Starting phenix.real_space_refine on Sat Dec 9 22:07:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6buz_7293/12_2023/6buz_7293.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6buz_7293/12_2023/6buz_7293.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6buz_7293/12_2023/6buz_7293.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6buz_7293/12_2023/6buz_7293.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6buz_7293/12_2023/6buz_7293.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6buz_7293/12_2023/6buz_7293.pdb" } resolution = 3.92 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= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 288 5.49 5 S 8 5.16 5 C 6962 2.51 5 N 2354 2.21 5 O 2897 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 69": "NH1" <-> "NH2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 100": "NH1" <-> "NH2" Residue "D ARG 34": "NH1" <-> "NH2" Residue "D TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "G ARG 43": "NH1" <-> "NH2" Residue "G ARG 100": "NH1" <-> "NH2" Residue "H ARG 100": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 12509 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 749 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "B" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 826 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 749 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 826 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "N" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 672 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 7 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 478 Unresolved non-hydrogen angles: 609 Unresolved non-hydrogen dihedrals: 409 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 3, 'ASP:plan': 4, 'PHE:plan': 6, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 262 Time building chain proxies: 6.61, per 1000 atoms: 0.53 Number of scatterers: 12509 At special positions: 0 Unit cell: (110.88, 134.4, 113.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 8 16.00 P 288 15.00 O 2897 8.00 N 2354 7.00 C 6962 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.12 Conformation dependent library (CDL) restraints added in 1.2 seconds 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1644 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 7 sheets defined 67.9% alpha, 1.6% beta 115 base pairs and 214 stacking pairs defined. Time for finding SS restraints: 6.85 Creating SS restraints... Processing helix chain 'A' and resid 46 through 55 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.813A pdb=" N LYS A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 116 removed outlier: 3.755A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A 93 " --> pdb=" O GLN A 89 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU A 99 " --> pdb=" O GLN A 95 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 134 removed outlier: 3.664A pdb=" N ALA A 129 " --> pdb=" O ASP A 125 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 30 removed outlier: 3.639A pdb=" N ILE B 30 " --> pdb=" O ILE B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 50 through 65 removed outlier: 3.706A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG B 56 " --> pdb=" O TYR B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 77 removed outlier: 3.601A pdb=" N THR B 72 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR B 73 " --> pdb=" O ASP B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 95 removed outlier: 3.504A pdb=" N VAL B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 27 through 38 removed outlier: 3.724A pdb=" N ARG C 36 " --> pdb=" O HIS C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 74 removed outlier: 4.770A pdb=" N ALA C 53 " --> pdb=" O PRO C 49 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA C 54 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL C 55 " --> pdb=" O TYR C 51 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU C 65 " --> pdb=" O ALA C 61 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN C 69 " --> pdb=" O GLU C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 91 removed outlier: 3.843A pdb=" N LEU C 84 " --> pdb=" O ILE C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 99 Processing helix chain 'D' and resid 38 through 50 Processing helix chain 'D' and resid 56 through 85 removed outlier: 3.732A pdb=" N MET D 60 " --> pdb=" O SER D 56 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG D 80 " --> pdb=" O GLY D 76 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 103 removed outlier: 3.760A pdb=" N ILE D 95 " --> pdb=" O THR D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 123 removed outlier: 4.346A pdb=" N HIS D 110 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA D 111 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER D 113 " --> pdb=" O LYS D 109 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA D 118 " --> pdb=" O GLU D 114 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.813A pdb=" N LYS E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 116 removed outlier: 3.756A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA E 93 " --> pdb=" O GLN E 89 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU E 94 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU E 99 " --> pdb=" O GLN E 95 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU E 111 " --> pdb=" O GLU E 107 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU E 112 " --> pdb=" O ASP E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 134 removed outlier: 3.664A pdb=" N ALA E 129 " --> pdb=" O ASP E 125 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY E 134 " --> pdb=" O ARG E 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 30 removed outlier: 3.640A pdb=" N ILE F 30 " --> pdb=" O ILE F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 42 Processing helix chain 'F' and resid 50 through 65 removed outlier: 3.706A pdb=" N GLU F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG F 56 " --> pdb=" O TYR F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 77 removed outlier: 3.600A pdb=" N THR F 72 " --> pdb=" O ARG F 68 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR F 73 " --> pdb=" O ASP F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 95 removed outlier: 3.505A pdb=" N VAL F 87 " --> pdb=" O THR F 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 23 Processing helix chain 'G' and resid 27 through 38 removed outlier: 3.724A pdb=" N ARG G 36 " --> pdb=" O HIS G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 74 removed outlier: 4.770A pdb=" N ALA G 53 " --> pdb=" O PRO G 49 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA G 54 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL G 55 " --> pdb=" O TYR G 51 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU G 65 " --> pdb=" O ALA G 61 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN G 69 " --> pdb=" O GLU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 91 removed outlier: 3.843A pdb=" N LEU G 84 " --> pdb=" O ILE G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 99 Processing helix chain 'H' and resid 38 through 50 removed outlier: 3.566A pdb=" N TYR H 43 " --> pdb=" O SER H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 85 removed outlier: 3.592A pdb=" N GLY H 61 " --> pdb=" O SER H 57 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG H 80 " --> pdb=" O GLY H 76 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU H 81 " --> pdb=" O GLU H 77 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA H 82 " --> pdb=" O ALA H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 103 removed outlier: 3.951A pdb=" N ILE H 95 " --> pdb=" O THR H 91 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG H 100 " --> pdb=" O GLN H 96 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU H 103 " --> pdb=" O VAL H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 125 removed outlier: 4.225A pdb=" N HIS H 110 " --> pdb=" O GLU H 106 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER H 113 " --> pdb=" O LYS H 109 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY H 115 " --> pdb=" O ALA H 111 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N THR H 116 " --> pdb=" O VAL H 112 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA H 125 " --> pdb=" O LYS H 121 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 16 removed outlier: 3.500A pdb=" N ILE N 16 " --> pdb=" O THR N 12 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 19 No H-bonds generated for 'chain 'N' and resid 17 through 19' Processing helix chain 'N' and resid 20 through 29 removed outlier: 3.585A pdb=" N ILE N 24 " --> pdb=" O GLU N 20 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP N 29 " --> pdb=" O LEU N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 56 removed outlier: 3.515A pdb=" N VAL N 49 " --> pdb=" O LYS N 45 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N HIS N 54 " --> pdb=" O GLN N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 67 through 74 removed outlier: 3.636A pdb=" N ILE N 71 " --> pdb=" O ALA N 67 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE N 72 " --> pdb=" O LEU N 68 " (cutoff:3.500A) Processing helix chain 'N' and resid 171 through 179 removed outlier: 4.141A pdb=" N GLY N 176 " --> pdb=" O THR N 172 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N GLN N 177 " --> pdb=" O PRO N 173 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU N 179 " --> pdb=" O LEU N 175 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 6.821A pdb=" N ASN A 85 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 43 through 44 removed outlier: 6.937A pdb=" N ARG C 43 " --> pdb=" O ILE D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA4, first strand: chain 'E' and resid 85 through 86 removed outlier: 6.848A pdb=" N ASN E 85 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 120 through 121 Processing sheet with id=AA6, first strand: chain 'G' and resid 43 through 44 removed outlier: 6.857A pdb=" N ARG G 43 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 78 through 79 355 hydrogen bonds defined for protein. 1059 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 275 hydrogen bonds 518 hydrogen bond angles 0 basepair planarities 115 basepair parallelities 214 stacking parallelities Total time for adding SS restraints: 4.54 Time building geometry restraints manager: 7.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1893 1.33 - 1.44: 4634 1.44 - 1.56: 6193 1.56 - 1.68: 576 1.68 - 1.80: 14 Bond restraints: 13310 Sorted by residual: bond pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 1.422 1.484 -0.062 3.00e-02 1.11e+03 4.25e+00 bond pdb=" C3' DT J 69 " pdb=" O3' DT J 69 " ideal model delta sigma weight residual 1.422 1.475 -0.053 3.00e-02 1.11e+03 3.12e+00 bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.474 -0.052 3.00e-02 1.11e+03 3.06e+00 bond pdb=" C3' DA J -38 " pdb=" O3' DA J -38 " ideal model delta sigma weight residual 1.422 1.473 -0.051 3.00e-02 1.11e+03 2.84e+00 bond pdb=" C3' DG J 21 " pdb=" O3' DG J 21 " ideal model delta sigma weight residual 1.422 1.471 -0.049 3.00e-02 1.11e+03 2.64e+00 ... (remaining 13305 not shown) Histogram of bond angle deviations from ideal: 97.75 - 105.00: 1268 105.00 - 112.26: 7456 112.26 - 119.51: 4167 119.51 - 126.76: 5541 126.76 - 134.01: 812 Bond angle restraints: 19244 Sorted by residual: angle pdb=" N VAL C 50 " pdb=" CA VAL C 50 " pdb=" C VAL C 50 " ideal model delta sigma weight residual 113.71 104.91 8.80 9.50e-01 1.11e+00 8.58e+01 angle pdb=" N VAL G 50 " pdb=" CA VAL G 50 " pdb=" C VAL G 50 " ideal model delta sigma weight residual 113.71 104.95 8.76 9.50e-01 1.11e+00 8.51e+01 angle pdb=" C VAL A 82 " pdb=" N ASP A 83 " pdb=" CA ASP A 83 " ideal model delta sigma weight residual 121.54 131.32 -9.78 1.91e+00 2.74e-01 2.62e+01 angle pdb=" C VAL E 82 " pdb=" N ASP E 83 " pdb=" CA ASP E 83 " ideal model delta sigma weight residual 121.54 131.30 -9.76 1.91e+00 2.74e-01 2.61e+01 angle pdb=" C VAL C 50 " pdb=" CA VAL C 50 " pdb=" CB VAL C 50 " ideal model delta sigma weight residual 110.63 114.10 -3.47 9.40e-01 1.13e+00 1.36e+01 ... (remaining 19239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 5867 35.76 - 71.52: 1298 71.52 - 107.29: 29 107.29 - 143.05: 7 143.05 - 178.81: 2 Dihedral angle restraints: 7203 sinusoidal: 4671 harmonic: 2532 Sorted by residual: dihedral pdb=" CA GLN G 113 " pdb=" C GLN G 113 " pdb=" N ALA G 114 " pdb=" CA ALA G 114 " ideal model delta harmonic sigma weight residual -180.00 -155.68 -24.32 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA GLN C 113 " pdb=" C GLN C 113 " pdb=" N ALA C 114 " pdb=" CA ALA C 114 " ideal model delta harmonic sigma weight residual -180.00 -155.69 -24.31 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA ALA B 77 " pdb=" C ALA B 77 " pdb=" N LYS B 78 " pdb=" CA LYS B 78 " ideal model delta harmonic sigma weight residual -180.00 -156.83 -23.17 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 7200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1660 0.051 - 0.102: 481 0.102 - 0.152: 68 0.152 - 0.203: 5 0.203 - 0.254: 2 Chirality restraints: 2216 Sorted by residual: chirality pdb=" CB VAL C 115 " pdb=" CA VAL C 115 " pdb=" CG1 VAL C 115 " pdb=" CG2 VAL C 115 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB VAL G 115 " pdb=" CA VAL G 115 " pdb=" CG1 VAL G 115 " pdb=" CG2 VAL G 115 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" P DT J -16 " pdb=" OP1 DT J -16 " pdb=" OP2 DT J -16 " pdb=" O5' DT J -16 " both_signs ideal model delta sigma weight residual True 2.35 -2.54 -0.19 2.00e-01 2.50e+01 9.44e-01 ... (remaining 2213 not shown) Planarity restraints: 1437 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN H 85 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.59e+00 pdb=" C ASN H 85 " -0.033 2.00e-02 2.50e+03 pdb=" O ASN H 85 " 0.012 2.00e-02 2.50e+03 pdb=" N LYS H 86 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 80 " 0.030 5.00e-02 4.00e+02 4.53e-02 3.29e+00 pdb=" N PRO C 81 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 81 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 81 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 80 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO G 81 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO G 81 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO G 81 " 0.025 5.00e-02 4.00e+02 ... (remaining 1434 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3607 2.83 - 3.34: 11779 3.34 - 3.86: 25178 3.86 - 4.38: 27440 4.38 - 4.90: 38393 Nonbonded interactions: 106397 Sorted by model distance: nonbonded pdb=" O TYR G 40 " pdb=" OG SER H 79 " model vdw 2.308 2.440 nonbonded pdb=" O TYR C 40 " pdb=" OG SER D 79 " model vdw 2.313 2.440 nonbonded pdb=" O TYR E 110 " pdb=" OG1 THR E 113 " model vdw 2.317 2.440 nonbonded pdb=" O TYR A 110 " pdb=" OG1 THR A 113 " model vdw 2.317 2.440 nonbonded pdb=" OH TYR D 41 " pdb=" OP1 DG J 48 " model vdw 2.325 2.440 ... (remaining 106392 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' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 36.800 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 42.340 Find NCS groups from input model: 0.530 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 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 : 0.008 0.063 13310 Z= 0.470 Angle : 0.877 9.776 19244 Z= 0.505 Chirality : 0.047 0.254 2216 Planarity : 0.005 0.045 1437 Dihedral : 27.458 178.809 5559 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.03 (0.19), residues: 846 helix: -3.52 (0.12), residues: 526 sheet: -6.89 (0.34), residues: 9 loop : -2.51 (0.30), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP E 86 HIS 0.009 0.003 HIS E 104 PHE 0.021 0.002 PHE A 106 TYR 0.011 0.002 TYR D 38 ARG 0.005 0.001 ARG G 30 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 411 time to evaluate : 1.132 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 outliers start: 0 outliers final: 0 residues processed: 411 average time/residue: 0.3855 time to fit residues: 200.7676 Evaluate side-chains 300 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 1.094 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 57 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 95 GLN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN D 83 HIS ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 13310 Z= 0.277 Angle : 0.724 7.718 19244 Z= 0.424 Chirality : 0.040 0.190 2216 Planarity : 0.005 0.066 1437 Dihedral : 31.390 179.702 4112 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 6.04 % Allowed : 22.02 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.25), residues: 846 helix: -0.91 (0.19), residues: 567 sheet: -6.95 (0.31), residues: 9 loop : -2.78 (0.32), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 47 HIS 0.005 0.001 HIS C 83 PHE 0.021 0.001 PHE H 66 TYR 0.030 0.003 TYR H 41 ARG 0.008 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 340 time to evaluate : 0.987 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 outliers start: 37 outliers final: 19 residues processed: 351 average time/residue: 0.3270 time to fit residues: 150.0037 Evaluate side-chains 311 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 292 time to evaluate : 1.036 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1344 time to fit residues: 5.5024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 111 optimal weight: 40.0000 chunk 91 optimal weight: 8.9990 chunk 101 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 ASN ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13310 Z= 0.260 Angle : 0.676 6.654 19244 Z= 0.395 Chirality : 0.037 0.163 2216 Planarity : 0.004 0.042 1437 Dihedral : 31.112 179.748 4112 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 4.57 % Allowed : 24.96 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.27), residues: 846 helix: 0.14 (0.20), residues: 571 sheet: None (None), residues: 0 loop : -2.86 (0.32), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 47 HIS 0.004 0.001 HIS F 76 PHE 0.020 0.002 PHE D 71 TYR 0.035 0.003 TYR H 41 ARG 0.007 0.001 ARG F 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 307 time to evaluate : 1.024 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: 28 outliers final: 15 residues processed: 311 average time/residue: 0.3208 time to fit residues: 132.1200 Evaluate side-chains 306 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 291 time to evaluate : 0.945 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1677 time to fit residues: 5.0395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 103 optimal weight: 20.0000 chunk 109 optimal weight: 40.0000 chunk 97 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 90 optimal weight: 8.9990 overall best weight: 3.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13310 Z= 0.280 Angle : 0.678 6.446 19244 Z= 0.396 Chirality : 0.038 0.161 2216 Planarity : 0.004 0.038 1437 Dihedral : 31.043 179.985 4112 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 20.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 4.24 % Allowed : 28.71 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.28), residues: 846 helix: 0.54 (0.21), residues: 574 sheet: None (None), residues: 0 loop : -2.65 (0.33), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 47 HIS 0.005 0.001 HIS F 76 PHE 0.023 0.002 PHE D 71 TYR 0.047 0.004 TYR F 89 ARG 0.006 0.001 ARG A 131 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 305 time to evaluate : 1.051 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 outliers start: 26 outliers final: 18 residues processed: 310 average time/residue: 0.3187 time to fit residues: 131.8618 Evaluate side-chains 307 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 289 time to evaluate : 1.036 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1184 time to fit residues: 5.2598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 0.9990 chunk 1 optimal weight: 0.4980 chunk 81 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 93 optimal weight: 8.9990 chunk 75 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 36 optimal weight: 0.3980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 ASN ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 HIS ** H 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.5254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13310 Z= 0.206 Angle : 0.643 8.176 19244 Z= 0.374 Chirality : 0.036 0.141 2216 Planarity : 0.004 0.074 1437 Dihedral : 30.897 178.624 4112 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.12 % Allowed : 29.69 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.28), residues: 846 helix: 0.92 (0.21), residues: 576 sheet: None (None), residues: 0 loop : -2.54 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 47 HIS 0.003 0.001 HIS F 76 PHE 0.016 0.001 PHE A 67 TYR 0.025 0.003 TYR H 41 ARG 0.009 0.001 ARG B 93 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 321 time to evaluate : 1.615 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: 13 outliers final: 9 residues processed: 324 average time/residue: 0.3117 time to fit residues: 133.2614 Evaluate side-chains 301 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 292 time to evaluate : 0.751 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1643 time to fit residues: 3.0431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 109 optimal weight: 40.0000 chunk 90 optimal weight: 8.9990 chunk 50 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 HIS ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.5324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 13310 Z= 0.353 Angle : 0.725 8.624 19244 Z= 0.417 Chirality : 0.040 0.186 2216 Planarity : 0.005 0.068 1437 Dihedral : 30.891 179.192 4112 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 24.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 4.73 % Allowed : 30.51 % Favored : 64.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.29), residues: 846 helix: 0.83 (0.21), residues: 576 sheet: -6.88 (0.31), residues: 9 loop : -2.32 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.004 TRP A 47 HIS 0.006 0.001 HIS D 83 PHE 0.028 0.002 PHE A 67 TYR 0.051 0.004 TYR H 84 ARG 0.007 0.001 ARG D 100 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 292 time to evaluate : 1.022 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: 29 outliers final: 26 residues processed: 299 average time/residue: 0.3207 time to fit residues: 128.0598 Evaluate side-chains 311 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 285 time to evaluate : 1.009 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1222 time to fit residues: 6.8626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.9980 chunk 62 optimal weight: 0.0270 chunk 79 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.5600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13310 Z= 0.232 Angle : 0.685 9.981 19244 Z= 0.391 Chirality : 0.037 0.151 2216 Planarity : 0.004 0.036 1437 Dihedral : 30.806 179.047 4112 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.63 % Allowed : 32.30 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.29), residues: 846 helix: 0.97 (0.21), residues: 574 sheet: None (None), residues: 0 loop : -2.37 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 47 HIS 0.002 0.001 HIS D 83 PHE 0.018 0.001 PHE A 67 TYR 0.072 0.004 TYR H 84 ARG 0.007 0.001 ARG H 100 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 303 time to evaluate : 0.922 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: 10 outliers final: 7 residues processed: 305 average time/residue: 0.3123 time to fit residues: 126.9813 Evaluate side-chains 295 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 288 time to evaluate : 0.986 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1912 time to fit residues: 3.0355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 74 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 overall best weight: 3.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 ASN D 83 HIS ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN ** H 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 ASN H 96 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.5680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13310 Z= 0.282 Angle : 0.707 10.521 19244 Z= 0.402 Chirality : 0.038 0.171 2216 Planarity : 0.004 0.037 1437 Dihedral : 30.724 179.969 4112 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 21.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 2.77 % Allowed : 34.42 % Favored : 62.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.29), residues: 846 helix: 0.93 (0.22), residues: 574 sheet: None (None), residues: 0 loop : -2.38 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP A 47 HIS 0.007 0.001 HIS B 76 PHE 0.023 0.002 PHE A 67 TYR 0.059 0.003 TYR H 84 ARG 0.007 0.001 ARG H 100 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 285 time to evaluate : 0.971 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: 17 outliers final: 13 residues processed: 287 average time/residue: 0.3146 time to fit residues: 120.8852 Evaluate side-chains 294 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 281 time to evaluate : 1.125 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1202 time to fit residues: 4.0772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 79 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 95 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 107 optimal weight: 0.0270 chunk 65 optimal weight: 9.9990 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN ** H 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.5820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13310 Z= 0.263 Angle : 0.715 10.408 19244 Z= 0.404 Chirality : 0.038 0.232 2216 Planarity : 0.004 0.040 1437 Dihedral : 30.658 179.854 4112 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 21.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.98 % Allowed : 35.07 % Favored : 63.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.29), residues: 846 helix: 0.96 (0.21), residues: 570 sheet: None (None), residues: 0 loop : -2.34 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.108 0.006 TRP A 47 HIS 0.004 0.001 HIS B 76 PHE 0.021 0.002 PHE A 67 TYR 0.053 0.003 TYR H 84 ARG 0.006 0.001 ARG D 100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 279 time to evaluate : 0.956 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 outliers start: 6 outliers final: 4 residues processed: 280 average time/residue: 0.3177 time to fit residues: 118.1832 Evaluate side-chains 281 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 277 time to evaluate : 1.059 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1101 time to fit residues: 1.9803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 112 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 chunk 89 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 54 optimal weight: 0.0980 chunk 71 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 chunk 27 optimal weight: 0.0060 overall best weight: 4.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 HIS D 85 ASN ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN ** H 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.5871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 13310 Z= 0.348 Angle : 0.761 11.383 19244 Z= 0.430 Chirality : 0.040 0.212 2216 Planarity : 0.005 0.045 1437 Dihedral : 30.724 178.887 4112 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 24.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 1.31 % Allowed : 36.38 % Favored : 62.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.29), residues: 846 helix: 0.80 (0.22), residues: 573 sheet: -6.83 (0.32), residues: 9 loop : -2.19 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.121 0.007 TRP A 47 HIS 0.005 0.001 HIS B 76 PHE 0.030 0.002 PHE A 67 TYR 0.059 0.004 TYR H 84 ARG 0.007 0.001 ARG D 100 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 280 time to evaluate : 1.069 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 outliers start: 8 outliers final: 5 residues processed: 281 average time/residue: 0.3132 time to fit residues: 118.4000 Evaluate side-chains 277 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 272 time to evaluate : 0.973 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1195 time to fit residues: 2.1484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 78 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN ** H 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.059808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.047195 restraints weight = 63904.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.048535 restraints weight = 31958.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.049424 restraints weight = 20175.498| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.6014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13310 Z= 0.275 Angle : 0.743 11.661 19244 Z= 0.418 Chirality : 0.038 0.222 2216 Planarity : 0.004 0.045 1437 Dihedral : 30.698 179.556 4112 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 22.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.65 % Allowed : 37.03 % Favored : 62.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.29), residues: 846 helix: 0.90 (0.22), residues: 570 sheet: None (None), residues: 0 loop : -2.33 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.118 0.007 TRP A 47 HIS 0.004 0.001 HIS H 83 PHE 0.029 0.002 PHE A 67 TYR 0.059 0.003 TYR H 84 ARG 0.006 0.001 ARG A 131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4422.65 seconds wall clock time: 82 minutes 23.90 seconds (4943.90 seconds total)