Starting phenix.real_space_refine on Fri Feb 16 14:04:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e0p_8949/02_2024/6e0p_8949.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e0p_8949/02_2024/6e0p_8949.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e0p_8949/02_2024/6e0p_8949.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e0p_8949/02_2024/6e0p_8949.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e0p_8949/02_2024/6e0p_8949.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e0p_8949/02_2024/6e0p_8949.pdb" } resolution = 2.6 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= 0.004 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 290 5.49 5 S 26 5.16 5 C 8921 2.51 5 N 2815 2.21 5 O 3515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 42": "NH1" <-> "NH2" Residue "A ARG 43": "NH1" <-> "NH2" Residue "A ARG 44": "NH1" <-> "NH2" Residue "A ARG 80": "NH1" <-> "NH2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 31": "NH1" <-> "NH2" Residue "E ARG 42": "NH1" <-> "NH2" Residue "E ARG 43": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 80": "NH1" <-> "NH2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 31": "NH1" <-> "NH2" Residue "M ARG 219": "NH1" <-> "NH2" Residue "N ARG 176": "NH1" <-> "NH2" Residue "N ARG 219": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15567 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} 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: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} 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: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} 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: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2957 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2988 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "M" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1789 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 1 Chain: "N" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1787 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 1 Time building chain proxies: 8.14, per 1000 atoms: 0.52 Number of scatterers: 15567 At special positions: 0 Unit cell: (132.66, 127.635, 116.58, 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 26 16.00 P 290 15.00 O 3515 8.00 N 2815 7.00 C 8921 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS M 44 " - pdb=" SG CYS M 118 " distance=2.03 Simple disulfide: pdb=" SG CYS M 181 " - pdb=" SG CYS M 246 " distance=2.03 Simple disulfide: pdb=" SG CYS N 44 " - pdb=" SG CYS N 118 " distance=2.02 Simple disulfide: pdb=" SG CYS N 181 " - pdb=" SG CYS N 246 " distance=2.03 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: 6.63 Conformation dependent library (CDL) restraints added in 1.7 seconds 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2254 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 24 sheets defined 46.1% alpha, 20.3% beta 137 base pairs and 268 stacking pairs defined. Time for finding SS restraints: 7.26 Creating SS restraints... Processing helix chain 'A' and resid 46 through 55 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.723A pdb=" N LYS A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 116 removed outlier: 3.598A pdb=" N LEU A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 134 removed outlier: 3.646A pdb=" N VAL A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.806A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.276A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.566A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.702A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.724A pdb=" N LYS E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 116 removed outlier: 3.599A pdb=" N LEU E 112 " --> pdb=" O ASP E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 134 removed outlier: 3.647A pdb=" N VAL E 126 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY E 134 " --> pdb=" O ARG E 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.807A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.308A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.535A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.526A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 123 removed outlier: 3.735A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 50 through 52 No H-bonds generated for 'chain 'M' and resid 50 through 52' Processing helix chain 'N' and resid 50 through 52 No H-bonds generated for 'chain 'N' and resid 50 through 52' Processing helix chain 'N' and resid 84 through 87 removed outlier: 3.825A pdb=" N LYS N 87 " --> pdb=" O GLU N 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 84 through 87' Processing helix chain 'N' and resid 109 through 113 removed outlier: 3.660A pdb=" N SER N 113 " --> pdb=" O SER N 110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 6.668A pdb=" N ASN A 85 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 121 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.521A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.179A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 85 through 86 removed outlier: 6.719A pdb=" N ASN E 85 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 120 through 121 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.905A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'M' and resid 25 through 28 removed outlier: 3.708A pdb=" N VAL M 101 " --> pdb=" O CYS M 44 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 32 through 34 removed outlier: 6.606A pdb=" N ILE M 56 " --> pdb=" O TYR M 72 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TYR M 72 " --> pdb=" O ILE M 56 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N TRP M 58 " --> pdb=" O ILE M 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 32 through 34 removed outlier: 3.725A pdb=" N TYR M 131 " --> pdb=" O ARG M 120 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N SER M 122 " --> pdb=" O LEU M 129 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU M 129 " --> pdb=" O SER M 122 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 163 through 164 removed outlier: 4.158A pdb=" N PHE M 229 " --> pdb=" O CYS M 181 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP M 228 " --> pdb=" O SER M 225 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 168 through 171 removed outlier: 3.944A pdb=" N GLU M 263 " --> pdb=" O MET M 169 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA M 171 " --> pdb=" O GLU M 263 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU M 191 " --> pdb=" O TYR M 207 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N TYR M 207 " --> pdb=" O LEU M 191 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TRP M 193 " --> pdb=" O LEU M 205 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 168 through 171 removed outlier: 3.944A pdb=" N GLU M 263 " --> pdb=" O MET M 169 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA M 171 " --> pdb=" O GLU M 263 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR M 255 " --> pdb=" O GLN M 248 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 25 through 28 Processing sheet with id=AB9, first strand: chain 'N' and resid 32 through 34 removed outlier: 6.447A pdb=" N GLU N 32 " --> pdb=" O THR N 139 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE N 56 " --> pdb=" O TYR N 72 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TYR N 72 " --> pdb=" O ILE N 56 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TRP N 58 " --> pdb=" O ILE N 70 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 32 through 34 removed outlier: 6.447A pdb=" N GLU N 32 " --> pdb=" O THR N 139 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR N 131 " --> pdb=" O ARG N 120 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N SER N 122 " --> pdb=" O LEU N 129 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU N 129 " --> pdb=" O SER N 122 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 39 through 40 removed outlier: 3.553A pdb=" N VAL N 40 " --> pdb=" O LEU N 105 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 162 through 163 Processing sheet with id=AC4, first strand: chain 'N' and resid 168 through 171 Processing sheet with id=AC5, first strand: chain 'N' and resid 177 through 180 removed outlier: 3.611A pdb=" N ASP N 228 " --> pdb=" O SER N 225 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 211 through 212 removed outlier: 6.543A pdb=" N TRP N 193 " --> pdb=" O LEU N 205 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N TYR N 207 " --> pdb=" O LEU N 191 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU N 191 " --> pdb=" O TYR N 207 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR N 255 " --> pdb=" O GLN N 248 " (cutoff:3.500A) 533 hydrogen bonds defined for protein. 1476 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 328 hydrogen bonds 656 hydrogen bond angles 0 basepair planarities 137 basepair parallelities 268 stacking parallelities Total time for adding SS restraints: 6.15 Time building geometry restraints manager: 7.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3679 1.34 - 1.46: 5588 1.46 - 1.58: 6571 1.58 - 1.71: 578 1.71 - 1.83: 42 Bond restraints: 16458 Sorted by residual: bond pdb=" CG1 ILE A 132 " pdb=" CD1 ILE A 132 " ideal model delta sigma weight residual 1.513 1.428 0.085 3.90e-02 6.57e+02 4.76e+00 bond pdb=" CG1 ILE E 132 " pdb=" CD1 ILE E 132 " ideal model delta sigma weight residual 1.513 1.428 0.085 3.90e-02 6.57e+02 4.76e+00 bond pdb=" CB THR H 96 " pdb=" CG2 THR H 96 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.32e+00 bond pdb=" C3' DG J 93 " pdb=" O3' DG J 93 " ideal model delta sigma weight residual 1.422 1.483 -0.061 3.00e-02 1.11e+03 4.19e+00 bond pdb=" CG LEU A 112 " pdb=" CD2 LEU A 112 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 4.05e+00 ... (remaining 16453 not shown) Histogram of bond angle deviations from ideal: 98.10 - 105.29: 1378 105.29 - 112.47: 8875 112.47 - 119.65: 5450 119.65 - 126.83: 6868 126.83 - 134.01: 909 Bond angle restraints: 23480 Sorted by residual: angle pdb=" C TYR M 208 " pdb=" N ALA M 209 " pdb=" CA ALA M 209 " ideal model delta sigma weight residual 121.54 129.66 -8.12 1.91e+00 2.74e-01 1.81e+01 angle pdb=" C TYR N 208 " pdb=" N ALA N 209 " pdb=" CA ALA N 209 " ideal model delta sigma weight residual 121.54 129.56 -8.02 1.91e+00 2.74e-01 1.76e+01 angle pdb=" C GLU N 251 " pdb=" N SER N 252 " pdb=" CA SER N 252 " ideal model delta sigma weight residual 120.06 124.78 -4.72 1.19e+00 7.06e-01 1.57e+01 angle pdb=" C3' DG J 93 " pdb=" O3' DG J 93 " pdb=" P DA J 94 " ideal model delta sigma weight residual 120.20 125.29 -5.09 1.50e+00 4.44e-01 1.15e+01 angle pdb=" N GLY D 104 " pdb=" CA GLY D 104 " pdb=" C GLY D 104 " ideal model delta sigma weight residual 110.86 116.55 -5.69 1.84e+00 2.95e-01 9.56e+00 ... (remaining 23475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 7721 35.86 - 71.72: 1463 71.72 - 107.57: 15 107.57 - 143.43: 1 143.43 - 179.29: 1 Dihedral angle restraints: 9201 sinusoidal: 5679 harmonic: 3522 Sorted by residual: dihedral pdb=" CA ASP N 186 " pdb=" C ASP N 186 " pdb=" N ILE N 187 " pdb=" CA ILE N 187 " ideal model delta harmonic sigma weight residual 180.00 155.58 24.42 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA LYS H 46 " pdb=" C LYS H 46 " pdb=" N GLN H 47 " pdb=" CA GLN H 47 " ideal model delta harmonic sigma weight residual 180.00 155.71 24.29 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA GLU M 251 " pdb=" C GLU M 251 " pdb=" N SER M 252 " pdb=" CA SER M 252 " ideal model delta harmonic sigma weight residual 180.00 -159.93 -20.07 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 9198 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1662 0.040 - 0.079: 692 0.079 - 0.119: 213 0.119 - 0.159: 58 0.159 - 0.198: 16 Chirality restraints: 2641 Sorted by residual: chirality pdb=" CB THR G 101 " pdb=" CA THR G 101 " pdb=" OG1 THR G 101 " pdb=" CG2 THR G 101 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.83e-01 chirality pdb=" CG LEU A 94 " pdb=" CB LEU A 94 " pdb=" CD1 LEU A 94 " pdb=" CD2 LEU A 94 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.19 2.00e-01 2.50e+01 9.16e-01 chirality pdb=" CA LYS H 46 " pdb=" N LYS H 46 " pdb=" C LYS H 46 " pdb=" CB LYS H 46 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.91e-01 ... (remaining 2638 not shown) Planarity restraints: 1956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR M 74 " -0.024 2.00e-02 2.50e+03 1.85e-02 6.82e+00 pdb=" CG TYR M 74 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR M 74 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR M 74 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR M 74 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR M 74 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR M 74 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR M 74 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR N 74 " 0.024 2.00e-02 2.50e+03 1.83e-02 6.73e+00 pdb=" CG TYR N 74 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR N 74 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR N 74 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR N 74 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR N 74 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR N 74 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR N 74 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 25 " -0.019 2.00e-02 2.50e+03 1.95e-02 6.65e+00 pdb=" CG PHE G 25 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE G 25 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE G 25 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE G 25 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE G 25 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE G 25 " -0.003 2.00e-02 2.50e+03 ... (remaining 1953 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2999 2.78 - 3.31: 12515 3.31 - 3.84: 30175 3.84 - 4.37: 36172 4.37 - 4.90: 52624 Nonbonded interactions: 134485 Sorted by model distance: nonbonded pdb=" OG SER M 165 " pdb=" OG1 THR M 180 " model vdw 2.253 2.440 nonbonded pdb=" OG SER D 32 " pdb=" OP1 DT J 103 " model vdw 2.272 2.440 nonbonded pdb=" OG1 THR E 79 " pdb=" O VAL E 82 " model vdw 2.291 2.440 nonbonded pdb=" OG1 THR A 79 " pdb=" O VAL A 82 " model vdw 2.291 2.440 nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.292 2.440 ... (remaining 134480 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' and resid 10 through 116) } ncs_group { reference = (chain 'D' and resid 31 through 124) selection = chain 'H' } ncs_group { reference = (chain 'M' and (resid 23 through 141 or resid 157 through 265)) selection = (chain 'N' and (resid 23 through 141 or resid 157 through 265)) } 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: 1.060 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: 0.020 Extract box with map and model: 4.620 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 48.190 Find NCS groups from input model: 0.660 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:12.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 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 0.085 16458 Z= 0.409 Angle : 0.852 12.286 23480 Z= 0.489 Chirality : 0.049 0.198 2641 Planarity : 0.007 0.057 1956 Dihedral : 25.474 179.291 6935 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % 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: -2.18 (0.20), residues: 1196 helix: -1.22 (0.17), residues: 514 sheet: -0.66 (0.35), residues: 237 loop : -1.99 (0.24), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP M 132 HIS 0.016 0.003 HIS B 75 PHE 0.045 0.004 PHE G 25 TYR 0.045 0.003 TYR M 74 ARG 0.020 0.002 ARG E 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 1.489 Fit side-chains revert: symmetry clash REVERT: G 91 GLU cc_start: 0.7582 (tm-30) cc_final: 0.7109 (tm-30) REVERT: N 112 ASP cc_start: 0.7859 (m-30) cc_final: 0.7571 (m-30) REVERT: N 185 GLN cc_start: 0.8598 (mt0) cc_final: 0.8340 (mt0) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 1.9197 time to fit residues: 554.2735 Evaluate side-chains 191 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 58 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN D 63 ASN D 84 ASN D 95 GLN E 127 GLN H 84 ASN N 134 GLN N 164 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16458 Z= 0.205 Angle : 0.621 9.943 23480 Z= 0.360 Chirality : 0.036 0.168 2641 Planarity : 0.005 0.047 1956 Dihedral : 29.534 176.792 4618 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.34 % Allowed : 11.59 % Favored : 86.08 % 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: -0.33 (0.22), residues: 1196 helix: 0.84 (0.21), residues: 522 sheet: -0.06 (0.35), residues: 222 loop : -1.53 (0.25), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 132 HIS 0.003 0.001 HIS B 75 PHE 0.012 0.002 PHE C 25 TYR 0.019 0.001 TYR M 74 ARG 0.006 0.001 ARG N 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 208 time to evaluate : 1.439 Fit side-chains REVERT: C 91 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7391 (tm-30) REVERT: M 219 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7048 (ptm-80) REVERT: N 173 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8241 (tt) REVERT: N 219 ARG cc_start: 0.8534 (ttp-110) cc_final: 0.8323 (mtp180) outliers start: 24 outliers final: 8 residues processed: 217 average time/residue: 1.8972 time to fit residues: 439.2758 Evaluate side-chains 196 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 185 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain M residue 137 SER Chi-restraints excluded: chain M residue 219 ARG Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 65 GLN Chi-restraints excluded: chain N residue 173 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 20.0000 chunk 40 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 141 optimal weight: 7.9990 chunk 116 optimal weight: 0.9990 chunk 129 optimal weight: 6.9990 chunk 44 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN H 49 HIS H 63 ASN N 61 GLN N 134 GLN N 185 GLN N 196 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16458 Z= 0.244 Angle : 0.602 6.820 23480 Z= 0.351 Chirality : 0.037 0.150 2641 Planarity : 0.005 0.044 1956 Dihedral : 29.425 174.599 4618 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.02 % Allowed : 12.37 % Favored : 84.62 % 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: 0.63 (0.24), residues: 1196 helix: 1.84 (0.22), residues: 521 sheet: 0.03 (0.36), residues: 222 loop : -1.06 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 132 HIS 0.004 0.001 HIS B 75 PHE 0.018 0.002 PHE C 25 TYR 0.017 0.002 TYR M 74 ARG 0.005 0.001 ARG E 118 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 213 time to evaluate : 1.424 Fit side-chains REVERT: A 124 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8810 (ptpt) REVERT: B 91 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8195 (ttpt) REVERT: C 99 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.8011 (mtp85) REVERT: E 108 ASP cc_start: 0.8227 (m-30) cc_final: 0.7926 (m-30) REVERT: G 35 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7513 (mtp180) REVERT: M 219 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7273 (ptm-80) REVERT: N 173 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8174 (tt) REVERT: N 219 ARG cc_start: 0.8583 (ttp-110) cc_final: 0.8215 (mtm110) outliers start: 31 outliers final: 11 residues processed: 224 average time/residue: 1.9506 time to fit residues: 466.9691 Evaluate side-chains 205 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 188 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain M residue 25 GLN Chi-restraints excluded: chain M residue 160 ILE Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 219 ARG Chi-restraints excluded: chain M residue 240 ASP Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 173 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 131 optimal weight: 8.9990 chunk 139 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 ASN E 127 GLN N 134 GLN N 185 GLN N 195 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 16458 Z= 0.365 Angle : 0.654 7.248 23480 Z= 0.374 Chirality : 0.040 0.146 2641 Planarity : 0.006 0.046 1956 Dihedral : 29.633 172.641 4618 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.99 % Allowed : 13.15 % Favored : 82.86 % 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: 0.74 (0.24), residues: 1196 helix: 1.80 (0.22), residues: 529 sheet: 0.09 (0.35), residues: 237 loop : -0.90 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 132 HIS 0.005 0.001 HIS D 109 PHE 0.021 0.002 PHE C 25 TYR 0.015 0.002 TYR C 57 ARG 0.007 0.001 ARG M 124 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 204 time to evaluate : 1.417 Fit side-chains REVERT: B 91 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8186 (ttpt) REVERT: C 99 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.8041 (mtp85) REVERT: E 108 ASP cc_start: 0.8290 (m-30) cc_final: 0.8016 (m-30) REVERT: H 99 ARG cc_start: 0.8297 (mtm-85) cc_final: 0.8096 (mtt180) REVERT: N 173 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8301 (tt) REVERT: N 219 ARG cc_start: 0.8621 (ttp-110) cc_final: 0.8253 (mtm110) outliers start: 41 outliers final: 16 residues processed: 220 average time/residue: 1.9475 time to fit residues: 457.7162 Evaluate side-chains 201 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 182 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain M residue 25 GLN Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 137 SER Chi-restraints excluded: chain M residue 158 MET Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 240 ASP Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 173 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 118 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 127 GLN M 164 GLN N 25 GLN N 134 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16458 Z= 0.208 Angle : 0.611 8.409 23480 Z= 0.355 Chirality : 0.036 0.151 2641 Planarity : 0.005 0.066 1956 Dihedral : 29.564 173.632 4618 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.31 % Allowed : 14.31 % Favored : 82.38 % 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: 0.99 (0.24), residues: 1196 helix: 2.11 (0.22), residues: 529 sheet: 0.17 (0.35), residues: 230 loop : -0.88 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 132 HIS 0.004 0.001 HIS B 75 PHE 0.009 0.001 PHE C 25 TYR 0.010 0.001 TYR N 74 ARG 0.004 0.000 ARG M 124 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 207 time to evaluate : 1.259 Fit side-chains REVERT: B 91 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8173 (ttpt) REVERT: C 99 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.8033 (mtp85) REVERT: E 108 ASP cc_start: 0.8264 (m-30) cc_final: 0.7970 (m-30) REVERT: N 111 GLU cc_start: 0.7459 (pm20) cc_final: 0.6962 (mp0) REVERT: N 169 MET cc_start: 0.7539 (ptp) cc_final: 0.6961 (ptp) REVERT: N 173 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8305 (tt) REVERT: N 219 ARG cc_start: 0.8592 (ttp-110) cc_final: 0.8310 (mtp180) outliers start: 34 outliers final: 20 residues processed: 219 average time/residue: 1.9308 time to fit residues: 451.6381 Evaluate side-chains 223 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 200 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain M residue 25 GLN Chi-restraints excluded: chain M residue 137 SER Chi-restraints excluded: chain M residue 158 MET Chi-restraints excluded: chain M residue 160 ILE Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 240 ASP Chi-restraints excluded: chain N residue 25 GLN Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 65 GLN Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 173 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 139 optimal weight: 0.0570 chunk 115 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 73 optimal weight: 8.9990 chunk 134 optimal weight: 0.2980 overall best weight: 1.6704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 127 GLN M 164 GLN N 134 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16458 Z= 0.250 Angle : 0.603 7.551 23480 Z= 0.349 Chirality : 0.037 0.140 2641 Planarity : 0.005 0.056 1956 Dihedral : 29.379 173.458 4618 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.21 % Allowed : 15.48 % Favored : 81.30 % 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: 1.12 (0.24), residues: 1196 helix: 2.21 (0.22), residues: 529 sheet: 0.13 (0.35), residues: 235 loop : -0.76 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 132 HIS 0.004 0.001 HIS B 75 PHE 0.012 0.001 PHE C 25 TYR 0.011 0.001 TYR C 57 ARG 0.011 0.001 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 194 time to evaluate : 1.269 Fit side-chains REVERT: B 91 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8201 (ttpt) REVERT: E 108 ASP cc_start: 0.8274 (m-30) cc_final: 0.8019 (m-30) REVERT: N 219 ARG cc_start: 0.8600 (ttp-110) cc_final: 0.8308 (mtp180) outliers start: 33 outliers final: 15 residues processed: 207 average time/residue: 1.9061 time to fit residues: 421.1021 Evaluate side-chains 206 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 190 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain M residue 25 GLN Chi-restraints excluded: chain M residue 137 SER Chi-restraints excluded: chain M residue 158 MET Chi-restraints excluded: chain M residue 160 ILE Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 240 ASP Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 65 GLN Chi-restraints excluded: chain N residue 68 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 chunk 86 optimal weight: 20.0000 chunk 84 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS D 63 ASN E 127 GLN H 95 GLN N 134 GLN N 195 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 16458 Z= 0.498 Angle : 0.713 6.882 23480 Z= 0.404 Chirality : 0.045 0.183 2641 Planarity : 0.006 0.052 1956 Dihedral : 29.996 169.767 4618 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.60 % Allowed : 15.29 % Favored : 81.11 % 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: 0.66 (0.24), residues: 1196 helix: 1.61 (0.21), residues: 542 sheet: 0.14 (0.35), residues: 234 loop : -0.89 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP N 199 HIS 0.005 0.002 HIS H 109 PHE 0.018 0.002 PHE G 25 TYR 0.019 0.002 TYR G 57 ARG 0.013 0.001 ARG M 124 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 187 time to evaluate : 1.404 Fit side-chains REVERT: B 91 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8234 (ttpt) REVERT: C 41 GLU cc_start: 0.7993 (tt0) cc_final: 0.7759 (tm-30) REVERT: C 99 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8055 (mtp85) REVERT: E 108 ASP cc_start: 0.8298 (m-30) cc_final: 0.8020 (m-30) REVERT: G 74 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8191 (mtpp) REVERT: N 219 ARG cc_start: 0.8637 (ttp-110) cc_final: 0.8363 (mtp-110) outliers start: 37 outliers final: 17 residues processed: 203 average time/residue: 1.9487 time to fit residues: 422.2514 Evaluate side-chains 209 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 189 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain M residue 25 GLN Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 137 SER Chi-restraints excluded: chain M residue 160 ILE Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 240 ASP Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 65 GLN Chi-restraints excluded: chain N residue 130 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 0.0970 chunk 88 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 68 optimal weight: 0.0870 chunk 12 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 overall best weight: 0.6362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 127 GLN M 61 GLN M 196 GLN N 25 GLN N 134 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16458 Z= 0.168 Angle : 0.579 7.836 23480 Z= 0.337 Chirality : 0.034 0.131 2641 Planarity : 0.004 0.052 1956 Dihedral : 29.173 174.741 4618 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.56 % Allowed : 17.23 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.25), residues: 1196 helix: 2.40 (0.22), residues: 535 sheet: 0.29 (0.36), residues: 226 loop : -0.67 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 132 HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE H 70 TYR 0.010 0.001 TYR N 72 ARG 0.014 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 195 time to evaluate : 1.588 Fit side-chains REVERT: B 91 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8192 (ttpt) REVERT: E 108 ASP cc_start: 0.8193 (m-30) cc_final: 0.7937 (m-30) REVERT: N 34 VAL cc_start: 0.8329 (m) cc_final: 0.8080 (t) REVERT: N 219 ARG cc_start: 0.8586 (ttp-110) cc_final: 0.8313 (mtp-110) outliers start: 16 outliers final: 7 residues processed: 199 average time/residue: 1.9120 time to fit residues: 406.3489 Evaluate side-chains 205 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 197 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain M residue 25 GLN Chi-restraints excluded: chain M residue 240 ASP Chi-restraints excluded: chain N residue 177 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 7.9990 chunk 121 optimal weight: 0.1980 chunk 129 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 116 optimal weight: 0.6980 chunk 122 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 ASN E 127 GLN H 63 ASN N 134 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16458 Z= 0.257 Angle : 0.622 13.320 23480 Z= 0.353 Chirality : 0.037 0.157 2641 Planarity : 0.005 0.053 1956 Dihedral : 29.356 172.301 4618 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.66 % Allowed : 17.62 % Favored : 80.72 % 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: 1.30 (0.25), residues: 1196 helix: 2.31 (0.22), residues: 535 sheet: 0.23 (0.35), residues: 233 loop : -0.62 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 132 HIS 0.003 0.001 HIS M 249 PHE 0.010 0.001 PHE A 67 TYR 0.012 0.002 TYR F 51 ARG 0.014 0.001 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 196 time to evaluate : 1.399 Fit side-chains REVERT: B 91 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8191 (ttpt) REVERT: E 108 ASP cc_start: 0.8268 (m-30) cc_final: 0.7986 (m-30) REVERT: N 111 GLU cc_start: 0.7655 (pm20) cc_final: 0.7363 (pm20) REVERT: N 219 ARG cc_start: 0.8597 (ttp-110) cc_final: 0.8312 (mtp-110) outliers start: 17 outliers final: 10 residues processed: 200 average time/residue: 2.0225 time to fit residues: 431.2087 Evaluate side-chains 206 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 195 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain M residue 25 GLN Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 240 ASP Chi-restraints excluded: chain N residue 65 GLN Chi-restraints excluded: chain N residue 177 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 143 optimal weight: 0.1980 chunk 132 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 127 GLN N 134 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16458 Z= 0.321 Angle : 0.650 10.842 23480 Z= 0.366 Chirality : 0.039 0.164 2641 Planarity : 0.005 0.055 1956 Dihedral : 29.521 170.411 4618 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.46 % Allowed : 17.72 % Favored : 80.82 % 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: 1.13 (0.24), residues: 1196 helix: 2.14 (0.22), residues: 535 sheet: 0.21 (0.35), residues: 232 loop : -0.72 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 132 HIS 0.004 0.001 HIS N 249 PHE 0.012 0.002 PHE G 25 TYR 0.013 0.002 TYR G 57 ARG 0.013 0.001 ARG A 80 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 197 time to evaluate : 1.547 Fit side-chains revert: symmetry clash REVERT: B 91 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8214 (ttpt) REVERT: C 41 GLU cc_start: 0.7963 (tt0) cc_final: 0.7713 (tm-30) REVERT: E 108 ASP cc_start: 0.8289 (m-30) cc_final: 0.8007 (m-30) REVERT: H 76 GLU cc_start: 0.8280 (tp30) cc_final: 0.7904 (tp30) REVERT: N 111 GLU cc_start: 0.7625 (pm20) cc_final: 0.7395 (pm20) REVERT: N 219 ARG cc_start: 0.8605 (ttp-110) cc_final: 0.8324 (mtp-110) outliers start: 15 outliers final: 10 residues processed: 201 average time/residue: 2.0759 time to fit residues: 443.7316 Evaluate side-chains 206 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 195 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain M residue 25 GLN Chi-restraints excluded: chain M residue 160 ILE Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 240 ASP Chi-restraints excluded: chain N residue 65 GLN Chi-restraints excluded: chain N residue 177 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN E 127 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 134 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.154878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.097090 restraints weight = 18868.120| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.46 r_work: 0.2900 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16458 Z= 0.220 Angle : 0.629 9.706 23480 Z= 0.357 Chirality : 0.036 0.149 2641 Planarity : 0.005 0.054 1956 Dihedral : 29.514 170.595 4618 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.27 % Allowed : 18.11 % Favored : 80.62 % 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: 1.22 (0.24), residues: 1196 helix: 2.25 (0.22), residues: 535 sheet: 0.19 (0.35), residues: 232 loop : -0.69 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 132 HIS 0.004 0.001 HIS F 75 PHE 0.010 0.001 PHE A 67 TYR 0.012 0.001 TYR N 76 ARG 0.012 0.001 ARG A 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7033.37 seconds wall clock time: 124 minutes 44.28 seconds (7484.28 seconds total)