Starting phenix.real_space_refine on Tue Feb 13 20:25:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ej6_31153/02_2024/7ej6_31153_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ej6_31153/02_2024/7ej6_31153.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ej6_31153/02_2024/7ej6_31153.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ej6_31153/02_2024/7ej6_31153.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ej6_31153/02_2024/7ej6_31153_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ej6_31153/02_2024/7ej6_31153_trim_updated.pdb" } resolution = 3.21 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= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 3 5.21 5 S 39 5.16 5 C 4674 2.51 5 N 1326 2.21 5 O 1524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 164": "NH1" <-> "NH2" Residue "B GLU 177": "OE1" <-> "OE2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B ARG 235": "NH1" <-> "NH2" Residue "B ARG 248": "NH1" <-> "NH2" Residue "B GLU 252": "OE1" <-> "OE2" Residue "B GLU 317": "OE1" <-> "OE2" Residue "C ARG 164": "NH1" <-> "NH2" Residue "C GLU 177": "OE1" <-> "OE2" Residue "C ARG 229": "NH1" <-> "NH2" Residue "C ARG 235": "NH1" <-> "NH2" Residue "C ARG 248": "NH1" <-> "NH2" Residue "C GLU 252": "OE1" <-> "OE2" Residue "C GLU 317": "OE1" <-> "OE2" Residue "A ARG 164": "NH1" <-> "NH2" Residue "A GLU 177": "OE1" <-> "OE2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A ARG 235": "NH1" <-> "NH2" Residue "A ARG 248": "NH1" <-> "NH2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "A GLU 317": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7584 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2436 Classifications: {'peptide': 316} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 306} Chain: "C" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2436 Classifications: {'peptide': 316} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 306} Chain: "A" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2436 Classifications: {'peptide': 316} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 306} Chain: "D" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.30, per 1000 atoms: 0.57 Number of scatterers: 7584 At special positions: 0 Unit cell: (84.96, 97.35, 111.51, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 39 16.00 P 18 15.00 Mg 3 11.99 O 1524 8.00 N 1326 7.00 C 4674 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.45 Conformation dependent library (CDL) restraints added in 1.4 seconds 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1716 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 3 sheets defined 41.0% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'B' and resid 21 through 24 Processing helix chain 'B' and resid 31 through 38 Processing helix chain 'B' and resid 44 through 47 No H-bonds generated for 'chain 'B' and resid 44 through 47' Processing helix chain 'B' and resid 51 through 56 removed outlier: 3.939A pdb=" N LYS B 56 " --> pdb=" O ARG B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 75 Processing helix chain 'B' and resid 84 through 92 removed outlier: 3.549A pdb=" N GLN B 91 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG B 92 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 107 Processing helix chain 'B' and resid 127 through 136 removed outlier: 3.981A pdb=" N HIS B 132 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL B 136 " --> pdb=" O HIS B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 144 No H-bonds generated for 'chain 'B' and resid 142 through 144' Processing helix chain 'B' and resid 162 through 172 Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'B' and resid 191 through 206 removed outlier: 3.594A pdb=" N VAL B 198 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU B 203 " --> pdb=" O GLU B 199 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU B 204 " --> pdb=" O GLN B 200 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER B 206 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 225 removed outlier: 3.727A pdb=" N VAL B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 252 Processing helix chain 'B' and resid 284 through 290 removed outlier: 3.579A pdb=" N ALA B 288 " --> pdb=" O GLY B 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 24 Processing helix chain 'C' and resid 31 through 38 Processing helix chain 'C' and resid 44 through 47 No H-bonds generated for 'chain 'C' and resid 44 through 47' Processing helix chain 'C' and resid 51 through 56 removed outlier: 3.938A pdb=" N LYS C 56 " --> pdb=" O ARG C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 75 Processing helix chain 'C' and resid 84 through 92 removed outlier: 3.549A pdb=" N GLN C 91 " --> pdb=" O LEU C 87 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ARG C 92 " --> pdb=" O ASP C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 107 Processing helix chain 'C' and resid 130 through 136 removed outlier: 3.668A pdb=" N VAL C 136 " --> pdb=" O HIS C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 144 No H-bonds generated for 'chain 'C' and resid 142 through 144' Processing helix chain 'C' and resid 162 through 172 Processing helix chain 'C' and resid 176 through 180 Processing helix chain 'C' and resid 191 through 206 removed outlier: 3.594A pdb=" N VAL C 198 " --> pdb=" O GLN C 194 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU C 203 " --> pdb=" O GLU C 199 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU C 204 " --> pdb=" O GLN C 200 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER C 206 " --> pdb=" O GLY C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 225 removed outlier: 3.727A pdb=" N VAL C 224 " --> pdb=" O ALA C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 252 Processing helix chain 'C' and resid 284 through 290 removed outlier: 3.579A pdb=" N ALA C 288 " --> pdb=" O GLY C 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 24 Processing helix chain 'A' and resid 31 through 38 Processing helix chain 'A' and resid 44 through 47 No H-bonds generated for 'chain 'A' and resid 44 through 47' Processing helix chain 'A' and resid 51 through 56 removed outlier: 3.939A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 75 Processing helix chain 'A' and resid 84 through 92 removed outlier: 3.549A pdb=" N GLN A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ARG A 92 " --> pdb=" O ASP A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 107 Processing helix chain 'A' and resid 128 through 136 removed outlier: 3.667A pdb=" N VAL A 136 " --> pdb=" O HIS A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 144 No H-bonds generated for 'chain 'A' and resid 142 through 144' Processing helix chain 'A' and resid 162 through 172 Processing helix chain 'A' and resid 176 through 180 Processing helix chain 'A' and resid 191 through 206 removed outlier: 3.594A pdb=" N VAL A 198 " --> pdb=" O GLN A 194 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU A 203 " --> pdb=" O GLU A 199 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU A 204 " --> pdb=" O GLN A 200 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 225 removed outlier: 3.727A pdb=" N VAL A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 252 Processing helix chain 'A' and resid 284 through 290 removed outlier: 3.579A pdb=" N ALA A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 318 through 323 removed outlier: 4.266A pdb=" N LYS B 318 " --> pdb=" O LEU B 309 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ARG B 294 " --> pdb=" O GLN B 310 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY B 121 " --> pdb=" O ASN B 261 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LYS B 150 " --> pdb=" O ARG B 211 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE B 213 " --> pdb=" O LYS B 150 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA B 152 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N VAL B 215 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE B 154 " --> pdb=" O VAL B 215 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 318 through 323 removed outlier: 4.266A pdb=" N LYS C 318 " --> pdb=" O LEU C 309 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ARG C 294 " --> pdb=" O GLN C 310 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY C 121 " --> pdb=" O ASN C 261 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LYS C 150 " --> pdb=" O ARG C 211 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE C 213 " --> pdb=" O LYS C 150 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA C 152 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL C 215 " --> pdb=" O ALA C 152 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE C 154 " --> pdb=" O VAL C 215 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 318 through 323 removed outlier: 4.267A pdb=" N LYS A 318 " --> pdb=" O LEU A 309 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ARG A 294 " --> pdb=" O GLN A 310 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY A 121 " --> pdb=" O ASN A 261 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LYS A 150 " --> pdb=" O ARG A 211 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE A 213 " --> pdb=" O LYS A 150 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA A 152 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL A 215 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ILE A 154 " --> pdb=" O VAL A 215 " (cutoff:3.500A) 271 hydrogen bonds defined for protein. 786 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: 1.90 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2215 1.33 - 1.45: 1087 1.45 - 1.57: 4303 1.57 - 1.69: 32 1.69 - 1.81: 60 Bond restraints: 7697 Sorted by residual: bond pdb=" C4 ATP B 602 " pdb=" C5 ATP B 602 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.73e+01 bond pdb=" C4 ATP C 402 " pdb=" C5 ATP C 402 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.70e+01 bond pdb=" C4 ATP C 401 " pdb=" C5 ATP C 401 " ideal model delta sigma weight residual 1.388 1.456 -0.068 1.00e-02 1.00e+04 4.67e+01 bond pdb=" C5 ATP C 402 " pdb=" C6 ATP C 402 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.29e+01 bond pdb=" C5 ATP B 602 " pdb=" C6 ATP B 602 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.28e+01 ... (remaining 7692 not shown) Histogram of bond angle deviations from ideal: 99.38 - 106.88: 231 106.88 - 114.37: 4625 114.37 - 121.87: 3934 121.87 - 129.37: 1598 129.37 - 136.86: 27 Bond angle restraints: 10415 Sorted by residual: angle pdb=" PA ATP B 602 " pdb=" O3A ATP B 602 " pdb=" PB ATP B 602 " ideal model delta sigma weight residual 136.83 117.84 18.99 1.00e+00 1.00e+00 3.61e+02 angle pdb=" PA ATP C 401 " pdb=" O3A ATP C 401 " pdb=" PB ATP C 401 " ideal model delta sigma weight residual 136.83 117.85 18.98 1.00e+00 1.00e+00 3.60e+02 angle pdb=" PA ATP C 402 " pdb=" O3A ATP C 402 " pdb=" PB ATP C 402 " ideal model delta sigma weight residual 136.83 117.86 18.97 1.00e+00 1.00e+00 3.60e+02 angle pdb=" PB ATP C 402 " pdb=" O3B ATP C 402 " pdb=" PG ATP C 402 " ideal model delta sigma weight residual 139.87 121.14 18.73 1.00e+00 1.00e+00 3.51e+02 angle pdb=" PB ATP C 401 " pdb=" O3B ATP C 401 " pdb=" PG ATP C 401 " ideal model delta sigma weight residual 139.87 121.17 18.70 1.00e+00 1.00e+00 3.50e+02 ... (remaining 10410 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 4134 17.88 - 35.76: 422 35.76 - 53.64: 132 53.64 - 71.53: 13 71.53 - 89.41: 24 Dihedral angle restraints: 4725 sinusoidal: 2037 harmonic: 2688 Sorted by residual: dihedral pdb=" CA PRO B 82 " pdb=" C PRO B 82 " pdb=" N ALA B 83 " pdb=" CA ALA B 83 " ideal model delta harmonic sigma weight residual 180.00 158.72 21.28 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA PRO A 82 " pdb=" C PRO A 82 " pdb=" N ALA A 83 " pdb=" CA ALA A 83 " ideal model delta harmonic sigma weight residual 180.00 158.75 21.25 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA PRO C 82 " pdb=" C PRO C 82 " pdb=" N ALA C 83 " pdb=" CA ALA C 83 " ideal model delta harmonic sigma weight residual 180.00 158.79 21.21 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 4722 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1002 0.066 - 0.131: 164 0.131 - 0.197: 9 0.197 - 0.263: 6 0.263 - 0.328: 1 Chirality restraints: 1182 Sorted by residual: chirality pdb=" CA THR C 128 " pdb=" N THR C 128 " pdb=" C THR C 128 " pdb=" CB THR C 128 " both_signs ideal model delta sigma weight residual False 2.53 2.20 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CA THR A 128 " pdb=" N THR A 128 " pdb=" C THR A 128 " pdb=" CB THR A 128 " both_signs ideal model delta sigma weight residual False 2.53 2.77 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" C2' ATP C 401 " pdb=" C1' ATP C 401 " pdb=" C3' ATP C 401 " pdb=" O2' ATP C 401 " both_signs ideal model delta sigma weight residual False -2.68 -2.47 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1179 not shown) Planarity restraints: 1314 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 124 " 0.024 2.00e-02 2.50e+03 5.02e-02 2.52e+01 pdb=" C ARG C 124 " -0.087 2.00e-02 2.50e+03 pdb=" O ARG C 124 " 0.034 2.00e-02 2.50e+03 pdb=" N CYS C 125 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 315 " 0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C MET A 315 " -0.059 2.00e-02 2.50e+03 pdb=" O MET A 315 " 0.022 2.00e-02 2.50e+03 pdb=" N PRO A 316 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 315 " -0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C MET B 315 " 0.059 2.00e-02 2.50e+03 pdb=" O MET B 315 " -0.022 2.00e-02 2.50e+03 pdb=" N PRO B 316 " -0.020 2.00e-02 2.50e+03 ... (remaining 1311 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 220 2.60 - 3.17: 7624 3.17 - 3.75: 11332 3.75 - 4.32: 16697 4.32 - 4.90: 27316 Nonbonded interactions: 63189 Sorted by model distance: nonbonded pdb="MG MG B 601 " pdb=" O3B ATP C 401 " model vdw 2.019 2.170 nonbonded pdb=" O3B ATP B 602 " pdb="MG MG A 601 " model vdw 2.020 2.170 nonbonded pdb=" O3B ATP C 402 " pdb="MG MG C 403 " model vdw 2.020 2.170 nonbonded pdb=" O TYR A 94 " pdb=" OG1 THR A 113 " model vdw 2.079 2.440 nonbonded pdb=" O TYR C 94 " pdb=" OG1 THR C 113 " model vdw 2.080 2.440 ... (remaining 63184 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 16 through 334) selection = (chain 'B' and resid 16 through 334) selection = (chain 'C' and resid 16 through 334) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.040 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: 12.900 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 24.570 Find NCS groups from input model: 0.500 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: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 7697 Z= 0.497 Angle : 1.028 18.994 10415 Z= 0.749 Chirality : 0.048 0.328 1182 Planarity : 0.004 0.050 1314 Dihedral : 16.919 89.407 3009 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 51.68 Ramachandran Plot: Outliers : 0.74 % Allowed : 12.10 % Favored : 87.15 % Rotamer: Outliers : 1.13 % Allowed : 6.02 % Favored : 92.86 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -4.78 (0.21), residues: 942 helix: -3.46 (0.16), residues: 435 sheet: 0.42 (0.43), residues: 153 loop : -4.39 (0.23), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 193 PHE 0.005 0.001 PHE A 123 TYR 0.010 0.001 TYR C 41 ARG 0.004 0.001 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 0.926 Fit side-chains REVERT: B 178 SER cc_start: 0.8980 (OUTLIER) cc_final: 0.8742 (m) REVERT: C 178 SER cc_start: 0.9059 (OUTLIER) cc_final: 0.8834 (t) REVERT: A 127 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.7994 (mtpt) REVERT: A 178 SER cc_start: 0.8918 (OUTLIER) cc_final: 0.8669 (m) outliers start: 9 outliers final: 4 residues processed: 85 average time/residue: 0.1696 time to fit residues: 20.9847 Evaluate side-chains 61 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 127 LYS Chi-restraints excluded: chain A residue 178 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 HIS B 182 ASN B 194 GLN B 236 GLN B 242 HIS B 289 HIS ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 HIS C 182 ASN C 194 GLN C 236 GLN C 242 HIS ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 ASN A 194 GLN A 236 GLN A 242 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7697 Z= 0.248 Angle : 0.675 7.878 10415 Z= 0.354 Chirality : 0.046 0.163 1182 Planarity : 0.005 0.038 1314 Dihedral : 15.592 86.340 1229 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.07 % Favored : 91.30 % Rotamer: Outliers : 2.01 % Allowed : 11.53 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -2.75 (0.25), residues: 942 helix: -1.29 (0.23), residues: 426 sheet: 1.04 (0.43), residues: 147 loop : -3.76 (0.27), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 193 PHE 0.007 0.001 PHE B 123 TYR 0.013 0.001 TYR C 94 ARG 0.003 0.001 ARG C 124 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 70 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: B 21 GLU cc_start: 0.7886 (mp0) cc_final: 0.7475 (mp0) REVERT: A 21 GLU cc_start: 0.7842 (mp0) cc_final: 0.7424 (mp0) REVERT: A 28 ASN cc_start: 0.8079 (p0) cc_final: 0.7744 (p0) outliers start: 16 outliers final: 6 residues processed: 85 average time/residue: 0.1594 time to fit residues: 20.0398 Evaluate side-chains 62 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain A residue 95 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 0.0070 chunk 26 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 91 optimal weight: 0.0870 chunk 75 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 241 GLN ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7697 Z= 0.157 Angle : 0.585 7.530 10415 Z= 0.302 Chirality : 0.043 0.152 1182 Planarity : 0.004 0.029 1314 Dihedral : 14.489 82.850 1220 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.26 % Favored : 93.21 % Rotamer: Outliers : 3.26 % Allowed : 12.28 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -1.70 (0.27), residues: 942 helix: -0.08 (0.25), residues: 447 sheet: 1.05 (0.42), residues: 147 loop : -3.64 (0.27), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 193 PHE 0.005 0.001 PHE B 123 TYR 0.007 0.001 TYR B 226 ARG 0.002 0.000 ARG B 161 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 63 time to evaluate : 0.878 Fit side-chains REVERT: B 21 GLU cc_start: 0.7868 (mp0) cc_final: 0.7499 (mp0) REVERT: C 21 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7844 (pm20) REVERT: C 28 ASN cc_start: 0.8225 (p0) cc_final: 0.7835 (p0) REVERT: A 21 GLU cc_start: 0.7889 (mp0) cc_final: 0.7583 (mp0) REVERT: A 28 ASN cc_start: 0.8117 (p0) cc_final: 0.7837 (p0) outliers start: 26 outliers final: 7 residues processed: 84 average time/residue: 0.1527 time to fit residues: 19.3904 Evaluate side-chains 61 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 113 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 43 optimal weight: 0.0570 chunk 9 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 56 optimal weight: 0.0980 chunk 84 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 24 optimal weight: 8.9990 overall best weight: 0.5100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 241 GLN ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7697 Z= 0.138 Angle : 0.570 7.617 10415 Z= 0.288 Chirality : 0.042 0.152 1182 Planarity : 0.003 0.028 1314 Dihedral : 14.010 75.937 1218 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.11 % Favored : 92.36 % Rotamer: Outliers : 3.51 % Allowed : 11.53 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -1.33 (0.28), residues: 942 helix: 0.35 (0.27), residues: 447 sheet: 1.04 (0.42), residues: 147 loop : -3.56 (0.26), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 193 PHE 0.005 0.001 PHE A 253 TYR 0.008 0.001 TYR A 41 ARG 0.002 0.000 ARG C 124 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 62 time to evaluate : 0.915 Fit side-chains revert: symmetry clash REVERT: B 21 GLU cc_start: 0.7907 (mp0) cc_final: 0.7605 (mp0) REVERT: C 21 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7852 (pm20) REVERT: C 28 ASN cc_start: 0.8189 (p0) cc_final: 0.7874 (p0) REVERT: C 125 CYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8664 (t) REVERT: A 21 GLU cc_start: 0.7847 (mp0) cc_final: 0.7647 (mp0) REVERT: A 28 ASN cc_start: 0.8181 (p0) cc_final: 0.7938 (p0) outliers start: 28 outliers final: 13 residues processed: 86 average time/residue: 0.1345 time to fit residues: 18.1492 Evaluate side-chains 68 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 53 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 125 CYS Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain A residue 24 ASN Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 212 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 37 optimal weight: 0.0370 chunk 76 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 overall best weight: 3.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 GLN B 289 HIS C 102 GLN C 241 GLN A 102 GLN ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 7697 Z= 0.372 Angle : 0.663 7.046 10415 Z= 0.341 Chirality : 0.046 0.229 1182 Planarity : 0.005 0.046 1314 Dihedral : 14.599 81.335 1218 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.70 % Favored : 90.66 % Rotamer: Outliers : 4.01 % Allowed : 11.28 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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 (0.28), residues: 942 helix: 0.23 (0.26), residues: 429 sheet: 0.61 (0.42), residues: 159 loop : -3.41 (0.28), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 193 PHE 0.010 0.001 PHE B 123 TYR 0.013 0.001 TYR A 94 ARG 0.003 0.001 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 62 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 17 residues processed: 90 average time/residue: 0.1401 time to fit residues: 19.3828 Evaluate side-chains 72 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 55 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 125 CYS Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain A residue 24 ASN Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 324 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 89 optimal weight: 0.0870 chunk 74 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 47 optimal weight: 0.0570 overall best weight: 0.5876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7697 Z= 0.145 Angle : 0.576 7.952 10415 Z= 0.295 Chirality : 0.043 0.155 1182 Planarity : 0.003 0.028 1314 Dihedral : 13.766 78.323 1218 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.37 % Favored : 93.10 % Rotamer: Outliers : 2.88 % Allowed : 12.41 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -1.19 (0.28), residues: 942 helix: 0.48 (0.27), residues: 441 sheet: 1.02 (0.43), residues: 147 loop : -3.39 (0.27), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 193 PHE 0.003 0.001 PHE C 80 TYR 0.008 0.001 TYR A 41 ARG 0.002 0.000 ARG C 124 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 61 time to evaluate : 0.859 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 15 residues processed: 81 average time/residue: 0.1375 time to fit residues: 17.2517 Evaluate side-chains 72 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 57 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain A residue 24 ASN Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 212 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 65 optimal weight: 0.2980 chunk 50 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 GLN ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7697 Z= 0.165 Angle : 0.569 7.598 10415 Z= 0.293 Chirality : 0.042 0.156 1182 Planarity : 0.003 0.028 1314 Dihedral : 13.642 76.290 1218 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.48 % Favored : 92.99 % Rotamer: Outliers : 2.26 % Allowed : 13.41 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.28), residues: 942 helix: 0.63 (0.27), residues: 426 sheet: 0.96 (0.43), residues: 147 loop : -3.07 (0.27), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 193 PHE 0.005 0.001 PHE B 123 TYR 0.007 0.001 TYR B 226 ARG 0.004 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 62 time to evaluate : 0.937 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 78 average time/residue: 0.1341 time to fit residues: 16.5887 Evaluate side-chains 67 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 56 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 212 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 56 optimal weight: 0.0050 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 overall best weight: 3.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 ASN B 200 GLN B 241 GLN ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7697 Z= 0.329 Angle : 0.646 7.795 10415 Z= 0.333 Chirality : 0.045 0.209 1182 Planarity : 0.004 0.044 1314 Dihedral : 14.379 81.097 1218 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.54 % Favored : 91.83 % Rotamer: Outliers : 2.63 % Allowed : 13.78 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -1.18 (0.28), residues: 942 helix: 0.46 (0.26), residues: 429 sheet: 0.68 (0.43), residues: 153 loop : -3.09 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 193 PHE 0.009 0.001 PHE B 123 TYR 0.014 0.001 TYR A 94 ARG 0.002 0.000 ARG C 142 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 62 time to evaluate : 0.853 Fit side-chains revert: symmetry clash REVERT: C 94 TYR cc_start: 0.7870 (OUTLIER) cc_final: 0.7143 (t80) REVERT: A 94 TYR cc_start: 0.7692 (OUTLIER) cc_final: 0.7291 (t80) outliers start: 21 outliers final: 12 residues processed: 78 average time/residue: 0.1322 time to fit residues: 16.3799 Evaluate side-chains 69 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 55 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 272 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 65 optimal weight: 0.4980 chunk 25 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 ASN B 200 GLN ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7697 Z= 0.276 Angle : 0.637 8.336 10415 Z= 0.326 Chirality : 0.044 0.186 1182 Planarity : 0.004 0.035 1314 Dihedral : 14.499 82.819 1218 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.11 % Favored : 92.25 % Rotamer: Outliers : 2.26 % Allowed : 14.16 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -1.14 (0.28), residues: 942 helix: 0.54 (0.27), residues: 423 sheet: 0.67 (0.43), residues: 153 loop : -3.07 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 193 PHE 0.008 0.001 PHE B 123 TYR 0.012 0.001 TYR A 94 ARG 0.002 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 57 time to evaluate : 0.969 Fit side-chains revert: symmetry clash REVERT: C 94 TYR cc_start: 0.7864 (OUTLIER) cc_final: 0.7206 (t80) REVERT: A 94 TYR cc_start: 0.7628 (OUTLIER) cc_final: 0.7213 (t80) outliers start: 18 outliers final: 14 residues processed: 71 average time/residue: 0.1314 time to fit residues: 15.0269 Evaluate side-chains 70 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 54 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 324 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 85 optimal weight: 0.0670 chunk 73 optimal weight: 0.6980 chunk 7 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 ASN ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7697 Z= 0.156 Angle : 0.584 8.788 10415 Z= 0.300 Chirality : 0.043 0.158 1182 Planarity : 0.003 0.033 1314 Dihedral : 13.683 79.293 1218 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.58 % Favored : 92.89 % Rotamer: Outliers : 1.50 % Allowed : 14.79 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -0.88 (0.28), residues: 942 helix: 0.79 (0.27), residues: 423 sheet: 0.89 (0.43), residues: 147 loop : -2.97 (0.28), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS C 193 PHE 0.006 0.001 PHE C 253 TYR 0.009 0.001 TYR B 226 ARG 0.002 0.000 ARG C 124 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 60 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: A 94 TYR cc_start: 0.7456 (OUTLIER) cc_final: 0.6930 (t80) outliers start: 12 outliers final: 10 residues processed: 69 average time/residue: 0.1578 time to fit residues: 16.4548 Evaluate side-chains 64 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 53 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 212 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 ASN ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.075170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.058792 restraints weight = 19826.649| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.98 r_work: 0.2745 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7697 Z= 0.227 Angle : 0.603 7.722 10415 Z= 0.310 Chirality : 0.043 0.174 1182 Planarity : 0.004 0.032 1314 Dihedral : 14.029 79.438 1218 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.11 % Favored : 92.25 % Rotamer: Outliers : 2.38 % Allowed : 14.29 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -0.95 (0.28), residues: 942 helix: 0.67 (0.27), residues: 426 sheet: 0.62 (0.42), residues: 153 loop : -2.90 (0.28), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 193 PHE 0.007 0.001 PHE B 123 TYR 0.010 0.001 TYR A 94 ARG 0.002 0.000 ARG B 161 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1629.27 seconds wall clock time: 30 minutes 31.54 seconds (1831.54 seconds total)