Starting phenix.real_space_refine on Thu Feb 22 06:30:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bod_12239/02_2024/7bod_12239_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bod_12239/02_2024/7bod_12239.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bod_12239/02_2024/7bod_12239_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bod_12239/02_2024/7bod_12239_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bod_12239/02_2024/7bod_12239_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bod_12239/02_2024/7bod_12239.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bod_12239/02_2024/7bod_12239.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bod_12239/02_2024/7bod_12239_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bod_12239/02_2024/7bod_12239_updated.pdb" } resolution = 2.88 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= 0.003 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 1078 5.49 5 Mg 101 5.21 5 S 41 5.16 5 C 16650 2.51 5 N 6220 2.21 5 O 9299 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 33389 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 23172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1078, 23172 Classifications: {'RNA': 1078} Modifications used: {'rna2p': 1, 'rna2p_pur': 77, 'rna2p_pyr': 52, 'rna3p': 7, 'rna3p_pur': 544, 'rna3p_pyr': 397} Link IDs: {'rna2p': 130, 'rna3p': 947} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "F" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 862 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "L" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D2T:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "T" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "U" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 430 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "A" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 101 Unusual residues: {' MG': 101} Classifications: {'undetermined': 101} Link IDs: {None: 100} Time building chain proxies: 17.81, per 1000 atoms: 0.53 Number of scatterers: 33389 At special positions: 0 Unit cell: (179.55, 148.05, 177.45, 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 41 16.00 P 1078 15.00 Mg 101 11.99 O 9299 8.00 N 6220 7.00 C 16650 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 17.07 Conformation dependent library (CDL) restraints added in 2.1 seconds 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2390 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 12 sheets defined 36.9% alpha, 18.3% beta 347 base pairs and 655 stacking pairs defined. Time for finding SS restraints: 20.49 Creating SS restraints... Processing helix chain 'D' and resid 9 through 15 Processing helix chain 'D' and resid 28 through 30 No H-bonds generated for 'chain 'D' and resid 28 through 30' Processing helix chain 'D' and resid 50 through 65 removed outlier: 3.764A pdb=" N TYR D 65 " --> pdb=" O VAL D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 81 Processing helix chain 'D' and resid 86 through 96 removed outlier: 3.543A pdb=" N LEU D 91 " --> pdb=" O GLY D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 105 Processing helix chain 'D' and resid 113 through 119 removed outlier: 4.133A pdb=" N VAL D 118 " --> pdb=" O ALA D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 149 No H-bonds generated for 'chain 'D' and resid 147 through 149' Processing helix chain 'D' and resid 153 through 164 removed outlier: 3.779A pdb=" N GLU D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLN D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 205 removed outlier: 3.926A pdb=" N SER D 205 " --> pdb=" O VAL D 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 67 Processing helix chain 'E' and resid 109 through 118 Processing helix chain 'E' and resid 133 through 146 Processing helix chain 'E' and resid 150 through 157 Processing helix chain 'E' and resid 161 through 164 No H-bonds generated for 'chain 'E' and resid 161 through 164' Processing helix chain 'F' and resid 12 through 31 removed outlier: 4.748A pdb=" N GLU F 16 " --> pdb=" O ASP F 13 " (cutoff:3.500A) Proline residue: F 19 - end of helix removed outlier: 3.600A pdb=" N ALA F 28 " --> pdb=" O TYR F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 80 Processing helix chain 'F' and resid 101 through 105 Processing helix chain 'H' and resid 6 through 19 Processing helix chain 'H' and resid 31 through 42 Processing helix chain 'H' and resid 89 through 91 No H-bonds generated for 'chain 'H' and resid 89 through 91' Processing helix chain 'H' and resid 113 through 118 Processing helix chain 'K' and resid 60 through 77 removed outlier: 4.469A pdb=" N GLU K 76 " --> pdb=" O ASP K 72 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N TYR K 77 " --> pdb=" O ALA K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 101 Processing helix chain 'L' and resid 4 through 9 Processing helix chain 'L' and resid 22 through 24 No H-bonds generated for 'chain 'L' and resid 22 through 24' Processing helix chain 'L' and resid 114 through 117 No H-bonds generated for 'chain 'L' and resid 114 through 117' Processing helix chain 'O' and resid 5 through 15 Processing helix chain 'O' and resid 25 through 45 removed outlier: 3.734A pdb=" N GLN O 40 " --> pdb=" O ILE O 36 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU O 45 " --> pdb=" O GLY O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 73 removed outlier: 4.057A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 84 Processing helix chain 'P' and resid 54 through 63 removed outlier: 3.593A pdb=" N GLN P 63 " --> pdb=" O HIS P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 81 Processing helix chain 'Q' and resid 49 through 51 No H-bonds generated for 'chain 'Q' and resid 49 through 51' Processing helix chain 'R' and resid 12 through 15 No H-bonds generated for 'chain 'R' and resid 12 through 15' Processing helix chain 'R' and resid 26 through 32 removed outlier: 4.160A pdb=" N ASN R 31 " --> pdb=" O ALA R 27 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR R 32 " --> pdb=" O THR R 28 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 45 No H-bonds generated for 'chain 'R' and resid 42 through 45' Processing helix chain 'R' and resid 49 through 64 removed outlier: 3.677A pdb=" N GLN R 54 " --> pdb=" O LYS R 50 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 38 removed outlier: 3.632A pdb=" N VAL T 35 " --> pdb=" O PHE T 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 47 through 63 removed outlier: 3.877A pdb=" N ASN T 52 " --> pdb=" O GLN T 48 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU T 53 " --> pdb=" O LYS T 49 " (cutoff:3.500A) Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 69 through 84 Processing helix chain 'U' and resid 13 through 16 No H-bonds generated for 'chain 'U' and resid 13 through 16' Processing helix chain 'U' and resid 19 through 25 removed outlier: 4.114A pdb=" N GLU U 24 " --> pdb=" O LYS U 20 " (cutoff:3.500A) Processing helix chain 'U' and resid 28 through 36 removed outlier: 3.509A pdb=" N ARG U 33 " --> pdb=" O LEU U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 41 through 57 Processing sheet with id= A, first strand: chain 'D' and resid 123 through 125 removed outlier: 4.140A pdb=" N ASP D 141 " --> pdb=" O PHE D 182 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU D 179 " --> pdb=" O ASP D 174 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 46 through 53 removed outlier: 6.649A pdb=" N VAL E 38 " --> pdb=" O LEU E 15 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N LEU E 15 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N GLY E 40 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N GLU E 13 " --> pdb=" O GLY E 40 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 85 through 89 Processing sheet with id= D, first strand: chain 'F' and resid 87 through 92 removed outlier: 3.544A pdb=" N MET F 88 " --> pdb=" O VAL F 7 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG F 2 " --> pdb=" O ALA F 66 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY F 43 " --> pdb=" O TYR F 59 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'F' and resid 35 through 41 removed outlier: 6.484A pdb=" N ASN F 63 " --> pdb=" O HIS F 37 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU F 39 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU F 61 " --> pdb=" O LEU F 39 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 24 through 28 removed outlier: 3.642A pdb=" N ASP H 48 " --> pdb=" O THR H 62 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 74 through 77 removed outlier: 6.717A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N TYR H 128 " --> pdb=" O ILE H 101 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE H 101 " --> pdb=" O TYR H 128 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'K' and resid 41 through 46 removed outlier: 6.756A pdb=" N ILE K 34 " --> pdb=" O LEU K 42 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TRP K 44 " --> pdb=" O VAL K 32 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL K 32 " --> pdb=" O TRP K 44 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N THR K 46 " --> pdb=" O THR K 30 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR K 30 " --> pdb=" O THR K 46 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'L' and resid 95 through 97 removed outlier: 6.619A pdb=" N ARG L 54 " --> pdb=" O THR L 35 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N VAL L 37 " --> pdb=" O VAL L 52 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL L 52 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N THR L 39 " --> pdb=" O ARG L 50 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ARG L 50 " --> pdb=" O THR L 39 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'P' and resid 2 through 9 removed outlier: 6.611A pdb=" N VAL P 21 " --> pdb=" O ARG P 35 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ARG P 35 " --> pdb=" O VAL P 21 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'Q' and resid 8 through 11 removed outlier: 9.230A pdb=" N SER Q 72 " --> pdb=" O LYS Q 43 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N HIS Q 45 " --> pdb=" O SER Q 72 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N THR Q 74 " --> pdb=" O HIS Q 45 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N HIS Q 47 " --> pdb=" O THR Q 74 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER Q 14 " --> pdb=" O VAL Q 22 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ALA Q 24 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N VAL Q 12 " --> pdb=" O ALA Q 24 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N GLU Q 26 " --> pdb=" O GLY Q 10 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLY Q 10 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'Q' and resid 58 through 60 removed outlier: 6.492A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N VAL Q 78 " --> pdb=" O GLU Q 60 " (cutoff:3.500A) 407 hydrogen bonds defined for protein. 1149 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 857 hydrogen bonds 1340 hydrogen bond angles 0 basepair planarities 347 basepair parallelities 655 stacking parallelities Total time for adding SS restraints: 28.19 Time building geometry restraints manager: 18.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3238 1.31 - 1.44: 16089 1.44 - 1.56: 14658 1.56 - 1.69: 2154 1.69 - 1.82: 70 Bond restraints: 36209 Sorted by residual: bond pdb=" C2 4OC A1402 " pdb=" N3 4OC A1402 " ideal model delta sigma weight residual 1.507 1.348 0.159 2.00e-02 2.50e+03 6.34e+01 bond pdb=" N3 2MG A1516 " pdb=" C4 2MG A1516 " ideal model delta sigma weight residual 1.496 1.346 0.150 2.00e-02 2.50e+03 5.61e+01 bond pdb=" C2 5MC A1407 " pdb=" N3 5MC A1407 " ideal model delta sigma weight residual 1.493 1.347 0.146 2.00e-02 2.50e+03 5.35e+01 bond pdb=" N1 4OC A1402 " pdb=" C6 4OC A1402 " ideal model delta sigma weight residual 1.467 1.332 0.135 2.00e-02 2.50e+03 4.57e+01 bond pdb=" C2 2MG A1516 " pdb=" N2 2MG A1516 " ideal model delta sigma weight residual 1.475 1.346 0.129 2.00e-02 2.50e+03 4.14e+01 ... (remaining 36204 not shown) Histogram of bond angle deviations from ideal: 99.33 - 106.88: 6722 106.88 - 114.44: 22951 114.44 - 121.99: 16741 121.99 - 129.54: 7129 129.54 - 137.10: 708 Bond angle restraints: 54251 Sorted by residual: angle pdb=" C1' G7M A 527 " pdb=" N9 G7M A 527 " pdb=" C8 G7M A 527 " ideal model delta sigma weight residual 94.96 131.29 -36.33 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C1' G7M A 527 " pdb=" N9 G7M A 527 " pdb=" C4 G7M A 527 " ideal model delta sigma weight residual 142.80 120.77 22.03 3.00e+00 1.11e-01 5.39e+01 angle pdb=" CA GLY H 109 " pdb=" C GLY H 109 " pdb=" O GLY H 109 " ideal model delta sigma weight residual 122.45 118.23 4.22 7.20e-01 1.93e+00 3.44e+01 angle pdb=" C1' 2MG A1516 " pdb=" N9 2MG A1516 " pdb=" C8 2MG A1516 " ideal model delta sigma weight residual 110.07 126.87 -16.80 3.00e+00 1.11e-01 3.14e+01 angle pdb=" CA GLY D 39 " pdb=" C GLY D 39 " pdb=" O GLY D 39 " ideal model delta sigma weight residual 122.52 118.29 4.23 7.90e-01 1.60e+00 2.87e+01 ... (remaining 54246 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.87: 20138 33.87 - 67.75: 2762 67.75 - 101.62: 288 101.62 - 135.49: 9 135.49 - 169.37: 6 Dihedral angle restraints: 23203 sinusoidal: 19503 harmonic: 3700 Sorted by residual: dihedral pdb=" O4' U A 365 " pdb=" C1' U A 365 " pdb=" N1 U A 365 " pdb=" C2 U A 365 " ideal model delta sinusoidal sigma weight residual 200.00 56.00 144.00 1 1.50e+01 4.44e-03 7.72e+01 dihedral pdb=" O4' C A 754 " pdb=" C1' C A 754 " pdb=" N1 C A 754 " pdb=" C2 C A 754 " ideal model delta sinusoidal sigma weight residual 200.00 61.50 138.50 1 1.50e+01 4.44e-03 7.46e+01 dihedral pdb=" O4' C A 183 " pdb=" C1' C A 183 " pdb=" N1 C A 183 " pdb=" C2 C A 183 " ideal model delta sinusoidal sigma weight residual -128.00 41.37 -169.37 1 1.70e+01 3.46e-03 6.59e+01 ... (remaining 23200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 6294 0.067 - 0.134: 474 0.134 - 0.201: 118 0.201 - 0.268: 23 0.268 - 0.335: 2 Chirality restraints: 6911 Sorted by residual: chirality pdb=" CB D2T L 89 " pdb=" CA D2T L 89 " pdb=" SB D2T L 89 " pdb=" CG D2T L 89 " both_signs ideal model delta sigma weight residual False -3.02 -3.35 0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CA THR E 90 " pdb=" N THR E 90 " pdb=" C THR E 90 " pdb=" CB THR E 90 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA ILE P 4 " pdb=" N ILE P 4 " pdb=" C ILE P 4 " pdb=" CB ILE P 4 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 6908 not shown) Planarity restraints: 2866 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MC A1407 " 0.035 2.00e-02 2.50e+03 5.47e-01 6.72e+03 pdb=" C4' 5MC A1407 " 0.428 2.00e-02 2.50e+03 pdb=" O4' 5MC A1407 " 0.560 2.00e-02 2.50e+03 pdb=" C3' 5MC A1407 " -0.583 2.00e-02 2.50e+03 pdb=" O3' 5MC A1407 " -0.543 2.00e-02 2.50e+03 pdb=" C2' 5MC A1407 " -0.217 2.00e-02 2.50e+03 pdb=" O2' 5MC A1407 " 0.892 2.00e-02 2.50e+03 pdb=" C1' 5MC A1407 " 0.239 2.00e-02 2.50e+03 pdb=" N1 5MC A1407 " -0.810 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1516 " 0.019 2.00e-02 2.50e+03 5.44e-01 6.66e+03 pdb=" C4' 2MG A1516 " 0.430 2.00e-02 2.50e+03 pdb=" O4' 2MG A1516 " 0.578 2.00e-02 2.50e+03 pdb=" C3' 2MG A1516 " -0.580 2.00e-02 2.50e+03 pdb=" O3' 2MG A1516 " -0.525 2.00e-02 2.50e+03 pdb=" C2' 2MG A1516 " -0.221 2.00e-02 2.50e+03 pdb=" O2' 2MG A1516 " 0.871 2.00e-02 2.50e+03 pdb=" C1' 2MG A1516 " 0.245 2.00e-02 2.50e+03 pdb=" N9 2MG A1516 " -0.817 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 MA6 A1518 " 0.126 2.00e-02 2.50e+03 2.08e-01 4.31e+02 pdb=" N6 MA6 A1518 " -0.360 2.00e-02 2.50e+03 pdb=" C10 MA6 A1518 " 0.119 2.00e-02 2.50e+03 pdb=" C9 MA6 A1518 " 0.115 2.00e-02 2.50e+03 ... (remaining 2863 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 197 2.51 - 3.11: 22339 3.11 - 3.71: 63426 3.71 - 4.30: 97888 4.30 - 4.90: 127883 Nonbonded interactions: 311733 Sorted by model distance: nonbonded pdb=" OP1 C A 770 " pdb="MG MG A1689 " model vdw 1.913 2.170 nonbonded pdb=" OP1 A A 59 " pdb="MG MG A1623 " model vdw 1.965 2.170 nonbonded pdb=" O LYS O 73 " pdb=" OD1 ASP O 74 " model vdw 1.983 3.040 nonbonded pdb=" OP1 G A 558 " pdb="MG MG A1633 " model vdw 1.985 2.170 nonbonded pdb=" OP2 G A 289 " pdb="MG MG A1687 " model vdw 1.999 2.170 ... (remaining 311728 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5.230 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: 0.030 Extract box with map and model: 15.320 Check model and map are aligned: 0.490 Set scattering table: 0.290 Process input model: 114.790 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 147.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.159 36209 Z= 0.423 Angle : 0.739 36.326 54251 Z= 0.459 Chirality : 0.043 0.335 6911 Planarity : 0.016 0.547 2866 Dihedral : 23.185 169.366 20813 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.47 % Allowed : 3.78 % Favored : 95.75 % 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: -1.72 (0.21), residues: 1262 helix: -1.26 (0.21), residues: 488 sheet: -0.88 (0.33), residues: 224 loop : -0.94 (0.24), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 44 HIS 0.010 0.001 HIS R 74 PHE 0.014 0.002 PHE O 43 TYR 0.016 0.002 TYR Q 34 ARG 0.009 0.001 ARG T 10 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 450 time to evaluate : 1.857 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: D 178 MET cc_start: 0.7321 (mtt) cc_final: 0.7105 (mtt) REVERT: E 73 ASN cc_start: 0.7600 (m-40) cc_final: 0.7331 (m-40) REVERT: F 52 ASN cc_start: 0.7605 (t0) cc_final: 0.7385 (t160) REVERT: F 93 LYS cc_start: 0.7901 (ttmt) cc_final: 0.7687 (ttmm) outliers start: 5 outliers final: 3 residues processed: 454 average time/residue: 1.7848 time to fit residues: 937.7166 Evaluate side-chains 352 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 349 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain H residue 14 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 194 optimal weight: 3.9990 chunk 174 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 180 optimal weight: 0.5980 chunk 69 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 134 optimal weight: 7.9990 chunk 208 optimal weight: 1.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 GLN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 GLN D 126 ASN E 82 GLN E 83 HIS E 135 ASN E 146 ASN E 148 ASN F 55 HIS H 18 GLN K 81 ASN K 101 ASN L 6 GLN L 96 HIS ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 HIS O 40 GLN O 80 GLN P 29 ASN P 59 HIS T 61 GLN T 78 ASN T 84 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 36209 Z= 0.326 Angle : 0.623 12.645 54251 Z= 0.334 Chirality : 0.038 0.361 6911 Planarity : 0.006 0.124 2866 Dihedral : 23.494 170.758 18272 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 4.91 % Allowed : 19.47 % Favored : 75.61 % 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: -0.68 (0.22), residues: 1262 helix: -0.23 (0.22), residues: 497 sheet: -0.60 (0.33), residues: 243 loop : -0.37 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP P 60 HIS 0.005 0.001 HIS F 11 PHE 0.020 0.002 PHE F 8 TYR 0.013 0.002 TYR F 49 ARG 0.011 0.001 ARG Q 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 358 time to evaluate : 1.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 46 GLN cc_start: 0.7608 (tp-100) cc_final: 0.7220 (tp40) REVERT: F 78 PHE cc_start: 0.7577 (OUTLIER) cc_final: 0.7289 (m-80) REVERT: H 43 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7645 (mm-30) REVERT: U 18 ARG cc_start: 0.5552 (OUTLIER) cc_final: 0.3882 (tmt170) outliers start: 52 outliers final: 31 residues processed: 379 average time/residue: 1.6514 time to fit residues: 729.6546 Evaluate side-chains 364 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 331 time to evaluate : 1.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 78 PHE Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain L residue 5 ASN Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain T residue 4 ILE Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain U residue 18 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 116 optimal weight: 0.7980 chunk 64 optimal weight: 7.9990 chunk 173 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 209 optimal weight: 0.0470 chunk 226 optimal weight: 7.9990 chunk 186 optimal weight: 5.9990 chunk 207 optimal weight: 0.7980 chunk 71 optimal weight: 8.9990 chunk 167 optimal weight: 20.0000 overall best weight: 2.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 ASN E 146 ASN F 52 ASN H 18 GLN L 5 ASN O 28 GLN O 40 GLN R 19 GLN U 56 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 36209 Z= 0.272 Angle : 0.582 12.739 54251 Z= 0.314 Chirality : 0.035 0.340 6911 Planarity : 0.006 0.120 2866 Dihedral : 23.334 170.272 18270 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 5.86 % Allowed : 21.17 % Favored : 72.97 % 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: -0.32 (0.23), residues: 1262 helix: 0.19 (0.23), residues: 501 sheet: -0.57 (0.33), residues: 241 loop : -0.22 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 60 HIS 0.004 0.001 HIS L 96 PHE 0.042 0.002 PHE U 19 TYR 0.012 0.002 TYR R 64 ARG 0.010 0.001 ARG Q 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 358 time to evaluate : 1.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 178 MET cc_start: 0.7172 (mtt) cc_final: 0.6928 (mtt) REVERT: F 46 GLN cc_start: 0.7470 (tp-100) cc_final: 0.7122 (tp-100) REVERT: F 78 PHE cc_start: 0.7492 (OUTLIER) cc_final: 0.7190 (m-80) REVERT: T 60 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8239 (ttp80) outliers start: 62 outliers final: 34 residues processed: 382 average time/residue: 1.6938 time to fit residues: 754.1341 Evaluate side-chains 369 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 333 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 78 PHE Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain T residue 4 ILE Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 60 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 206 optimal weight: 2.9990 chunk 157 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 140 optimal weight: 4.9990 chunk 209 optimal weight: 4.9990 chunk 222 optimal weight: 0.8980 chunk 109 optimal weight: 9.9990 chunk 199 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 ASN E 61 GLN E 146 ASN F 52 ASN K 40 ASN K 119 ASN O 80 GLN U 56 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 36209 Z= 0.356 Angle : 0.619 12.657 54251 Z= 0.331 Chirality : 0.038 0.385 6911 Planarity : 0.006 0.121 2866 Dihedral : 23.310 169.574 18270 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 5.95 % Allowed : 23.25 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.23), residues: 1262 helix: 0.36 (0.23), residues: 501 sheet: -0.55 (0.32), residues: 246 loop : -0.20 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 60 HIS 0.004 0.001 HIS R 74 PHE 0.030 0.002 PHE U 19 TYR 0.012 0.002 TYR R 64 ARG 0.007 0.001 ARG Q 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 348 time to evaluate : 2.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 118 GLN cc_start: 0.7363 (OUTLIER) cc_final: 0.6631 (tp40) REVERT: P 31 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.8127 (ttp-170) REVERT: T 60 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8262 (ttp80) outliers start: 63 outliers final: 41 residues processed: 375 average time/residue: 1.7314 time to fit residues: 755.2310 Evaluate side-chains 379 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 335 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 5 ASN Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain P residue 31 ARG Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 39 LYS Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain T residue 4 ILE Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 60 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 185 optimal weight: 9.9990 chunk 126 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 165 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 chunk 189 optimal weight: 0.8980 chunk 153 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 113 optimal weight: 0.9980 chunk 199 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 overall best weight: 2.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 ASN F 46 GLN F 52 ASN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN O 80 GLN T 70 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 36209 Z= 0.276 Angle : 0.588 12.859 54251 Z= 0.316 Chirality : 0.035 0.340 6911 Planarity : 0.005 0.119 2866 Dihedral : 23.299 170.222 18269 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 5.58 % Allowed : 25.90 % Favored : 68.53 % 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: -0.01 (0.23), residues: 1262 helix: 0.50 (0.23), residues: 500 sheet: -0.38 (0.34), residues: 237 loop : -0.13 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 42 HIS 0.003 0.001 HIS F 11 PHE 0.023 0.002 PHE F 8 TYR 0.012 0.002 TYR R 64 ARG 0.011 0.001 ARG U 55 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 341 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 118 GLN cc_start: 0.7311 (OUTLIER) cc_final: 0.6555 (tp40) REVERT: O 45 GLU cc_start: 0.6048 (pt0) cc_final: 0.5846 (pt0) REVERT: P 31 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8085 (ttp-170) REVERT: Q 19 LYS cc_start: 0.8369 (mttt) cc_final: 0.7924 (mttt) REVERT: T 60 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8263 (ttp80) outliers start: 59 outliers final: 42 residues processed: 368 average time/residue: 1.6855 time to fit residues: 723.1628 Evaluate side-chains 382 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 337 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain H residue 27 MET Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 113 VAL Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 5 ASN Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain P residue 31 ARG Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 39 LYS Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain T residue 4 ILE Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 53 GLU Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 60 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 74 optimal weight: 8.9990 chunk 200 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 222 optimal weight: 4.9990 chunk 184 optimal weight: 0.6980 chunk 103 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 ASN E 146 ASN F 52 ASN ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN O 40 GLN O 80 GLN P 26 ASN T 70 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 36209 Z= 0.354 Angle : 0.618 12.827 54251 Z= 0.330 Chirality : 0.038 0.334 6911 Planarity : 0.006 0.121 2866 Dihedral : 23.272 170.780 18269 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 6.43 % Allowed : 25.71 % Favored : 67.86 % 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: 0.00 (0.23), residues: 1262 helix: 0.52 (0.23), residues: 503 sheet: -0.40 (0.34), residues: 238 loop : -0.12 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 42 HIS 0.004 0.001 HIS L 96 PHE 0.017 0.002 PHE R 13 TYR 0.011 0.002 TYR L 95 ARG 0.010 0.001 ARG Q 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 335 time to evaluate : 1.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 78 PHE cc_start: 0.7416 (OUTLIER) cc_final: 0.7154 (m-80) REVERT: H 118 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.6558 (tp40) REVERT: K 76 GLU cc_start: 0.6308 (pm20) cc_final: 0.6094 (pm20) REVERT: O 45 GLU cc_start: 0.6271 (pt0) cc_final: 0.6042 (pt0) REVERT: O 48 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7591 (mtpp) REVERT: P 31 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8111 (ttp-170) REVERT: T 60 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8263 (ttp80) outliers start: 68 outliers final: 45 residues processed: 368 average time/residue: 1.6865 time to fit residues: 724.0250 Evaluate side-chains 374 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 324 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 78 PHE Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain H residue 27 MET Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain P residue 31 ARG Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 39 LYS Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain T residue 4 ILE Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 53 GLU Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 60 ARG Chi-restraints excluded: chain U residue 22 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 214 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 126 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 125 optimal weight: 0.0170 chunk 187 optimal weight: 0.0040 chunk 124 optimal weight: 0.9990 chunk 221 optimal weight: 8.9990 chunk 138 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 chunk 102 optimal weight: 20.0000 overall best weight: 1.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 ASN E 146 ASN ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN K 38 GLN L 5 ASN O 20 ASN T 70 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 36209 Z= 0.176 Angle : 0.580 13.024 54251 Z= 0.314 Chirality : 0.033 0.340 6911 Planarity : 0.007 0.150 2866 Dihedral : 23.337 170.749 18269 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 5.67 % Allowed : 27.22 % Favored : 67.11 % 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 (0.24), residues: 1262 helix: 0.63 (0.23), residues: 503 sheet: -0.31 (0.34), residues: 236 loop : -0.13 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 42 HIS 0.003 0.001 HIS O 46 PHE 0.016 0.002 PHE U 19 TYR 0.010 0.001 TYR R 64 ARG 0.011 0.001 ARG Q 11 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 341 time to evaluate : 1.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 78 PHE cc_start: 0.7281 (OUTLIER) cc_final: 0.6961 (m-80) REVERT: H 118 GLN cc_start: 0.7239 (OUTLIER) cc_final: 0.6462 (tp40) REVERT: O 45 GLU cc_start: 0.6280 (pt0) cc_final: 0.6074 (pt0) REVERT: T 60 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8249 (ttp80) outliers start: 60 outliers final: 36 residues processed: 367 average time/residue: 1.6604 time to fit residues: 711.2498 Evaluate side-chains 371 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 332 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 78 PHE Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain H residue 27 MET Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain K residue 34 ILE Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 113 VAL Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 39 LYS Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 53 GLU Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 60 ARG Chi-restraints excluded: chain U residue 22 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 137 optimal weight: 0.8980 chunk 88 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 140 optimal weight: 0.9990 chunk 151 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 174 optimal weight: 9.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 19 ASN E 146 ASN F 52 ASN L 5 ASN O 20 ASN O 80 GLN T 70 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 36209 Z= 0.324 Angle : 0.609 12.847 54251 Z= 0.326 Chirality : 0.037 0.333 6911 Planarity : 0.006 0.120 2866 Dihedral : 23.241 171.789 18269 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 5.39 % Allowed : 27.98 % Favored : 66.64 % 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: 0.13 (0.24), residues: 1262 helix: 0.74 (0.23), residues: 498 sheet: -0.35 (0.34), residues: 238 loop : -0.17 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 42 HIS 0.003 0.001 HIS F 11 PHE 0.020 0.002 PHE F 8 TYR 0.010 0.002 TYR L 95 ARG 0.014 0.001 ARG Q 11 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 338 time to evaluate : 1.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 78 PHE cc_start: 0.7410 (OUTLIER) cc_final: 0.7162 (m-80) REVERT: H 118 GLN cc_start: 0.7280 (OUTLIER) cc_final: 0.6539 (tp40) REVERT: O 45 GLU cc_start: 0.6365 (pt0) cc_final: 0.6164 (pt0) REVERT: O 48 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7586 (mtpp) REVERT: T 60 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8283 (ttp80) outliers start: 57 outliers final: 41 residues processed: 365 average time/residue: 1.6749 time to fit residues: 713.1824 Evaluate side-chains 372 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 327 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 78 PHE Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain H residue 27 MET Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 39 LYS Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 53 GLU Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 60 ARG Chi-restraints excluded: chain U residue 22 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 201 optimal weight: 0.0970 chunk 212 optimal weight: 6.9990 chunk 193 optimal weight: 0.9990 chunk 206 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 162 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 186 optimal weight: 4.9990 chunk 195 optimal weight: 0.8980 chunk 205 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 19 ASN E 146 ASN F 52 ASN K 38 GLN L 5 ASN O 20 ASN O 80 GLN T 70 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 36209 Z= 0.143 Angle : 0.579 13.139 54251 Z= 0.312 Chirality : 0.033 0.325 6911 Planarity : 0.006 0.116 2866 Dihedral : 23.312 171.925 18269 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.88 % Allowed : 30.43 % Favored : 65.69 % 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: 0.20 (0.24), residues: 1262 helix: 0.80 (0.23), residues: 498 sheet: -0.17 (0.34), residues: 231 loop : -0.21 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 42 HIS 0.003 0.001 HIS F 11 PHE 0.015 0.002 PHE U 37 TYR 0.009 0.001 TYR L 95 ARG 0.015 0.001 ARG Q 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 340 time to evaluate : 2.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 78 PHE cc_start: 0.7265 (OUTLIER) cc_final: 0.7020 (m-80) REVERT: H 43 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7549 (mm-30) REVERT: H 118 GLN cc_start: 0.7220 (OUTLIER) cc_final: 0.6443 (tp40) REVERT: O 45 GLU cc_start: 0.6311 (pt0) cc_final: 0.6048 (pt0) outliers start: 41 outliers final: 30 residues processed: 356 average time/residue: 1.7043 time to fit residues: 708.4469 Evaluate side-chains 366 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 334 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 78 PHE Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain H residue 27 MET Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 113 VAL Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 39 LYS Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 53 GLU Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain U residue 22 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 135 optimal weight: 1.9990 chunk 218 optimal weight: 0.7980 chunk 133 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 151 optimal weight: 9.9990 chunk 229 optimal weight: 6.9990 chunk 210 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 140 optimal weight: 0.9990 chunk 111 optimal weight: 0.0470 overall best weight: 0.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 19 ASN E 146 ASN F 52 ASN ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN L 5 ASN O 20 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 36209 Z= 0.146 Angle : 0.561 13.091 54251 Z= 0.302 Chirality : 0.032 0.324 6911 Planarity : 0.005 0.116 2866 Dihedral : 23.190 174.395 18269 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.78 % Allowed : 30.15 % 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: 0.39 (0.24), residues: 1262 helix: 1.01 (0.23), residues: 491 sheet: -0.21 (0.34), residues: 234 loop : -0.07 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 42 HIS 0.004 0.001 HIS U 56 PHE 0.013 0.002 PHE K 52 TYR 0.009 0.001 TYR U 38 ARG 0.015 0.001 ARG Q 11 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 343 time to evaluate : 2.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 162 GLU cc_start: 0.6192 (tp30) cc_final: 0.5934 (mm-30) REVERT: F 78 PHE cc_start: 0.7221 (OUTLIER) cc_final: 0.6974 (m-80) REVERT: O 45 GLU cc_start: 0.6303 (pt0) cc_final: 0.6078 (pt0) REVERT: O 48 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7549 (mtpp) REVERT: U 18 ARG cc_start: 0.6111 (tmt170) cc_final: 0.5718 (ptm160) outliers start: 40 outliers final: 25 residues processed: 360 average time/residue: 1.7015 time to fit residues: 715.0014 Evaluate side-chains 361 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 334 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 78 PHE Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain H residue 27 MET Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 113 VAL Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 39 LYS Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 53 GLU Chi-restraints excluded: chain T residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 144 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 168 optimal weight: 0.0570 chunk 26 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 182 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 187 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 GLN E 19 ASN E 61 GLN E 146 ASN F 52 ASN ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN L 20 ASN O 20 ASN O 40 GLN O 80 GLN T 70 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.066539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.048317 restraints weight = 90491.320| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 1.10 r_work: 0.2580 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2486 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9031 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 36209 Z= 0.264 Angle : 0.585 12.881 54251 Z= 0.313 Chirality : 0.034 0.308 6911 Planarity : 0.006 0.119 2866 Dihedral : 23.141 174.688 18269 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.21 % Allowed : 31.10 % Favored : 65.69 % 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: 0.34 (0.24), residues: 1262 helix: 0.95 (0.23), residues: 493 sheet: -0.23 (0.35), residues: 232 loop : -0.09 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 42 HIS 0.003 0.001 HIS L 96 PHE 0.012 0.002 PHE R 13 TYR 0.010 0.001 TYR L 95 ARG 0.016 0.001 ARG Q 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11411.77 seconds wall clock time: 204 minutes 20.96 seconds (12260.96 seconds total)