Starting phenix.real_space_refine on Tue Jun 25 07:25:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tuy_26135/06_2024/7tuy_26135_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tuy_26135/06_2024/7tuy_26135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tuy_26135/06_2024/7tuy_26135.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tuy_26135/06_2024/7tuy_26135.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tuy_26135/06_2024/7tuy_26135_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tuy_26135/06_2024/7tuy_26135_updated.pdb" } resolution = 2.98 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= 0.006 sd= 0.055 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 S 36 5.16 5 Cl 3 4.86 5 C 4575 2.51 5 N 1201 2.21 5 O 1342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 162": "OE1" <-> "OE2" Residue "K ARG 27": "NH1" <-> "NH2" Residue "K ARG 53": "NH1" <-> "NH2" Residue "L TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 145": "OE1" <-> "OE2" Residue "L TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 187": "OD1" <-> "OD2" Residue "L TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 60": "NH1" <-> "NH2" Residue "R ARG 129": "NH1" <-> "NH2" Residue "R ARG 144": "NH1" <-> "NH2" Residue "R TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 1007": "OD1" <-> "OD2" Residue "R ASP 1010": "OD1" <-> "OD2" Residue "R TYR 1106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 1113": "NH1" <-> "NH2" Residue "R ARG 1115": "NH1" <-> "NH2" Residue "R PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 7157 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1682 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 921 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1624 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 201} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "R" Number of atoms: 2930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2930 Unusual residues: {'KKF': 1} Classifications: {'peptide': 371, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 11, 'TRANS': 359, None: 1} Not linked: pdbres="MET R 310 " pdbres="KKF R1301 " Chain breaks: 8 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Time building chain proxies: 4.64, per 1000 atoms: 0.65 Number of scatterers: 7157 At special positions: 0 Unit cell: (64.74, 100.43, 141.93, 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) Cl 3 17.00 S 36 16.00 O 1342 8.00 N 1201 7.00 C 4575 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 154 " - pdb=" SG CYS H 210 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.03 Simple disulfide: pdb=" SG CYS R 104 " - pdb=" SG CYS R 181 " 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: 2.64 Conformation dependent library (CDL) restraints added in 1.2 seconds 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1742 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 22 helices and 12 sheets defined 33.1% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'H' and resid 91 through 93 No H-bonds generated for 'chain 'H' and resid 91 through 93' Processing helix chain 'H' and resid 108 through 111 No H-bonds generated for 'chain 'H' and resid 108 through 111' Processing helix chain 'H' and resid 202 through 205 Processing helix chain 'H' and resid 215 through 217 No H-bonds generated for 'chain 'H' and resid 215 through 217' Processing helix chain 'L' and resid 124 through 129 removed outlier: 4.263A pdb=" N SER L 129 " --> pdb=" O SER L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 188 No H-bonds generated for 'chain 'L' and resid 185 through 188' Processing helix chain 'R' and resid 27 through 59 removed outlier: 3.901A pdb=" N ILE R 32 " --> pdb=" O SER R 28 " (cutoff:3.500A) Proline residue: R 35 - end of helix Processing helix chain 'R' and resid 67 through 82 Processing helix chain 'R' and resid 102 through 132 removed outlier: 4.031A pdb=" N ALA R 117 " --> pdb=" O ILE R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 142 Processing helix chain 'R' and resid 145 through 164 removed outlier: 3.861A pdb=" N LEU R 164 " --> pdb=" O PHE R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 196 through 204 Processing helix chain 'R' and resid 206 through 1024 removed outlier: 3.836A pdb=" N ARG R1002 " --> pdb=" O LEU R 223 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU R1005 " --> pdb=" O ALA R1001 " (cutoff:3.500A) Processing helix chain 'R' and resid 1031 through 1045 removed outlier: 3.620A pdb=" N LYS R1037 " --> pdb=" O ASP R1033 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP R1044 " --> pdb=" O ALA R1040 " (cutoff:3.500A) Processing helix chain 'R' and resid 1063 through 1086 removed outlier: 3.547A pdb=" N GLY R1069 " --> pdb=" O ASP R1065 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE R1070 " --> pdb=" O PHE R1066 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU R1083 " --> pdb=" O ASP R1079 " (cutoff:3.500A) Processing helix chain 'R' and resid 1091 through 1094 No H-bonds generated for 'chain 'R' and resid 1091 through 1094' Processing helix chain 'R' and resid 1097 through 1106 removed outlier: 3.537A pdb=" N LYS R1100 " --> pdb=" O GLU R1097 " (cutoff:3.500A) Processing helix chain 'R' and resid 1108 through 1116 removed outlier: 4.081A pdb=" N GLU R1112 " --> pdb=" O GLN R1108 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ARG R1113 " --> pdb=" O LYS R1109 " (cutoff:3.500A) Processing helix chain 'R' and resid 228 through 246 Processing helix chain 'R' and resid 248 through 259 Processing helix chain 'R' and resid 277 through 301 removed outlier: 4.963A pdb=" N CYS R 291 " --> pdb=" O MET R 287 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N CYS R 292 " --> pdb=" O ASN R 288 " (cutoff:3.500A) Proline residue: R 295 - end of helix removed outlier: 3.527A pdb=" N TYR R 298 " --> pdb=" O ASP R 294 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE R 300 " --> pdb=" O PHE R 296 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 309 Processing sheet with id= A, first strand: chain 'H' and resid 6 through 10 removed outlier: 3.610A pdb=" N THR H 81 " --> pdb=" O ASP H 76 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'H' and resid 121 through 123 removed outlier: 3.646A pdb=" N ALA H 95 " --> pdb=" O VAL H 123 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS H 38 " --> pdb=" O ALA H 100 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA H 52 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 134 through 138 removed outlier: 3.798A pdb=" N LYS H 157 " --> pdb=" O SER H 134 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY H 153 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL H 198 " --> pdb=" O ALA H 150 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 165 through 168 removed outlier: 3.908A pdb=" N THR H 165 " --> pdb=" O ASN H 213 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN H 213 " --> pdb=" O THR H 165 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS H 223 " --> pdb=" O CYS H 210 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'K' and resid 3 through 7 removed outlier: 3.843A pdb=" N GLN K 3 " --> pdb=" O SER K 25 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER K 21 " --> pdb=" O SER K 7 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'K' and resid 96 through 98 removed outlier: 3.601A pdb=" N ALA K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ARG K 38 " --> pdb=" O PHE K 47 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'K' and resid 69 through 73 removed outlier: 3.510A pdb=" N TYR K 80 " --> pdb=" O SER K 71 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'L' and resid 5 through 7 Processing sheet with id= I, first strand: chain 'L' and resid 11 through 14 removed outlier: 5.974A pdb=" N LYS L 105 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ALA L 14 " --> pdb=" O LYS L 105 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N GLU L 107 " --> pdb=" O ALA L 14 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'L' and resid 89 through 91 removed outlier: 3.514A pdb=" N ILE L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'L' and resid 118 through 120 removed outlier: 3.556A pdb=" N VAL L 135 " --> pdb=" O PHE L 120 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'L' and resid 147 through 152 305 hydrogen bonds defined for protein. 861 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.00 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2242 1.34 - 1.46: 1464 1.46 - 1.58: 3557 1.58 - 1.69: 1 1.69 - 1.81: 51 Bond restraints: 7315 Sorted by residual: bond pdb=" C17 KKF R1301 " pdb=" N07 KKF R1301 " ideal model delta sigma weight residual 1.352 1.425 -0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C22 KKF R1301 " pdb=" C26 KKF R1301 " ideal model delta sigma weight residual 1.460 1.524 -0.064 2.00e-02 2.50e+03 1.04e+01 bond pdb=" C13 KKF R1301 " pdb=" N07 KKF R1301 " ideal model delta sigma weight residual 1.459 1.514 -0.055 2.00e-02 2.50e+03 7.61e+00 bond pdb=" C15 KKF R1301 " pdb=" O05 KKF R1301 " ideal model delta sigma weight residual 1.207 1.257 -0.050 2.00e-02 2.50e+03 6.17e+00 bond pdb=" C16 KKF R1301 " pdb=" N08 KKF R1301 " ideal model delta sigma weight residual 1.438 1.487 -0.049 2.00e-02 2.50e+03 5.92e+00 ... (remaining 7310 not shown) Histogram of bond angle deviations from ideal: 98.43 - 105.54: 144 105.54 - 112.65: 3832 112.65 - 119.77: 2361 119.77 - 126.88: 3502 126.88 - 133.99: 100 Bond angle restraints: 9939 Sorted by residual: angle pdb=" N VAL R 206 " pdb=" CA VAL R 206 " pdb=" C VAL R 206 " ideal model delta sigma weight residual 110.42 117.64 -7.22 9.60e-01 1.09e+00 5.65e+01 angle pdb=" C GLU R 183 " pdb=" N TYR R 184 " pdb=" CA TYR R 184 " ideal model delta sigma weight residual 120.44 126.13 -5.69 1.30e+00 5.92e-01 1.91e+01 angle pdb=" N TYR R 205 " pdb=" CA TYR R 205 " pdb=" C TYR R 205 " ideal model delta sigma weight residual 112.72 118.18 -5.46 1.28e+00 6.10e-01 1.82e+01 angle pdb=" CA LEU R 207 " pdb=" C LEU R 207 " pdb=" N PRO R 208 " ideal model delta sigma weight residual 120.93 116.62 4.31 1.06e+00 8.90e-01 1.65e+01 angle pdb=" C17 KKF R1301 " pdb=" C19 KKF R1301 " pdb=" C22 KKF R1301 " ideal model delta sigma weight residual 120.00 132.06 -12.06 3.00e+00 1.11e-01 1.62e+01 ... (remaining 9934 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 4009 17.80 - 35.59: 296 35.59 - 53.39: 45 53.39 - 71.19: 4 71.19 - 88.99: 6 Dihedral angle restraints: 4360 sinusoidal: 1657 harmonic: 2703 Sorted by residual: dihedral pdb=" CB CYS K 22 " pdb=" SG CYS K 22 " pdb=" SG CYS K 96 " pdb=" CB CYS K 96 " ideal model delta sinusoidal sigma weight residual 93.00 28.93 64.07 1 1.00e+01 1.00e-02 5.40e+01 dihedral pdb=" CB CYS R 104 " pdb=" SG CYS R 104 " pdb=" SG CYS R 181 " pdb=" CB CYS R 181 " ideal model delta sinusoidal sigma weight residual 93.00 138.60 -45.60 1 1.00e+01 1.00e-02 2.88e+01 dihedral pdb=" CA GLU K 44 " pdb=" C GLU K 44 " pdb=" N ARG K 45 " pdb=" CA ARG K 45 " ideal model delta harmonic sigma weight residual 180.00 154.97 25.03 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 4357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 724 0.041 - 0.082: 286 0.082 - 0.122: 102 0.122 - 0.163: 15 0.163 - 0.204: 8 Chirality restraints: 1135 Sorted by residual: chirality pdb=" CA TYR R 205 " pdb=" N TYR R 205 " pdb=" C TYR R 205 " pdb=" CB TYR R 205 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ILE R 210 " pdb=" N ILE R 210 " pdb=" C ILE R 210 " pdb=" CB ILE R 210 " both_signs ideal model delta sigma weight residual False 2.43 2.23 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA TYR L 142 " pdb=" N TYR L 142 " pdb=" C TYR L 142 " pdb=" CB TYR L 142 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.94e-01 ... (remaining 1132 not shown) Planarity restraints: 1250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 108 " -0.039 5.00e-02 4.00e+02 5.78e-02 5.35e+00 pdb=" N PRO H 109 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO H 109 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO H 109 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP R 294 " -0.036 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO R 295 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO R 295 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO R 295 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 164 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO R 165 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO R 165 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO R 165 " -0.029 5.00e-02 4.00e+02 ... (remaining 1247 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 697 2.74 - 3.28: 7206 3.28 - 3.82: 11665 3.82 - 4.36: 14002 4.36 - 4.90: 23827 Nonbonded interactions: 57397 Sorted by model distance: nonbonded pdb=" OH TYR R 38 " pdb=" OD1 ASN R 288 " model vdw 2.202 2.440 nonbonded pdb=" OE1 GLU L 107 " pdb=" OH TYR L 175 " model vdw 2.276 2.440 nonbonded pdb=" OH TYR R 205 " pdb=" OG1 THR R 248 " model vdw 2.295 2.440 nonbonded pdb=" NH2 ARG H 70 " pdb=" OD2 ASP H 93 " model vdw 2.305 2.520 nonbonded pdb=" OE2 GLU K 6 " pdb=" N GLY K 114 " model vdw 2.307 2.520 ... (remaining 57392 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: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.700 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.160 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 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:12.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 7315 Z= 0.331 Angle : 0.868 12.057 9939 Z= 0.452 Chirality : 0.051 0.204 1135 Planarity : 0.006 0.058 1250 Dihedral : 12.817 88.986 2600 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.26 % Allowed : 3.24 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -3.71 (0.24), residues: 904 helix: -1.93 (0.24), residues: 316 sheet: -2.09 (0.31), residues: 238 loop : -3.08 (0.28), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 50 HIS 0.008 0.001 HIS R 251 PHE 0.013 0.002 PHE H 114 TYR 0.018 0.001 TYR H 53 ARG 0.002 0.000 ARG R1039 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 147 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 76 ASP cc_start: 0.7819 (t0) cc_final: 0.7489 (t0) REVERT: H 92 GLU cc_start: 0.8639 (pm20) cc_final: 0.8316 (pm20) REVERT: H 185 GLN cc_start: 0.8579 (tt0) cc_final: 0.8193 (mt0) REVERT: H 209 ILE cc_start: 0.8768 (pt) cc_final: 0.8443 (pp) REVERT: H 226 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8478 (mt-10) REVERT: K 30 SER cc_start: 0.8593 (p) cc_final: 0.8287 (m) REVERT: K 34 MET cc_start: 0.7706 (mmt) cc_final: 0.7419 (mmt) REVERT: K 46 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7350 (mp0) REVERT: K 98 ILE cc_start: 0.8458 (tp) cc_final: 0.8052 (tp) REVERT: K 101 ASP cc_start: 0.8694 (t0) cc_final: 0.8341 (t0) REVERT: L 124 ASP cc_start: 0.9072 (p0) cc_final: 0.8817 (m-30) REVERT: L 128 LYS cc_start: 0.9215 (mptt) cc_final: 0.9007 (mmtm) REVERT: L 167 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8083 (tp30) REVERT: L 192 LYS cc_start: 0.8498 (pttp) cc_final: 0.8170 (mmtt) REVERT: R 37 HIS cc_start: 0.7186 (t70) cc_final: 0.6812 (t-170) REVERT: R 156 TRP cc_start: 0.8127 (t-100) cc_final: 0.7871 (m100) REVERT: R 202 PHE cc_start: 0.7816 (t80) cc_final: 0.7364 (m-80) REVERT: R 1091 GLU cc_start: 0.8037 (mp0) cc_final: 0.7706 (mp0) REVERT: R 288 ASN cc_start: 0.7678 (m110) cc_final: 0.7220 (m110) outliers start: 2 outliers final: 0 residues processed: 147 average time/residue: 1.1145 time to fit residues: 173.8233 Evaluate side-chains 105 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.5980 chunk 69 optimal weight: 0.0020 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 0.0000 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 13 GLN K 39 GLN L 126 GLN ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R1104 ASN R1108 GLN R 234 ASN R 251 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7315 Z= 0.167 Angle : 0.643 12.528 9939 Z= 0.321 Chirality : 0.043 0.188 1135 Planarity : 0.005 0.045 1250 Dihedral : 5.513 53.950 1030 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.68 % Allowed : 12.95 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -2.58 (0.26), residues: 904 helix: -0.65 (0.27), residues: 306 sheet: -1.91 (0.31), residues: 248 loop : -2.38 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 117 HIS 0.003 0.001 HIS R 37 PHE 0.008 0.001 PHE R 289 TYR 0.022 0.001 TYR R 298 ARG 0.007 0.000 ARG K 31 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 76 ASP cc_start: 0.7822 (t0) cc_final: 0.7324 (t0) REVERT: H 79 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8466 (mttm) REVERT: H 92 GLU cc_start: 0.8598 (pm20) cc_final: 0.8290 (pm20) REVERT: H 119 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8496 (pt0) REVERT: H 185 GLN cc_start: 0.8713 (tt0) cc_final: 0.8351 (mt0) REVERT: H 209 ILE cc_start: 0.8860 (pt) cc_final: 0.8602 (pp) REVERT: H 226 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8519 (mt-10) REVERT: K 31 ARG cc_start: 0.8210 (ptm160) cc_final: 0.7809 (ttm170) REVERT: K 46 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7309 (mp0) REVERT: K 101 ASP cc_start: 0.8633 (t0) cc_final: 0.8278 (t0) REVERT: L 192 LYS cc_start: 0.8513 (pttp) cc_final: 0.8124 (mmtt) REVERT: R 34 MET cc_start: 0.3734 (ttt) cc_final: 0.3269 (ttt) REVERT: R 202 PHE cc_start: 0.7879 (t80) cc_final: 0.7356 (m-10) REVERT: R 1091 GLU cc_start: 0.8037 (mp0) cc_final: 0.7674 (mp0) REVERT: R 288 ASN cc_start: 0.7639 (m110) cc_final: 0.7005 (m110) REVERT: R 289 PHE cc_start: 0.8592 (t80) cc_final: 0.8392 (t80) outliers start: 13 outliers final: 5 residues processed: 124 average time/residue: 1.1674 time to fit residues: 153.0937 Evaluate side-chains 110 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 103 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 119 GLN Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain R residue 1005 LEU Chi-restraints excluded: chain R residue 284 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 37 HIS ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 234 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 7315 Z= 0.460 Angle : 0.758 9.263 9939 Z= 0.384 Chirality : 0.048 0.166 1135 Planarity : 0.005 0.043 1250 Dihedral : 5.960 58.528 1030 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 3.50 % Allowed : 17.23 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -2.56 (0.26), residues: 904 helix: -0.73 (0.27), residues: 313 sheet: -1.91 (0.30), residues: 271 loop : -2.25 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 168 HIS 0.004 0.001 HIS L 191 PHE 0.011 0.002 PHE R 296 TYR 0.021 0.002 TYR L 142 ARG 0.005 0.001 ARG L 213 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 100 time to evaluate : 0.818 Fit side-chains REVERT: H 76 ASP cc_start: 0.7835 (t0) cc_final: 0.7231 (t0) REVERT: H 79 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8315 (mtpt) REVERT: H 92 GLU cc_start: 0.8639 (pm20) cc_final: 0.8325 (pm20) REVERT: H 185 GLN cc_start: 0.8658 (tt0) cc_final: 0.8332 (mt0) REVERT: H 209 ILE cc_start: 0.8873 (pt) cc_final: 0.8607 (pp) REVERT: H 226 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8451 (mt-10) REVERT: K 30 SER cc_start: 0.8544 (p) cc_final: 0.8262 (m) REVERT: K 46 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7396 (mp0) REVERT: K 74 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7707 (m-30) REVERT: K 87 LYS cc_start: 0.8202 (mtmm) cc_final: 0.7912 (mtmm) REVERT: K 101 ASP cc_start: 0.8744 (t0) cc_final: 0.8284 (t0) REVERT: L 192 LYS cc_start: 0.8538 (pttp) cc_final: 0.8044 (mmtt) REVERT: R 34 MET cc_start: 0.4187 (ttt) cc_final: 0.3697 (ttt) REVERT: R 156 TRP cc_start: 0.8276 (t-100) cc_final: 0.8032 (m100) REVERT: R 202 PHE cc_start: 0.7979 (t80) cc_final: 0.7474 (m-10) REVERT: R 1091 GLU cc_start: 0.8165 (mp0) cc_final: 0.7814 (mp0) REVERT: R 288 ASN cc_start: 0.7710 (m110) cc_final: 0.7166 (m110) outliers start: 27 outliers final: 12 residues processed: 121 average time/residue: 0.9832 time to fit residues: 126.9171 Evaluate side-chains 103 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 62 ASP Chi-restraints excluded: chain K residue 74 ASP Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain L residue 191 HIS Chi-restraints excluded: chain L residue 199 THR Chi-restraints excluded: chain R residue 1005 LEU Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 284 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 1.9990 chunk 62 optimal weight: 20.0000 chunk 43 optimal weight: 0.1980 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 56 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 88 optimal weight: 20.0000 chunk 79 optimal weight: 0.5980 chunk 23 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R1018 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7315 Z= 0.182 Angle : 0.647 12.018 9939 Z= 0.323 Chirality : 0.044 0.150 1135 Planarity : 0.004 0.052 1250 Dihedral : 5.337 58.930 1030 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.63 % Allowed : 19.17 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -2.04 (0.27), residues: 904 helix: -0.26 (0.29), residues: 304 sheet: -1.57 (0.31), residues: 247 loop : -2.04 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 156 HIS 0.006 0.001 HIS R 281 PHE 0.009 0.001 PHE L 141 TYR 0.014 0.001 TYR R 69 ARG 0.008 0.001 ARG K 31 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 99 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 6 GLN cc_start: 0.8152 (tt0) cc_final: 0.7921 (tt0) REVERT: H 76 ASP cc_start: 0.7723 (t0) cc_final: 0.7167 (t0) REVERT: H 79 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8383 (mtpt) REVERT: H 92 GLU cc_start: 0.8607 (pm20) cc_final: 0.8306 (pm20) REVERT: H 185 GLN cc_start: 0.8656 (tt0) cc_final: 0.8355 (mt0) REVERT: H 209 ILE cc_start: 0.8897 (pt) cc_final: 0.8661 (OUTLIER) REVERT: H 226 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8457 (mt-10) REVERT: K 31 ARG cc_start: 0.8121 (ptm160) cc_final: 0.7660 (ttp-170) REVERT: K 46 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7361 (mp0) REVERT: K 101 ASP cc_start: 0.8667 (t0) cc_final: 0.8173 (t0) REVERT: L 192 LYS cc_start: 0.8539 (pttp) cc_final: 0.8021 (mmtt) REVERT: R 156 TRP cc_start: 0.8224 (t-100) cc_final: 0.7940 (m100) REVERT: R 198 LEU cc_start: 0.6620 (OUTLIER) cc_final: 0.6405 (tp) REVERT: R 202 PHE cc_start: 0.7962 (t80) cc_final: 0.7484 (m-10) REVERT: R 1091 GLU cc_start: 0.8083 (mp0) cc_final: 0.7738 (mp0) REVERT: R 243 PHE cc_start: 0.7165 (OUTLIER) cc_final: 0.5625 (t80) REVERT: R 288 ASN cc_start: 0.7598 (m110) cc_final: 0.7014 (m110) outliers start: 28 outliers final: 10 residues processed: 119 average time/residue: 0.9630 time to fit residues: 122.3477 Evaluate side-chains 102 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain K residue 62 ASP Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain L residue 191 HIS Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 1005 LEU Chi-restraints excluded: chain R residue 239 ILE Chi-restraints excluded: chain R residue 243 PHE Chi-restraints excluded: chain R residue 284 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 4.9990 chunk 1 optimal weight: 0.0870 chunk 66 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 22 optimal weight: 20.0000 chunk 29 optimal weight: 4.9990 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R1018 ASN R 281 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7315 Z= 0.249 Angle : 0.662 10.259 9939 Z= 0.331 Chirality : 0.044 0.163 1135 Planarity : 0.004 0.053 1250 Dihedral : 5.087 48.704 1030 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.50 % Allowed : 21.11 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -1.97 (0.28), residues: 904 helix: -0.24 (0.29), residues: 304 sheet: -1.53 (0.31), residues: 265 loop : -1.94 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 50 HIS 0.005 0.001 HIS R 281 PHE 0.010 0.001 PHE R 289 TYR 0.018 0.001 TYR L 142 ARG 0.006 0.000 ARG K 31 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 97 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: H 76 ASP cc_start: 0.7781 (t0) cc_final: 0.7183 (t0) REVERT: H 79 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8365 (mtpt) REVERT: H 92 GLU cc_start: 0.8611 (pm20) cc_final: 0.8308 (pm20) REVERT: H 185 GLN cc_start: 0.8669 (tt0) cc_final: 0.8368 (mt0) REVERT: H 209 ILE cc_start: 0.8899 (pt) cc_final: 0.8661 (OUTLIER) REVERT: H 222 ASP cc_start: 0.8669 (m-30) cc_final: 0.8464 (m-30) REVERT: H 226 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8456 (mt-10) REVERT: K 18 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7197 (mp) REVERT: K 46 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7342 (mp0) REVERT: K 101 ASP cc_start: 0.8656 (t0) cc_final: 0.8159 (t0) REVERT: L 192 LYS cc_start: 0.8535 (pttp) cc_final: 0.7974 (mmtt) REVERT: R 156 TRP cc_start: 0.8237 (t-100) cc_final: 0.7984 (m100) REVERT: R 162 GLN cc_start: 0.7838 (tp-100) cc_final: 0.7635 (tm-30) REVERT: R 198 LEU cc_start: 0.6635 (OUTLIER) cc_final: 0.5957 (tt) REVERT: R 202 PHE cc_start: 0.7943 (t80) cc_final: 0.7448 (m-10) REVERT: R 1091 GLU cc_start: 0.8088 (mp0) cc_final: 0.7742 (mp0) REVERT: R 243 PHE cc_start: 0.7217 (OUTLIER) cc_final: 0.5651 (t80) REVERT: R 281 HIS cc_start: 0.7751 (t-170) cc_final: 0.7380 (t70) REVERT: R 285 CYS cc_start: 0.8256 (m) cc_final: 0.7591 (m) REVERT: R 288 ASN cc_start: 0.7449 (m110) cc_final: 0.7129 (m110) outliers start: 27 outliers final: 14 residues processed: 115 average time/residue: 1.0194 time to fit residues: 124.7795 Evaluate side-chains 109 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 92 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 62 ASP Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 191 HIS Chi-restraints excluded: chain L residue 199 THR Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 1005 LEU Chi-restraints excluded: chain R residue 239 ILE Chi-restraints excluded: chain R residue 243 PHE Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 287 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 7 optimal weight: 0.0370 chunk 29 optimal weight: 4.9990 chunk 46 optimal weight: 0.0770 chunk 85 optimal weight: 0.9980 overall best weight: 1.2220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7315 Z= 0.234 Angle : 0.649 9.629 9939 Z= 0.323 Chirality : 0.043 0.155 1135 Planarity : 0.004 0.055 1250 Dihedral : 4.876 39.126 1030 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 4.27 % Allowed : 20.85 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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 (0.28), residues: 904 helix: -0.12 (0.30), residues: 304 sheet: -1.32 (0.32), residues: 254 loop : -1.78 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 50 HIS 0.003 0.001 HIS R 281 PHE 0.009 0.001 PHE L 141 TYR 0.016 0.001 TYR L 142 ARG 0.010 0.001 ARG K 31 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 100 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 76 ASP cc_start: 0.7760 (t0) cc_final: 0.7146 (t0) REVERT: H 79 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8398 (mtpt) REVERT: H 92 GLU cc_start: 0.8618 (pm20) cc_final: 0.8351 (pm20) REVERT: H 185 GLN cc_start: 0.8651 (tt0) cc_final: 0.8340 (mt0) REVERT: H 209 ILE cc_start: 0.8898 (pt) cc_final: 0.8628 (pp) REVERT: H 226 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8460 (mt-10) REVERT: K 18 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7286 (mp) REVERT: K 31 ARG cc_start: 0.8148 (ptm160) cc_final: 0.7598 (ttp-170) REVERT: K 46 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7335 (mp0) REVERT: K 87 LYS cc_start: 0.8114 (mtmm) cc_final: 0.7898 (mtmm) REVERT: K 101 ASP cc_start: 0.8656 (t0) cc_final: 0.8144 (t0) REVERT: R 156 TRP cc_start: 0.8235 (t-100) cc_final: 0.8032 (m100) REVERT: R 198 LEU cc_start: 0.6711 (OUTLIER) cc_final: 0.6019 (tt) REVERT: R 202 PHE cc_start: 0.7950 (t80) cc_final: 0.7451 (m-10) REVERT: R 223 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8070 (mm) REVERT: R 1091 GLU cc_start: 0.8081 (mp0) cc_final: 0.7696 (mp0) REVERT: R 281 HIS cc_start: 0.7389 (t-170) cc_final: 0.6848 (t70) REVERT: R 285 CYS cc_start: 0.8245 (m) cc_final: 0.7530 (m) REVERT: R 288 ASN cc_start: 0.7415 (m110) cc_final: 0.7045 (m110) outliers start: 33 outliers final: 18 residues processed: 125 average time/residue: 0.9043 time to fit residues: 121.2566 Evaluate side-chains 110 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 88 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 191 HIS Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 199 THR Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 1005 LEU Chi-restraints excluded: chain R residue 239 ILE Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 287 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 88 optimal weight: 0.0040 chunk 55 optimal weight: 0.0070 chunk 54 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 overall best weight: 1.1014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7315 Z= 0.228 Angle : 0.668 13.264 9939 Z= 0.333 Chirality : 0.044 0.156 1135 Planarity : 0.004 0.053 1250 Dihedral : 4.801 33.577 1030 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 4.02 % Allowed : 22.02 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -1.58 (0.28), residues: 904 helix: -0.06 (0.30), residues: 303 sheet: -1.24 (0.32), residues: 254 loop : -1.64 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 50 HIS 0.002 0.001 HIS L 191 PHE 0.010 0.001 PHE R 289 TYR 0.015 0.001 TYR L 142 ARG 0.009 0.000 ARG K 31 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 90 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 76 ASP cc_start: 0.7756 (t0) cc_final: 0.7131 (t0) REVERT: H 79 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8394 (mtpt) REVERT: H 92 GLU cc_start: 0.8619 (pm20) cc_final: 0.8353 (pm20) REVERT: H 185 GLN cc_start: 0.8656 (tt0) cc_final: 0.8369 (mt0) REVERT: H 209 ILE cc_start: 0.8910 (pt) cc_final: 0.8632 (pp) REVERT: H 226 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8439 (mt-10) REVERT: K 18 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7265 (mp) REVERT: K 31 ARG cc_start: 0.8223 (ptm160) cc_final: 0.7714 (ttp-170) REVERT: K 46 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7259 (mp0) REVERT: K 87 LYS cc_start: 0.8094 (mtmm) cc_final: 0.7747 (mtmm) REVERT: K 101 ASP cc_start: 0.8650 (t0) cc_final: 0.8140 (t0) REVERT: R 156 TRP cc_start: 0.8268 (t-100) cc_final: 0.7990 (m100) REVERT: R 202 PHE cc_start: 0.7961 (t80) cc_final: 0.7483 (m-10) REVERT: R 223 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8077 (mm) REVERT: R 1091 GLU cc_start: 0.8070 (mp0) cc_final: 0.7623 (mp0) REVERT: R 243 PHE cc_start: 0.7268 (OUTLIER) cc_final: 0.5834 (t80) REVERT: R 281 HIS cc_start: 0.7398 (t-170) cc_final: 0.6870 (t70) REVERT: R 285 CYS cc_start: 0.8224 (m) cc_final: 0.7546 (m) REVERT: R 288 ASN cc_start: 0.7455 (m110) cc_final: 0.7140 (m110) outliers start: 31 outliers final: 20 residues processed: 117 average time/residue: 1.0569 time to fit residues: 132.2790 Evaluate side-chains 108 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 84 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 191 HIS Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 1005 LEU Chi-restraints excluded: chain R residue 1107 ILE Chi-restraints excluded: chain R residue 239 ILE Chi-restraints excluded: chain R residue 243 PHE Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 248 THR Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 287 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 0.9980 chunk 17 optimal weight: 8.9990 chunk 56 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 82 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7315 Z= 0.228 Angle : 0.669 12.461 9939 Z= 0.334 Chirality : 0.044 0.163 1135 Planarity : 0.004 0.050 1250 Dihedral : 4.739 29.764 1030 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.63 % Allowed : 22.41 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -1.48 (0.29), residues: 904 helix: -0.01 (0.30), residues: 303 sheet: -1.14 (0.32), residues: 254 loop : -1.58 (0.36), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 111 HIS 0.002 0.001 HIS L 191 PHE 0.009 0.001 PHE L 141 TYR 0.016 0.001 TYR R 69 ARG 0.008 0.000 ARG K 31 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 92 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 76 ASP cc_start: 0.7757 (t0) cc_final: 0.7129 (t0) REVERT: H 79 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8388 (mtpt) REVERT: H 92 GLU cc_start: 0.8624 (pm20) cc_final: 0.8356 (pm20) REVERT: H 185 GLN cc_start: 0.8650 (tt0) cc_final: 0.8372 (mt0) REVERT: H 209 ILE cc_start: 0.8879 (pt) cc_final: 0.8603 (pp) REVERT: H 226 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8449 (mt-10) REVERT: K 18 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7246 (mp) REVERT: K 29 ILE cc_start: 0.7393 (OUTLIER) cc_final: 0.7025 (mp) REVERT: K 31 ARG cc_start: 0.8147 (ptm160) cc_final: 0.7625 (ttp-170) REVERT: K 46 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7245 (mp0) REVERT: K 87 LYS cc_start: 0.8070 (mtmm) cc_final: 0.7792 (mtmm) REVERT: K 101 ASP cc_start: 0.8634 (t0) cc_final: 0.8114 (t0) REVERT: R 202 PHE cc_start: 0.7969 (t80) cc_final: 0.7487 (m-10) REVERT: R 223 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8078 (mm) REVERT: R 1091 GLU cc_start: 0.8059 (mp0) cc_final: 0.7613 (mp0) REVERT: R 243 PHE cc_start: 0.7234 (OUTLIER) cc_final: 0.5776 (t80) REVERT: R 281 HIS cc_start: 0.7343 (t-170) cc_final: 0.6803 (t70) REVERT: R 285 CYS cc_start: 0.8236 (m) cc_final: 0.7516 (m) REVERT: R 288 ASN cc_start: 0.7301 (m110) cc_final: 0.6949 (m110) outliers start: 28 outliers final: 18 residues processed: 114 average time/residue: 0.9881 time to fit residues: 120.4161 Evaluate side-chains 113 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 90 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 29 ILE Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 199 THR Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 1005 LEU Chi-restraints excluded: chain R residue 1107 ILE Chi-restraints excluded: chain R residue 239 ILE Chi-restraints excluded: chain R residue 243 PHE Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 248 THR Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 287 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 7315 Z= 0.310 Angle : 0.701 11.770 9939 Z= 0.353 Chirality : 0.045 0.188 1135 Planarity : 0.004 0.049 1250 Dihedral : 4.987 33.838 1030 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.40 % Allowed : 22.28 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.29), residues: 904 helix: -0.08 (0.30), residues: 302 sheet: -1.10 (0.33), residues: 245 loop : -1.56 (0.35), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 50 HIS 0.003 0.001 HIS R 27 PHE 0.010 0.001 PHE R 289 TYR 0.019 0.001 TYR L 142 ARG 0.006 0.000 ARG K 31 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 90 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 6 GLN cc_start: 0.8204 (tt0) cc_final: 0.7948 (pt0) REVERT: H 76 ASP cc_start: 0.7774 (t0) cc_final: 0.7122 (t0) REVERT: H 79 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8363 (mtpt) REVERT: H 92 GLU cc_start: 0.8652 (pm20) cc_final: 0.8385 (pm20) REVERT: H 185 GLN cc_start: 0.8644 (tt0) cc_final: 0.8339 (mt0) REVERT: H 209 ILE cc_start: 0.8848 (pt) cc_final: 0.8556 (pp) REVERT: H 226 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8426 (mt-10) REVERT: K 18 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7335 (mp) REVERT: K 29 ILE cc_start: 0.7361 (OUTLIER) cc_final: 0.7060 (mp) REVERT: K 31 ARG cc_start: 0.8216 (ptm160) cc_final: 0.7721 (ttp-170) REVERT: K 46 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7285 (mp0) REVERT: K 87 LYS cc_start: 0.8060 (mtmm) cc_final: 0.7758 (mtmm) REVERT: K 101 ASP cc_start: 0.8642 (t0) cc_final: 0.8103 (t0) REVERT: R 146 GLU cc_start: 0.7131 (tm-30) cc_final: 0.6883 (pp20) REVERT: R 202 PHE cc_start: 0.7966 (t80) cc_final: 0.7467 (m-10) REVERT: R 223 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8100 (mm) REVERT: R 1013 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7912 (tp30) REVERT: R 1091 GLU cc_start: 0.8108 (mp0) cc_final: 0.7654 (mp0) REVERT: R 243 PHE cc_start: 0.7212 (OUTLIER) cc_final: 0.5768 (t80) REVERT: R 288 ASN cc_start: 0.7502 (m110) cc_final: 0.6893 (m110) outliers start: 34 outliers final: 17 residues processed: 113 average time/residue: 0.9344 time to fit residues: 113.1271 Evaluate side-chains 108 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 85 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 29 ILE Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 199 THR Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 1005 LEU Chi-restraints excluded: chain R residue 1013 GLU Chi-restraints excluded: chain R residue 1107 ILE Chi-restraints excluded: chain R residue 239 ILE Chi-restraints excluded: chain R residue 243 PHE Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 248 THR Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 287 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 91 optimal weight: 0.0370 chunk 84 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 22 optimal weight: 20.0000 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 27 HIS ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7315 Z= 0.209 Angle : 0.670 14.623 9939 Z= 0.333 Chirality : 0.044 0.164 1135 Planarity : 0.004 0.057 1250 Dihedral : 4.701 27.023 1030 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.72 % Allowed : 24.22 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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 (0.29), residues: 904 helix: 0.04 (0.30), residues: 302 sheet: -1.07 (0.32), residues: 254 loop : -1.45 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 50 HIS 0.003 0.001 HIS R 27 PHE 0.009 0.001 PHE L 141 TYR 0.016 0.001 TYR R 69 ARG 0.013 0.001 ARG R 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 94 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 76 ASP cc_start: 0.7772 (t0) cc_final: 0.7119 (t0) REVERT: H 79 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8375 (mtpt) REVERT: H 92 GLU cc_start: 0.8643 (pm20) cc_final: 0.8374 (pm20) REVERT: H 185 GLN cc_start: 0.8646 (tt0) cc_final: 0.8376 (mt0) REVERT: H 209 ILE cc_start: 0.8819 (pt) cc_final: 0.8523 (pp) REVERT: H 226 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8421 (mt-10) REVERT: K 18 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7374 (mp) REVERT: K 29 ILE cc_start: 0.7304 (OUTLIER) cc_final: 0.7080 (mp) REVERT: K 31 ARG cc_start: 0.8169 (ptm160) cc_final: 0.7748 (ttm170) REVERT: K 46 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7308 (mp0) REVERT: K 87 LYS cc_start: 0.8021 (mtmm) cc_final: 0.7801 (mtmm) REVERT: K 101 ASP cc_start: 0.8624 (t0) cc_final: 0.8097 (t0) REVERT: R 146 GLU cc_start: 0.7129 (tm-30) cc_final: 0.6892 (pp20) REVERT: R 202 PHE cc_start: 0.7983 (t80) cc_final: 0.7480 (m-10) REVERT: R 223 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8089 (mm) REVERT: R 1013 GLU cc_start: 0.8268 (tt0) cc_final: 0.7935 (tp30) REVERT: R 1091 GLU cc_start: 0.8042 (mp0) cc_final: 0.7614 (mp0) REVERT: R 243 PHE cc_start: 0.7254 (OUTLIER) cc_final: 0.5905 (t80) REVERT: R 285 CYS cc_start: 0.8199 (m) cc_final: 0.7497 (m) REVERT: R 288 ASN cc_start: 0.7382 (m110) cc_final: 0.6799 (m110) outliers start: 21 outliers final: 13 residues processed: 112 average time/residue: 1.0192 time to fit residues: 121.6436 Evaluate side-chains 109 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 91 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 29 ILE Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 199 THR Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 1005 LEU Chi-restraints excluded: chain R residue 1107 ILE Chi-restraints excluded: chain R residue 243 PHE Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 284 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 73 optimal weight: 8.9990 chunk 30 optimal weight: 0.1980 chunk 75 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 64 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.131857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.086403 restraints weight = 12513.219| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 3.37 r_work: 0.3152 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7315 Z= 0.245 Angle : 0.682 14.427 9939 Z= 0.341 Chirality : 0.044 0.175 1135 Planarity : 0.004 0.049 1250 Dihedral : 4.751 27.556 1030 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.98 % Allowed : 24.22 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -1.31 (0.29), residues: 904 helix: 0.04 (0.30), residues: 302 sheet: -1.00 (0.33), residues: 245 loop : -1.43 (0.36), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 50 HIS 0.002 0.001 HIS R 37 PHE 0.010 0.001 PHE R 289 TYR 0.035 0.001 TYR R 69 ARG 0.009 0.001 ARG R 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2804.07 seconds wall clock time: 50 minutes 29.63 seconds (3029.63 seconds total)