00 O 1902 8.00 N 1666 7.00 C 6060 6.00 H 9507 1.00 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: 5.63 Conformation dependent library (CDL) restraints added in 1.6 seconds 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1918 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 2 sheets defined 49.6% alpha, 13.4% beta 15 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 9.10 Creating SS restraints... Processing helix chain 'A' and resid 34 through 38 Processing helix chain 'A' and resid 65 through 77 removed outlier: 3.676A pdb=" N LYS A 77 " --> pdb=" O LYS A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 93 Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 106 through 112 removed outlier: 3.632A pdb=" N LEU A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 133 removed outlier: 4.631A pdb=" N ASP A 130 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ARG A 131 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE A 132 " --> pdb=" O MET A 128 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYS A 133 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 38 Processing helix chain 'B' and resid 65 through 77 removed outlier: 3.646A pdb=" N LYS B 77 " --> pdb=" O LYS B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'B' and resid 94 through 105 Processing helix chain 'B' and resid 106 through 112 removed outlier: 3.582A pdb=" N LEU B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 133 removed outlier: 4.598A pdb=" N ASP B 130 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ARG B 131 " --> pdb=" O GLU B 127 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE B 132 " --> pdb=" O MET B 128 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LYS B 133 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 38 removed outlier: 3.753A pdb=" N TYR C 36 " --> pdb=" O THR C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 77 removed outlier: 3.623A pdb=" N LYS C 77 " --> pdb=" O LYS C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 93 Processing helix chain 'C' and resid 94 through 105 Processing helix chain 'C' and resid 106 through 112 removed outlier: 3.651A pdb=" N LEU C 110 " --> pdb=" O GLU C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 133 removed outlier: 4.582A pdb=" N ASP C 130 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG C 131 " --> pdb=" O GLU C 127 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE C 132 " --> pdb=" O MET C 128 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LYS C 133 " --> pdb=" O LYS C 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 38 Processing helix chain 'D' and resid 65 through 77 removed outlier: 3.673A pdb=" N LYS D 77 " --> pdb=" O LYS D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 93 Processing helix chain 'D' and resid 94 through 105 Processing helix chain 'D' and resid 106 through 112 removed outlier: 3.628A pdb=" N LEU D 110 " --> pdb=" O GLU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 133 removed outlier: 4.626A pdb=" N ASP D 130 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG D 131 " --> pdb=" O GLU D 127 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE D 132 " --> pdb=" O MET D 128 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS D 133 " --> pdb=" O LYS D 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 38 Processing helix chain 'F' and resid 65 through 77 removed outlier: 3.612A pdb=" N LYS F 77 " --> pdb=" O LYS F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'F' and resid 94 through 105 Processing helix chain 'F' and resid 106 through 112 removed outlier: 3.646A pdb=" N LEU F 110 " --> pdb=" O GLU F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 133 removed outlier: 4.586A pdb=" N ASP F 130 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG F 131 " --> pdb=" O GLU F 127 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE F 132 " --> pdb=" O MET F 128 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LYS F 133 " --> pdb=" O LYS F 129 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 38 Processing helix chain 'H' and resid 65 through 77 removed outlier: 3.631A pdb=" N LYS H 77 " --> pdb=" O LYS H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 93 Processing helix chain 'H' and resid 94 through 105 Processing helix chain 'H' and resid 106 through 112 removed outlier: 3.681A pdb=" N LEU H 110 " --> pdb=" O GLU H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 129 Processing helix chain 'J' and resid 34 through 38 Processing helix chain 'J' and resid 65 through 78 removed outlier: 3.574A pdb=" N LYS J 77 " --> pdb=" O LYS J 73 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR J 78 " --> pdb=" O GLU J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 93 Processing helix chain 'J' and resid 94 through 105 Processing helix chain 'J' and resid 106 through 112 removed outlier: 3.638A pdb=" N LEU J 110 " --> pdb=" O GLU J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 117 through 133 removed outlier: 4.592A pdb=" N ASP J 130 " --> pdb=" O VAL J 126 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ARG J 131 " --> pdb=" O GLU J 127 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE J 132 " --> pdb=" O MET J 128 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LYS J 133 " --> pdb=" O LYS J 129 " (cutoff:3.500A) Processing helix chain 'L' and resid 33 through 38 removed outlier: 3.646A pdb=" N TYR L 36 " --> pdb=" O THR L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 65 through 77 removed outlier: 3.661A pdb=" N LYS L 77 " --> pdb=" O LYS L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 93 Processing helix chain 'L' and resid 94 through 105 Processing helix chain 'L' and resid 106 through 112 removed outlier: 3.640A pdb=" N LEU L 110 " --> pdb=" O GLU L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 117 through 133 removed outlier: 4.584A pdb=" N ASP L 130 " --> pdb=" O VAL L 126 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG L 131 " --> pdb=" O GLU L 127 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE L 132 " --> pdb=" O MET L 128 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS L 133 " --> pdb=" O LYS L 129 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 13 removed outlier: 6.820A pdb=" N LEU A 18 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LYS A 12 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ILE A 16 " --> pdb=" O LYS A 12 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 24 through 29 current: chain 'A' and resid 58 through 63 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 58 through 63 current: chain 'B' and resid 16 through 21 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 24 through 29 current: chain 'B' and resid 58 through 63 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 58 through 63 current: chain 'C' and resid 16 through 21 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 24 through 29 current: chain 'C' and resid 58 through 63 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 58 through 63 current: chain 'D' and resid 16 through 21 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 24 through 29 current: chain 'D' and resid 58 through 63 Processing sheet with id=AA2, first strand: chain 'F' and resid 2 through 13 removed outlier: 6.788A pdb=" N LEU F 18 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LYS F 12 " --> pdb=" O ILE F 16 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ILE F 16 " --> pdb=" O LYS F 12 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 24 through 29 current: chain 'F' and resid 58 through 63 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 58 through 63 current: chain 'H' and resid 16 through 21 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 24 through 29 current: chain 'H' and resid 58 through 63 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 58 through 63 current: chain 'J' and resid 16 through 21 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 24 through 29 current: chain 'J' and resid 58 through 63 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 58 through 63 current: chain 'L' and resid 16 through 21 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 24 through 29 current: chain 'L' and resid 58 through 63 350 hydrogen bonds defined for protein. 978 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 64 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 7.48 Time building geometry restraints manager: 6.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9499 1.03 - 1.22: 36 1.22 - 1.42: 3958 1.42 - 1.61: 5939 1.61 - 1.80: 113 Bond restraints: 19545 Sorted by residual: bond pdb=" C4' DT E 27 " pdb=" C3' DT E 27 " ideal model delta sigma weight residual 1.523 1.502 0.021 2.00e-02 2.50e+03 1.10e+00 bond pdb=" C4' DT G 27 " pdb=" C3' DT G 27 " ideal model delta sigma weight residual 1.523 1.504 0.019 2.00e-02 2.50e+03 8.63e-01 bond pdb=" C3' DA E 33 " pdb=" O3' DA E 33 " ideal model delta sigma weight residual 1.422 1.450 -0.028 3.00e-02 1.11e+03 8.48e-01 bond pdb=" CB LEU C 60 " pdb=" CG LEU C 60 " ideal model delta sigma weight residual 1.530 1.512 0.018 2.00e-02 2.50e+03 8.32e-01 bond pdb=" CB LEU D 60 " pdb=" CG LEU D 60 " ideal model delta sigma weight residual 1.530 1.512 0.018 2.00e-02 2.50e+03 8.24e-01 ... (remaining 19540 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 31711 1.11 - 2.21: 3488 2.21 - 3.32: 339 3.32 - 4.42: 72 4.42 - 5.53: 12 Bond angle restraints: 35622 Sorted by residual: angle pdb=" C5' DT K 7 " pdb=" C4' DT K 7 " pdb=" O4' DT K 7 " ideal model delta sigma weight residual 109.40 113.89 -4.49 1.50e+00 4.44e-01 8.97e+00 angle pdb=" C3' DA G 33 " pdb=" C2' DA G 33 " pdb=" C1' DA G 33 " ideal model delta sigma weight residual 101.60 105.98 -4.38 1.50e+00 4.44e-01 8.53e+00 angle pdb=" C4' DT E 25 " pdb=" O4' DT E 25 " pdb=" C1' DT E 25 " ideal model delta sigma weight residual 109.70 105.71 3.99 1.50e+00 4.44e-01 7.09e+00 angle pdb=" C3' DA E 34 " pdb=" C2' DA E 34 " pdb=" C1' DA E 34 " ideal model delta sigma weight residual 101.60 105.57 -3.97 1.50e+00 4.44e-01 7.00e+00 angle pdb=" C4' DT G 25 " pdb=" O4' DT G 25 " pdb=" C1' DT G 25 " ideal model delta sigma weight residual 109.70 105.74 3.96 1.50e+00 4.44e-01 6.97e+00 ... (remaining 35617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 7840 17.86 - 35.73: 551 35.73 - 53.59: 280 53.59 - 71.45: 132 71.45 - 89.31: 11 Dihedral angle restraints: 8814 sinusoidal: 5393 harmonic: 3421 Sorted by residual: dihedral pdb=" CA LYS D 84 " pdb=" CB LYS D 84 " pdb=" CG LYS D 84 " pdb=" CD LYS D 84 " ideal model delta sinusoidal sigma weight residual 180.00 126.48 53.52 3 1.50e+01 4.44e-03 9.21e+00 dihedral pdb=" CB GLU A 106 " pdb=" CG GLU A 106 " pdb=" CD GLU A 106 " pdb=" OE1 GLU A 106 " ideal model delta sinusoidal sigma weight residual 0.00 73.71 -73.71 1 3.00e+01 1.11e-03 7.68e+00 dihedral pdb=" CG ARG J 54 " pdb=" CD ARG J 54 " pdb=" NE ARG J 54 " pdb=" CZ ARG J 54 " ideal model delta sinusoidal sigma weight residual -90.00 -124.88 34.88 2 1.50e+01 4.44e-03 6.98e+00 ... (remaining 8811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1125 0.046 - 0.092: 326 0.092 - 0.138: 110 0.138 - 0.185: 10 0.185 - 0.231: 4 Chirality restraints: 1575 Sorted by residual: chirality pdb=" C3' DT E 30 " pdb=" C4' DT E 30 " pdb=" O3' DT E 30 " pdb=" C2' DT E 30 " both_signs ideal model delta sigma weight residual False -2.66 -2.43 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" C3' DT G 30 " pdb=" C4' DT G 30 " pdb=" O3' DT G 30 " pdb=" C2' DT G 30 " both_signs ideal model delta sigma weight residual False -2.66 -2.44 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" C3' DT G 28 " pdb=" C4' DT G 28 " pdb=" O3' DT G 28 " pdb=" C2' DT G 28 " both_signs ideal model delta sigma weight residual False -2.66 -2.47 -0.19 2.00e-01 2.50e+01 9.13e-01 ... (remaining 1572 not shown) Planarity restraints: 2585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 64 " 0.015 2.00e-02 2.50e+03 2.68e-02 1.08e+01 pdb=" CG ASN A 64 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN A 64 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 64 " 0.047 2.00e-02 2.50e+03 pdb="HD21 ASN A 64 " 0.000 2.00e-02 2.50e+03 pdb="HD22 ASN A 64 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 64 " -0.015 2.00e-02 2.50e+03 2.68e-02 1.08e+01 pdb=" CG ASN F 64 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN F 64 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN F 64 " -0.047 2.00e-02 2.50e+03 pdb="HD21 ASN F 64 " -0.001 2.00e-02 2.50e+03 pdb="HD22 ASN F 64 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 64 " 0.015 2.00e-02 2.50e+03 2.56e-02 9.86e+00 pdb=" CG ASN D 64 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN D 64 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN D 64 " 0.045 2.00e-02 2.50e+03 pdb="HD21 ASN D 64 " 0.000 2.00e-02 2.50e+03 pdb="HD22 ASN D 64 " -0.029 2.00e-02 2.50e+03 ... (remaining 2582 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 1445 2.24 - 2.83: 41587 2.83 - 3.42: 45307 3.42 - 4.01: 63119 4.01 - 4.60: 98727 Nonbonded interactions: 250185 Sorted by model distance: nonbonded pdb=" OE1 GLU A 74 " pdb=" HE ARG A 131 " model vdw 1.649 2.450 nonbonded pdb=" OE1 GLU C 74 " pdb=" HE ARG C 131 " model vdw 1.684 2.450 nonbonded pdb=" OE1 GLU L 74 " pdb=" HE ARG L 131 " model vdw 1.714 2.450 nonbonded pdb=" OE1 GLU D 74 " pdb=" HE ARG D 131 " model vdw 1.732 2.450 nonbonded pdb=" OE2 GLU D 127 " pdb="HH11 ARG F 123 " model vdw 1.742 2.450 ... (remaining 250180 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 132) selection = (chain 'B' and resid 1 through 132) selection = (chain 'C' and resid 1 through 132) selection = (chain 'D' and resid 1 through 132) selection = (chain 'F' and resid 1 through 132) selection = chain 'H' selection = (chain 'J' and resid 1 through 132) selection = (chain 'L' and resid 1 through 132) } ncs_group { reference = (chain 'E' and resid 25 through 40) selection = (chain 'G' and resid 25 through 40) selection = (chain 'I' and resid 2 through 17) selection = (chain 'K' and resid 2 through 17) } 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: 2.380 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: 0.300 Extract box with map and model: 0.710 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 51.980 Find NCS groups from input model: 0.680 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: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 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 : 0.005 0.033 10038 Z= 0.331 Angle : 0.819 5.529 13809 Z= 0.494 Chirality : 0.049 0.231 1575 Planarity : 0.007 0.054 1538 Dihedral : 16.547 89.314 4038 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.25), residues: 1047 helix: -0.89 (0.20), residues: 472 sheet: 0.77 (0.25), residues: 336 loop : 2.15 (0.46), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.005 HIS J 29 PHE 0.012 0.002 PHE L 48 TYR 0.011 0.003 TYR D 36 ARG 0.008 0.002 ARG L 4 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 416 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLN cc_start: 0.8017 (mt0) cc_final: 0.7776 (mp10) REVERT: A 84 LYS cc_start: 0.8694 (tptt) cc_final: 0.8441 (tttt) REVERT: A 100 ASN cc_start: 0.7390 (m-40) cc_final: 0.7182 (m110) REVERT: B 13 GLN cc_start: 0.7059 (mt0) cc_final: 0.6773 (mt0) REVERT: B 100 ASN cc_start: 0.7356 (m-40) cc_final: 0.7104 (m110) REVERT: C 67 GLN cc_start: 0.8036 (mt0) cc_final: 0.7666 (mp10) REVERT: C 100 ASN cc_start: 0.7338 (m-40) cc_final: 0.7110 (m110) REVERT: D 13 GLN cc_start: 0.7163 (mt0) cc_final: 0.6919 (mt0) REVERT: D 67 GLN cc_start: 0.8055 (mt0) cc_final: 0.7736 (mp10) REVERT: D 100 ASN cc_start: 0.7326 (m-40) cc_final: 0.7082 (m110) REVERT: F 100 ASN cc_start: 0.7284 (m-40) cc_final: 0.6925 (m-40) REVERT: H 67 GLN cc_start: 0.8165 (mt0) cc_final: 0.7799 (mp10) REVERT: H 100 ASN cc_start: 0.7322 (m-40) cc_final: 0.7050 (m110) REVERT: J 67 GLN cc_start: 0.8097 (mt0) cc_final: 0.7852 (mp10) REVERT: J 100 ASN cc_start: 0.7415 (m-40) cc_final: 0.7132 (m110) REVERT: L 13 GLN cc_start: 0.7068 (mt0) cc_final: 0.6816 (mt0) REVERT: L 59 LEU cc_start: 0.9092 (mt) cc_final: 0.8892 (mp) REVERT: L 67 GLN cc_start: 0.8017 (mt0) cc_final: 0.7725 (mp10) REVERT: L 100 ASN cc_start: 0.7376 (m-40) cc_final: 0.7144 (m110) outliers start: 0 outliers final: 0 residues processed: 416 average time/residue: 0.6360 time to fit residues: 343.4465 Evaluate side-chains 319 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 319 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.1980 chunk 55 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN B 97 GLN C 65 ASN D 65 ASN D 97 GLN F 97 GLN H 65 ASN H 97 GLN J 65 ASN J 97 GLN L 65 ASN L 97 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 10038 Z= 0.287 Angle : 0.658 5.577 13809 Z= 0.378 Chirality : 0.044 0.155 1575 Planarity : 0.005 0.032 1538 Dihedral : 19.540 89.366 1922 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.48 % Allowed : 12.18 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.68 (0.27), residues: 1047 helix: 0.89 (0.25), residues: 480 sheet: 0.48 (0.25), residues: 329 loop : 3.17 (0.49), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS H 29 PHE 0.008 0.002 PHE B 63 TYR 0.007 0.001 TYR H 61 ARG 0.002 0.000 ARG L 4 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 324 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.7988 (m-80) REVERT: A 68 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7318 (mt-10) REVERT: A 100 ASN cc_start: 0.7275 (m-40) cc_final: 0.7001 (m110) REVERT: B 35 PHE cc_start: 0.8375 (OUTLIER) cc_final: 0.7981 (m-80) REVERT: B 40 GLU cc_start: 0.7322 (mp0) cc_final: 0.7073 (pm20) REVERT: B 74 GLU cc_start: 0.8304 (mm-30) cc_final: 0.8102 (mm-30) REVERT: C 35 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.7953 (m-80) REVERT: C 67 GLN cc_start: 0.7920 (mt0) cc_final: 0.7715 (mt0) REVERT: C 116 ILE cc_start: 0.8675 (mt) cc_final: 0.8435 (mp) REVERT: D 35 PHE cc_start: 0.8306 (OUTLIER) cc_final: 0.8058 (m-80) REVERT: D 77 LYS cc_start: 0.8467 (mtmt) cc_final: 0.8212 (mtmm) REVERT: F 35 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.8004 (m-80) REVERT: F 100 ASN cc_start: 0.7309 (m-40) cc_final: 0.6969 (m-40) REVERT: H 35 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.7967 (m-80) REVERT: H 100 ASN cc_start: 0.7178 (m-40) cc_final: 0.6754 (m110) REVERT: J 35 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.8188 (m-80) REVERT: L 35 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.8017 (m-80) REVERT: L 40 GLU cc_start: 0.7297 (mp0) cc_final: 0.7034 (pm20) REVERT: L 68 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7283 (mt-10) REVERT: L 100 ASN cc_start: 0.7299 (m-40) cc_final: 0.7018 (m110) outliers start: 22 outliers final: 11 residues processed: 331 average time/residue: 0.6896 time to fit residues: 293.0625 Evaluate side-chains 305 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 286 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 35 PHE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 35 PHE Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain H residue 35 PHE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 112 LYS Chi-restraints excluded: chain J residue 35 PHE Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain L residue 35 PHE Chi-restraints excluded: chain L residue 102 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 0.3980 chunk 98 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 97 optimal weight: 0.2980 chunk 33 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 ASN C 100 ASN D 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 10038 Z= 0.224 Angle : 0.599 4.983 13809 Z= 0.343 Chirality : 0.043 0.137 1575 Planarity : 0.004 0.035 1538 Dihedral : 19.741 88.053 1922 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 4.40 % Allowed : 14.09 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.60 (0.27), residues: 1047 helix: 1.16 (0.25), residues: 480 sheet: 0.12 (0.29), residues: 233 loop : 2.05 (0.39), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS L 29 PHE 0.006 0.001 PHE H 35 TYR 0.005 0.001 TYR H 61 ARG 0.002 0.000 ARG L 4 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 308 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.8131 (m-80) REVERT: A 68 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7212 (mt-10) REVERT: B 35 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.8131 (m-80) REVERT: C 35 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.8106 (m-80) REVERT: C 68 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7304 (mt-10) REVERT: C 122 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6949 (mp0) REVERT: D 77 LYS cc_start: 0.8378 (mtmt) cc_final: 0.8169 (mtmm) REVERT: F 35 PHE cc_start: 0.8450 (OUTLIER) cc_final: 0.8100 (m-80) REVERT: H 32 MET cc_start: 0.7797 (mmm) cc_final: 0.7584 (mmm) REVERT: H 35 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.8139 (m-80) REVERT: L 35 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.8083 (m-80) REVERT: L 68 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7252 (mt-10) REVERT: L 122 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.7028 (mp0) outliers start: 39 outliers final: 18 residues processed: 314 average time/residue: 0.6970 time to fit residues: 279.7323 Evaluate side-chains 314 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 288 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain B residue 1 VAL Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 35 PHE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 1 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain H residue 35 PHE Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 112 LYS Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain L residue 35 PHE Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 122 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 104 optimal weight: 0.4980 chunk 51 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN C 100 ASN D 100 ASN H 100 ASN L 100 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10038 Z= 0.260 Angle : 0.605 5.495 13809 Z= 0.343 Chirality : 0.043 0.128 1575 Planarity : 0.004 0.032 1538 Dihedral : 19.898 87.851 1922 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 4.85 % Allowed : 15.22 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.09 (0.27), residues: 1047 helix: 0.98 (0.25), residues: 480 sheet: -0.45 (0.29), residues: 240 loop : 1.71 (0.39), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS L 29 PHE 0.009 0.001 PHE C 35 TYR 0.007 0.001 TYR H 61 ARG 0.003 0.001 ARG F 104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 297 time to evaluate : 2.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 122 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7015 (mp0) REVERT: D 11 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7291 (mt-10) REVERT: D 13 GLN cc_start: 0.7538 (mp10) cc_final: 0.7330 (mp10) REVERT: D 77 LYS cc_start: 0.8408 (mtmt) cc_final: 0.8189 (mtmm) REVERT: F 35 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.8126 (m-80) outliers start: 43 outliers final: 22 residues processed: 304 average time/residue: 0.7010 time to fit residues: 274.7054 Evaluate side-chains 302 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 278 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain B residue 1 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 1 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 112 LYS Chi-restraints excluded: chain J residue 1 VAL Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain L residue 1 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 102 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 72 optimal weight: 0.4980 chunk 0 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN C 100 ASN D 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 10038 Z= 0.263 Angle : 0.594 5.641 13809 Z= 0.336 Chirality : 0.042 0.127 1575 Planarity : 0.004 0.030 1538 Dihedral : 19.938 89.273 1922 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 4.51 % Allowed : 16.35 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.27), residues: 1047 helix: 0.92 (0.25), residues: 480 sheet: -0.79 (0.28), residues: 240 loop : 1.52 (0.39), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS L 29 PHE 0.006 0.001 PHE F 35 TYR 0.006 0.001 TYR H 61 ARG 0.003 0.001 ARG C 123 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 282 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.8274 (tttt) cc_final: 0.8016 (ttmt) REVERT: C 122 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7001 (mp0) REVERT: D 77 LYS cc_start: 0.8364 (mtmt) cc_final: 0.8152 (mtmm) REVERT: D 106 GLU cc_start: 0.7882 (tp30) cc_final: 0.7647 (tp30) REVERT: F 35 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.8249 (m-80) REVERT: H 68 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7238 (mt-10) REVERT: L 122 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7036 (mp0) outliers start: 40 outliers final: 27 residues processed: 286 average time/residue: 0.6501 time to fit residues: 237.8824 Evaluate side-chains 310 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 279 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain B residue 1 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 1 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain F residue 1 VAL Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain H residue 1 VAL Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain J residue 1 VAL Chi-restraints excluded: chain J residue 11 GLU Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain L residue 1 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 122 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 0.0870 chunk 54 optimal weight: 0.6980 overall best weight: 0.7358 ------------------------------------------------------------------------------- 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: 0.7718 moved from start: 0.5018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 10038 Z= 0.256 Angle : 0.582 4.339 13809 Z= 0.329 Chirality : 0.042 0.128 1575 Planarity : 0.004 0.032 1538 Dihedral : 19.814 87.654 1922 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 4.17 % Allowed : 16.23 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.27), residues: 1047 helix: 0.92 (0.25), residues: 480 sheet: -1.16 (0.28), residues: 240 loop : 1.37 (0.38), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 29 PHE 0.006 0.001 PHE F 35 TYR 0.007 0.001 TYR J 26 ARG 0.002 0.000 ARG L 4 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 284 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 106 GLU cc_start: 0.7924 (tp30) cc_final: 0.7534 (tp30) REVERT: C 122 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7031 (mp0) REVERT: D 77 LYS cc_start: 0.8377 (mtmt) cc_final: 0.8150 (mtmm) REVERT: F 35 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.8313 (m-80) REVERT: H 68 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7242 (mt-10) REVERT: J 106 GLU cc_start: 0.7889 (tp30) cc_final: 0.7499 (tp30) REVERT: J 119 LYS cc_start: 0.7526 (tttm) cc_final: 0.7318 (tttt) REVERT: L 103 GLU cc_start: 0.6629 (tm-30) cc_final: 0.6394 (tm-30) REVERT: L 106 GLU cc_start: 0.8059 (tp30) cc_final: 0.7631 (tp30) outliers start: 37 outliers final: 27 residues processed: 287 average time/residue: 0.6285 time to fit residues: 232.1464 Evaluate side-chains 311 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 281 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain B residue 1 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 1 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain F residue 1 VAL Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain H residue 1 VAL Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain J residue 1 VAL Chi-restraints excluded: chain J residue 11 GLU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain L residue 1 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 102 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 87 optimal weight: 0.2980 chunk 58 optimal weight: 0.4980 chunk 104 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 64 optimal weight: 0.0980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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: 0.7705 moved from start: 0.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 10038 Z= 0.195 Angle : 0.553 4.366 13809 Z= 0.313 Chirality : 0.042 0.128 1575 Planarity : 0.004 0.033 1538 Dihedral : 19.678 85.617 1922 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 4.28 % Allowed : 15.78 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.27), residues: 1047 helix: 1.08 (0.25), residues: 480 sheet: -1.04 (0.28), residues: 240 loop : 1.54 (0.39), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS L 29 PHE 0.006 0.001 PHE F 35 TYR 0.005 0.001 TYR H 61 ARG 0.002 0.000 ARG H 104 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 295 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 GLU cc_start: 0.7887 (tp30) cc_final: 0.7654 (tp30) REVERT: C 122 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.6987 (mp0) REVERT: D 77 LYS cc_start: 0.8370 (mtmt) cc_final: 0.8127 (mtmm) REVERT: F 106 GLU cc_start: 0.8025 (tp30) cc_final: 0.7588 (tp30) REVERT: H 68 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7203 (mt-10) REVERT: J 106 GLU cc_start: 0.7878 (tp30) cc_final: 0.7643 (tp30) REVERT: J 119 LYS cc_start: 0.7439 (tttm) cc_final: 0.7233 (tttt) REVERT: L 33 THR cc_start: 0.9003 (t) cc_final: 0.8696 (m) REVERT: L 106 GLU cc_start: 0.7897 (tp30) cc_final: 0.7524 (tp30) REVERT: L 122 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7119 (mp0) outliers start: 38 outliers final: 29 residues processed: 298 average time/residue: 0.6085 time to fit residues: 236.4275 Evaluate side-chains 320 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 288 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain B residue 1 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain D residue 1 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain F residue 1 VAL Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain H residue 1 VAL Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain J residue 1 VAL Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain L residue 1 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 122 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 20 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 0.0980 chunk 51 optimal weight: 0.0980 chunk 9 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.5223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10038 Z= 0.207 Angle : 0.555 4.400 13809 Z= 0.313 Chirality : 0.042 0.128 1575 Planarity : 0.004 0.033 1538 Dihedral : 19.539 82.487 1922 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 3.95 % Allowed : 16.01 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.27), residues: 1047 helix: 1.14 (0.25), residues: 480 sheet: -1.01 (0.29), residues: 240 loop : 1.57 (0.39), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS L 29 PHE 0.005 0.001 PHE A 72 TYR 0.005 0.001 TYR J 26 ARG 0.005 0.000 ARG D 104 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 287 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 GLU cc_start: 0.7914 (tp30) cc_final: 0.7535 (tp30) REVERT: B 122 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7025 (mp0) REVERT: C 122 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7010 (mp0) REVERT: D 77 LYS cc_start: 0.8349 (mtmt) cc_final: 0.8099 (mtmm) REVERT: D 106 GLU cc_start: 0.7948 (tp30) cc_final: 0.7705 (tp30) REVERT: F 106 GLU cc_start: 0.8035 (tp30) cc_final: 0.7796 (tp30) REVERT: H 68 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7167 (mt-10) REVERT: J 106 GLU cc_start: 0.7879 (tp30) cc_final: 0.7643 (tp30) REVERT: L 33 THR cc_start: 0.8997 (t) cc_final: 0.8725 (m) REVERT: L 106 GLU cc_start: 0.7897 (tp30) cc_final: 0.7531 (tp30) REVERT: L 122 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.6968 (mp0) outliers start: 35 outliers final: 28 residues processed: 290 average time/residue: 0.5888 time to fit residues: 222.6891 Evaluate side-chains 313 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 281 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain B residue 1 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain D residue 1 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain F residue 1 VAL Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain H residue 1 VAL Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain J residue 1 VAL Chi-restraints excluded: chain J residue 11 GLU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain L residue 1 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 122 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 42 optimal weight: 0.0670 chunk 76 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 87 optimal weight: 0.3980 chunk 91 optimal weight: 0.9990 chunk 96 optimal weight: 0.1980 chunk 63 optimal weight: 0.0870 overall best weight: 0.3296 ------------------------------------------------------------------------------- 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: 0.7693 moved from start: 0.5329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 10038 Z= 0.170 Angle : 0.537 4.270 13809 Z= 0.304 Chirality : 0.041 0.128 1575 Planarity : 0.004 0.030 1538 Dihedral : 19.475 78.003 1922 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Rotamer: Outliers : 3.49 % Allowed : 16.69 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.49 (0.28), residues: 1047 helix: 1.39 (0.25), residues: 480 sheet: -0.15 (0.27), residues: 315 loop : 2.25 (0.48), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS L 29 PHE 0.004 0.001 PHE B 51 TYR 0.004 0.001 TYR H 61 ARG 0.005 0.000 ARG H 104 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 287 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 THR cc_start: 0.8968 (t) cc_final: 0.8667 (m) REVERT: B 103 GLU cc_start: 0.6634 (tm-30) cc_final: 0.6419 (tm-30) REVERT: B 106 GLU cc_start: 0.7886 (tp30) cc_final: 0.7519 (tp30) REVERT: B 122 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.6961 (mp0) REVERT: C 122 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7035 (mp0) REVERT: D 77 LYS cc_start: 0.8347 (mtmt) cc_final: 0.8120 (mtmm) REVERT: D 106 GLU cc_start: 0.7979 (tp30) cc_final: 0.7566 (tp30) REVERT: F 106 GLU cc_start: 0.7998 (tp30) cc_final: 0.7759 (tp30) REVERT: J 103 GLU cc_start: 0.6615 (tm-30) cc_final: 0.6402 (tm-30) REVERT: J 106 GLU cc_start: 0.7833 (tp30) cc_final: 0.7464 (tp30) REVERT: L 33 THR cc_start: 0.9021 (t) cc_final: 0.8776 (m) REVERT: L 106 GLU cc_start: 0.7852 (tp30) cc_final: 0.7498 (tp30) REVERT: L 122 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7074 (mp0) outliers start: 31 outliers final: 25 residues processed: 289 average time/residue: 0.5683 time to fit residues: 218.2318 Evaluate side-chains 306 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 278 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain B residue 1 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain D residue 1 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain F residue 1 VAL Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain H residue 1 VAL Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain J residue 1 VAL Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain L residue 1 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 122 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN C 64 ASN H 64 ASN J 64 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.5413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 10038 Z= 0.284 Angle : 0.590 4.264 13809 Z= 0.331 Chirality : 0.043 0.135 1575 Planarity : 0.004 0.036 1538 Dihedral : 19.402 71.705 1922 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.93 % Allowed : 16.80 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.27), residues: 1047 helix: 1.15 (0.25), residues: 480 sheet: -1.35 (0.28), residues: 240 loop : 1.36 (0.39), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS L 29 PHE 0.008 0.002 PHE L 48 TYR 0.010 0.002 TYR J 26 ARG 0.004 0.000 ARG C 123 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 274 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 33 THR cc_start: 0.8992 (t) cc_final: 0.8757 (m) REVERT: B 106 GLU cc_start: 0.7943 (tp30) cc_final: 0.7706 (tp30) REVERT: B 122 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6939 (mp0) REVERT: C 122 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7021 (mp0) REVERT: D 77 LYS cc_start: 0.8406 (mtmt) cc_final: 0.8137 (mtmm) REVERT: F 106 GLU cc_start: 0.7906 (tp30) cc_final: 0.7660 (tp30) REVERT: H 33 THR cc_start: 0.9071 (t) cc_final: 0.8808 (m) REVERT: J 33 THR cc_start: 0.9060 (t) cc_final: 0.8784 (m) REVERT: J 106 GLU cc_start: 0.7900 (tp30) cc_final: 0.7509 (tp30) REVERT: J 119 LYS cc_start: 0.7546 (tttm) cc_final: 0.7332 (tttt) REVERT: L 33 THR cc_start: 0.9036 (t) cc_final: 0.8831 (m) REVERT: L 103 GLU cc_start: 0.6579 (tm-30) cc_final: 0.6374 (tm-30) REVERT: L 122 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.6897 (mp0) outliers start: 26 outliers final: 16 residues processed: 277 average time/residue: 0.6064 time to fit residues: 218.5037 Evaluate side-chains 288 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 269 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain B residue 1 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 1 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain F residue 1 VAL Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain H residue 1 VAL Chi-restraints excluded: chain J residue 1 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 122 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.3980 chunk 26 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 12 optimal weight: 0.3980 chunk 23 optimal weight: 0.0970 chunk 85 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 = 0.3899 r_free = 0.3899 target = 0.162424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.110609 restraints weight = 32537.310| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.73 r_work: 0.3126 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.5467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 10038 Z= 0.193 Angle : 0.555 4.127 13809 Z= 0.312 Chirality : 0.041 0.129 1575 Planarity : 0.004 0.033 1538 Dihedral : 19.373 69.712 1922 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.48 % Allowed : 17.47 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.27), residues: 1047 helix: 1.20 (0.24), residues: 480 sheet: -0.82 (0.25), residues: 336 loop : 2.41 (0.51), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS L 29 PHE 0.004 0.001 PHE A 72 TYR 0.005 0.001 TYR H 61 ARG 0.002 0.000 ARG D 123 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6106.84 seconds wall clock time: 107 minutes 4.65 seconds (6424.65 seconds total)