Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 03:00:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbu_13303/04_2023/7pbu_13303_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbu_13303/04_2023/7pbu_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_13303/04_2023/7pbu_13303.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbu_13303/04_2023/7pbu_13303.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbu_13303/04_2023/7pbu_13303_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbu_13303/04_2023/7pbu_13303_neut.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Residue "B TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 8.36, per 1000 atoms: 0.43 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.17 Conformation dependent library (CDL) restraints added in 1.3 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: 8.26 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: 6.81 Time building geometry restraints manager: 16.65 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: 100.29 - 106.73: 689 106.73 - 113.17: 23219 113.17 - 119.61: 4524 119.61 - 126.04: 6867 126.04 - 132.48: 323 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: 6813 17.86 - 35.73: 363 35.73 - 53.59: 166 53.59 - 71.45: 94 71.45 - 89.31: 11 Dihedral angle restraints: 7447 sinusoidal: 4026 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 7444 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 1.850 nonbonded pdb=" OE1 GLU C 74 " pdb=" HE ARG C 131 " model vdw 1.684 1.850 nonbonded pdb=" OE1 GLU L 74 " pdb=" HE ARG L 131 " model vdw 1.714 1.850 nonbonded pdb=" OE1 GLU D 74 " pdb=" HE ARG D 131 " model vdw 1.732 1.850 nonbonded pdb=" OE2 GLU D 127 " pdb="HH11 ARG F 123 " model vdw 1.742 1.850 ... (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 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: 3.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.270 Extract box with map and model: 10.890 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 66.900 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.070 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.160 ------------------------------------------------------------------------------- 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 : 16.248 89.314 3926 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 % 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 *********************** 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 : 1.468 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 outliers start: 0 outliers final: 0 residues processed: 416 average time/residue: 0.6258 time to fit residues: 336.9773 Evaluate side-chains 317 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 317 time to evaluate : 1.473 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8054 ------------------------------------------------------------------------------- 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: 0.9980 chunk 27 optimal weight: 0.0970 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN A 100 ASN B 13 GLN B 97 GLN B 100 ASN C 65 ASN C 97 GLN C 100 ASN D 13 GLN D 65 ASN D 97 GLN D 100 ASN F 97 GLN H 65 ASN H 97 GLN H 100 ASN J 65 ASN J 97 GLN J 100 ASN L 13 GLN L 65 ASN L 97 GLN L 100 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 10038 Z= 0.278 Angle : 0.647 5.678 13809 Z= 0.373 Chirality : 0.044 0.151 1575 Planarity : 0.005 0.030 1538 Dihedral : 19.322 89.539 1810 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer Outliers : 2.37 % 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: 1.65 (0.27), residues: 1047 helix: 0.85 (0.25), residues: 480 sheet: 0.50 (0.25), residues: 336 loop : 3.22 (0.49), residues: 231 *********************** 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 351 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 330 time to evaluate : 1.397 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 outliers start: 21 outliers final: 11 residues processed: 337 average time/residue: 0.6592 time to fit residues: 285.6353 Evaluate side-chains 303 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 292 time to evaluate : 1.433 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2583 time to fit residues: 6.6302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 0.3980 chunk 30 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 98 optimal weight: 0.0040 chunk 106 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 97 optimal weight: 0.2980 chunk 33 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN B 100 ASN C 100 ASN D 100 ASN H 100 ASN L 13 GLN L 100 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 10038 Z= 0.207 Angle : 0.579 5.368 13809 Z= 0.331 Chirality : 0.042 0.133 1575 Planarity : 0.004 0.031 1538 Dihedral : 19.506 88.016 1810 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer Outliers : 2.48 % 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: 1.64 (0.27), residues: 1047 helix: 1.18 (0.26), residues: 480 sheet: 0.03 (0.29), residues: 240 loop : 2.23 (0.39), residues: 327 *********************** 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 331 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 309 time to evaluate : 1.408 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 outliers start: 22 outliers final: 12 residues processed: 309 average time/residue: 0.6857 time to fit residues: 273.7285 Evaluate side-chains 312 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 300 time to evaluate : 1.479 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 3 residues processed: 12 average time/residue: 0.3499 time to fit residues: 8.2085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 50 optimal weight: 0.0970 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 104 optimal weight: 0.1980 chunk 51 optimal weight: 0.4980 chunk 93 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 J 100 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 10038 Z= 0.203 Angle : 0.563 4.974 13809 Z= 0.320 Chirality : 0.041 0.128 1575 Planarity : 0.004 0.028 1538 Dihedral : 19.610 89.710 1810 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer Outliers : 2.93 % 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: 1.62 (0.27), residues: 1047 helix: 1.24 (0.25), residues: 480 sheet: -0.09 (0.29), residues: 240 loop : 2.19 (0.39), residues: 327 *********************** 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 328 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 302 time to evaluate : 1.472 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 outliers start: 26 outliers final: 16 residues processed: 303 average time/residue: 0.6390 time to fit residues: 250.2666 Evaluate side-chains 308 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 292 time to evaluate : 1.451 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 16 outliers final: 1 residues processed: 16 average time/residue: 0.2769 time to fit residues: 9.0717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 1 optimal weight: 0.2980 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 89 optimal weight: 0.3980 chunk 72 optimal weight: 0.8980 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: 0.6180 ------------------------------------------------------------------------------- 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: 0.7690 moved from start: 0.4754 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= 0.228 Angle : 0.568 4.668 13809 Z= 0.321 Chirality : 0.042 0.127 1575 Planarity : 0.003 0.027 1538 Dihedral : 19.591 87.030 1810 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer Outliers : 1.24 % 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: 1.36 (0.27), residues: 1047 helix: 1.12 (0.25), residues: 480 sheet: -0.27 (0.29), residues: 240 loop : 1.94 (0.38), residues: 327 *********************** 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 305 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 294 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 294 average time/residue: 0.6351 time to fit residues: 241.4095 Evaluate side-chains 286 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 282 time to evaluate : 1.501 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2124 time to fit residues: 3.3970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 0.3980 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 D 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.5009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 10038 Z= 0.263 Angle : 0.584 4.342 13809 Z= 0.328 Chirality : 0.042 0.130 1575 Planarity : 0.003 0.029 1538 Dihedral : 19.525 88.869 1810 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer Outliers : 2.14 % 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: 0.98 (0.27), residues: 1047 helix: 0.97 (0.25), residues: 480 sheet: -0.69 (0.28), residues: 240 loop : 1.66 (0.38), residues: 327 *********************** 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 299 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 280 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 13 residues processed: 282 average time/residue: 0.6408 time to fit residues: 232.8101 Evaluate side-chains 291 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 278 time to evaluate : 1.378 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2121 time to fit residues: 6.6201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.2980 chunk 59 optimal weight: 0.2980 chunk 76 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.7708 moved from start: 0.5175 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= 0.223 Angle : 0.564 4.336 13809 Z= 0.317 Chirality : 0.042 0.127 1575 Planarity : 0.003 0.029 1538 Dihedral : 19.415 88.986 1810 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer Outliers : 1.47 % 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: 1.01 (0.27), residues: 1047 helix: 1.04 (0.24), residues: 480 sheet: -0.74 (0.28), residues: 238 loop : 1.66 (0.39), residues: 329 *********************** 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 302 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 289 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 291 average time/residue: 0.6116 time to fit residues: 231.2346 Evaluate side-chains 293 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 285 time to evaluate : 1.514 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2076 time to fit residues: 4.8482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 0.0030 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 0.0870 overall best weight: 0.5372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.5281 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= 0.210 Angle : 0.558 4.266 13809 Z= 0.314 Chirality : 0.041 0.128 1575 Planarity : 0.003 0.028 1538 Dihedral : 19.311 86.022 1810 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer Outliers : 1.24 % 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: 1.04 (0.27), residues: 1047 helix: 1.07 (0.24), residues: 480 sheet: -0.72 (0.28), residues: 238 loop : 1.64 (0.39), residues: 329 *********************** 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 305 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 294 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 295 average time/residue: 0.5856 time to fit residues: 226.2429 Evaluate side-chains 299 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 291 time to evaluate : 1.342 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2021 time to fit residues: 4.7644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 99 optimal weight: 0.3980 chunk 58 optimal weight: 0.0970 chunk 42 optimal weight: 0.0980 chunk 76 optimal weight: 0.9990 chunk 29 optimal weight: 0.2980 chunk 87 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 96 optimal weight: 0.0970 chunk 63 optimal weight: 0.8980 overall best weight: 0.1976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 64 ASN H 64 ASN J 64 ASN L 64 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.5409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 10038 Z= 0.163 Angle : 0.539 4.526 13809 Z= 0.305 Chirality : 0.041 0.125 1575 Planarity : 0.003 0.030 1538 Dihedral : 19.225 83.922 1810 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Rotamer Outliers : 0.68 % 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: 1.66 (0.28), residues: 1047 helix: 1.33 (0.25), residues: 480 sheet: 0.06 (0.26), residues: 334 loop : 2.81 (0.52), residues: 233 *********************** 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 308 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 302 time to evaluate : 1.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 302 average time/residue: 0.5768 time to fit residues: 228.9460 Evaluate side-chains 294 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 291 time to evaluate : 1.462 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2057 time to fit residues: 2.9111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 107 optimal weight: 0.9990 chunk 99 optimal weight: 0.3980 chunk 85 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.5472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 10038 Z= 0.235 Angle : 0.559 4.299 13809 Z= 0.316 Chirality : 0.042 0.128 1575 Planarity : 0.003 0.030 1538 Dihedral : 19.129 80.194 1810 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer Outliers : 0.11 % 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: 1.27 (0.27), residues: 1047 helix: 1.26 (0.25), residues: 480 sheet: -0.63 (0.29), residues: 238 loop : 1.78 (0.40), residues: 329 ********************** 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 285 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 284 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 284 average time/residue: 0.5840 time to fit residues: 217.8821 Evaluate side-chains 279 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 1.483 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 75 optimal weight: 0.0370 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 ASN C 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.163389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.111603 restraints weight = 32701.866| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.74 r_work: 0.3124 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.5535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 10038 Z= 0.244 Angle : 0.565 4.385 13809 Z= 0.318 Chirality : 0.042 0.128 1575 Planarity : 0.003 0.031 1538 Dihedral : 19.087 76.405 1810 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer Outliers : 0.23 % 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: 1.21 (0.24), residues: 480 sheet: -0.83 (0.29), residues: 238 loop : 1.62 (0.39), residues: 329 =============================================================================== Job complete usr+sys time: 5923.76 seconds wall clock time: 104 minutes 34.28 seconds (6274.28 seconds total)