Starting phenix.real_space_refine on Wed Feb 4 04:52:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o1e_70004/02_2026/9o1e_70004_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o1e_70004/02_2026/9o1e_70004.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o1e_70004/02_2026/9o1e_70004.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o1e_70004/02_2026/9o1e_70004.map" model { file = "/net/cci-nas-00/data/ceres_data/9o1e_70004/02_2026/9o1e_70004_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o1e_70004/02_2026/9o1e_70004_neut.cif" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 sd= 0.011 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 Zn 1 6.06 5 S 64 5.16 5 C 5958 2.51 5 N 1392 2.21 5 O 1497 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8912 Number of models: 1 Model: "" Number of chains: 14 Chain: "I" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 591 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "J" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "L" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "M" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "N" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "O" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "P" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 591 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "R" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "S" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 594 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "X" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 367 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "Y" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 367 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "a" Number of atoms: 2243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2243 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 275} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.11, per 1000 atoms: 0.24 Number of scatterers: 8912 At special positions: 0 Unit cell: (91.3, 100.43, 97.11, 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) Zn 1 29.99 S 64 16.00 O 1497 8.00 N 1392 7.00 C 5958 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 - 3.00 Amino acid : True - 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: 0.76 Conformation dependent library (CDL) restraints added in 397.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN a 301 " pdb="ZN ZN a 301 " - pdb=" ND1 HIS a 186 " pdb="ZN ZN a 301 " - pdb=" ND1 HIS a 289 " 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2108 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 1 sheets defined 89.3% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'I' and resid 1 through 41 removed outlier: 3.715A pdb=" N GLY I 19 " --> pdb=" O LEU I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 60 removed outlier: 3.670A pdb=" N GLY I 57 " --> pdb=" O PHE I 53 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU I 58 " --> pdb=" O ILE I 54 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP I 60 " --> pdb=" O ALA I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 76 Processing helix chain 'J' and resid 2 through 41 Processing helix chain 'J' and resid 44 through 60 removed outlier: 3.560A pdb=" N LEU J 58 " --> pdb=" O ILE J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 76 removed outlier: 3.624A pdb=" N ILE J 65 " --> pdb=" O ALA J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 82 removed outlier: 4.032A pdb=" N GLY J 81 " --> pdb=" O ASN J 77 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN J 82 " --> pdb=" O PRO J 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 77 through 82' Processing helix chain 'L' and resid 2 through 17 Processing helix chain 'L' and resid 18 through 41 removed outlier: 3.524A pdb=" N LYS L 33 " --> pdb=" O LEU L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 76 removed outlier: 3.550A pdb=" N VAL L 50 " --> pdb=" O PRO L 46 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU L 58 " --> pdb=" O ILE L 54 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N VAL L 62 " --> pdb=" O LEU L 58 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N THR L 63 " --> pdb=" O LEU L 59 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'M' and resid 2 through 41 removed outlier: 3.684A pdb=" N GLY M 19 " --> pdb=" O LEU M 15 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 76 removed outlier: 3.567A pdb=" N VAL M 50 " --> pdb=" O PRO M 46 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU M 58 " --> pdb=" O ILE M 54 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N VAL M 62 " --> pdb=" O LEU M 58 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N THR M 63 " --> pdb=" O LEU M 59 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE M 65 " --> pdb=" O ALA M 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 41 removed outlier: 3.901A pdb=" N GLY N 19 " --> pdb=" O LEU N 15 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 60 removed outlier: 3.584A pdb=" N LEU N 58 " --> pdb=" O ILE N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 60 through 76 removed outlier: 3.529A pdb=" N MET N 64 " --> pdb=" O ASP N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'O' and resid 2 through 41 removed outlier: 3.646A pdb=" N GLY O 19 " --> pdb=" O LEU O 15 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS O 33 " --> pdb=" O LEU O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 76 removed outlier: 3.912A pdb=" N LEU O 58 " --> pdb=" O ILE O 54 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL O 62 " --> pdb=" O LEU O 58 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N THR O 63 " --> pdb=" O LEU O 59 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE O 65 " --> pdb=" O ALA O 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 41 removed outlier: 3.730A pdb=" N GLY P 19 " --> pdb=" O LEU P 15 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS P 33 " --> pdb=" O LEU P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 60 removed outlier: 3.579A pdb=" N VAL P 50 " --> pdb=" O PRO P 46 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU P 58 " --> pdb=" O ILE P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 60 through 76 removed outlier: 3.530A pdb=" N ILE P 65 " --> pdb=" O ALA P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 78 through 82 Processing helix chain 'Q' and resid 2 through 41 removed outlier: 3.606A pdb=" N GLY Q 19 " --> pdb=" O LEU Q 15 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS Q 33 " --> pdb=" O LEU Q 29 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 60 removed outlier: 3.555A pdb=" N LEU Q 58 " --> pdb=" O ILE Q 54 " (cutoff:3.500A) Processing helix chain 'Q' and resid 60 through 76 Processing helix chain 'Q' and resid 79 through 83 removed outlier: 3.618A pdb=" N ILE Q 83 " --> pdb=" O VAL Q 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 41 removed outlier: 3.517A pdb=" N ILE R 10 " --> pdb=" O GLY R 6 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY R 19 " --> pdb=" O LEU R 15 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS R 33 " --> pdb=" O LEU R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 60 removed outlier: 3.523A pdb=" N LEU R 58 " --> pdb=" O ILE R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 75 removed outlier: 3.737A pdb=" N ILE R 65 " --> pdb=" O ALA R 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 3 through 41 removed outlier: 6.067A pdb=" N ALA S 9 " --> pdb=" O VAL S 5 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY S 19 " --> pdb=" O LEU S 15 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 76 removed outlier: 3.632A pdb=" N VAL S 50 " --> pdb=" O PRO S 46 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU S 58 " --> pdb=" O ILE S 54 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N VAL S 62 " --> pdb=" O LEU S 58 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N THR S 63 " --> pdb=" O LEU S 59 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 83 Processing helix chain 'X' and resid 5 through 25 removed outlier: 3.586A pdb=" N SER X 11 " --> pdb=" O LEU X 7 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS X 23 " --> pdb=" O LEU X 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 45 removed outlier: 3.738A pdb=" N VAL X 29 " --> pdb=" O VAL X 25 " (cutoff:3.500A) Processing helix chain 'Y' and resid 5 through 25 Processing helix chain 'Y' and resid 25 through 47 removed outlier: 3.707A pdb=" N VAL Y 29 " --> pdb=" O VAL Y 25 " (cutoff:3.500A) Processing helix chain 'a' and resid 5 through 14 Processing helix chain 'a' and resid 32 through 39 Processing helix chain 'a' and resid 46 through 69 removed outlier: 3.533A pdb=" N ALA a 66 " --> pdb=" O ILE a 62 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS a 69 " --> pdb=" O LEU a 65 " (cutoff:3.500A) Processing helix chain 'a' and resid 76 through 95 removed outlier: 3.583A pdb=" N PHE a 81 " --> pdb=" O GLY a 77 " (cutoff:3.500A) Processing helix chain 'a' and resid 103 through 121 removed outlier: 3.793A pdb=" N ILE a 121 " --> pdb=" O LEU a 117 " (cutoff:3.500A) Processing helix chain 'a' and resid 122 through 124 No H-bonds generated for 'chain 'a' and resid 122 through 124' Processing helix chain 'a' and resid 127 through 138 Processing helix chain 'a' and resid 147 through 150 removed outlier: 3.681A pdb=" N THR a 150 " --> pdb=" O VAL a 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 147 through 150' Processing helix chain 'a' and resid 151 through 185 removed outlier: 3.704A pdb=" N THR a 155 " --> pdb=" O ASP a 151 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ILE a 176 " --> pdb=" O LYS a 172 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N GLY a 177 " --> pdb=" O VAL a 173 " (cutoff:3.500A) Processing helix chain 'a' and resid 192 through 242 Proline residue: a 201 - end of helix removed outlier: 4.108A pdb=" N VAL a 209 " --> pdb=" O LEU a 205 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR a 210 " --> pdb=" O LEU a 206 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS a 214 " --> pdb=" O THR a 210 " (cutoff:3.500A) Proline residue: a 215 - end of helix removed outlier: 3.853A pdb=" N LEU a 222 " --> pdb=" O LEU a 218 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN a 225 " --> pdb=" O ARG a 221 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL a 238 " --> pdb=" O ILE a 234 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N MET a 239 " --> pdb=" O LEU a 235 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE a 240 " --> pdb=" O ILE a 236 " (cutoff:3.500A) Processing helix chain 'a' and resid 244 through 285 removed outlier: 3.616A pdb=" N ALA a 253 " --> pdb=" O ALA a 249 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU a 264 " --> pdb=" O VAL a 260 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE a 265 " --> pdb=" O PHE a 261 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA a 270 " --> pdb=" O ILE a 266 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N HIS a 285 " --> pdb=" O LEU a 281 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 18 through 20 818 hydrogen bonds defined for protein. 2427 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: 1.29 Time building geometry restraints manager: 1.02 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: 2684 1.34 - 1.45: 1096 1.45 - 1.57: 5174 1.57 - 1.69: 0 1.69 - 1.81: 126 Bond restraints: 9080 Sorted by residual: bond pdb=" N HIS a 285 " pdb=" CA HIS a 285 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.33e-02 5.65e+03 5.77e+00 bond pdb=" N GLN R 82 " pdb=" CA GLN R 82 " ideal model delta sigma weight residual 1.455 1.480 -0.025 1.38e-02 5.25e+03 3.29e+00 bond pdb=" C ALA a 284 " pdb=" N HIS a 285 " ideal model delta sigma weight residual 1.332 1.360 -0.028 1.53e-02 4.27e+03 3.27e+00 bond pdb=" CA ILE a 200 " pdb=" CB ILE a 200 " ideal model delta sigma weight residual 1.534 1.546 -0.011 6.80e-03 2.16e+04 2.76e+00 bond pdb=" CA VAL Q 45 " pdb=" CB VAL Q 45 " ideal model delta sigma weight residual 1.534 1.544 -0.010 6.80e-03 2.16e+04 1.97e+00 ... (remaining 9075 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 12085 1.67 - 3.34: 171 3.34 - 5.02: 40 5.02 - 6.69: 10 6.69 - 8.36: 4 Bond angle restraints: 12310 Sorted by residual: angle pdb=" C ALA L 76 " pdb=" N ASN L 77 " pdb=" CA ASN L 77 " ideal model delta sigma weight residual 122.26 115.50 6.76 1.10e+00 8.26e-01 3.78e+01 angle pdb=" C ALA N 76 " pdb=" N ASN N 77 " pdb=" CA ASN N 77 " ideal model delta sigma weight residual 122.26 115.99 6.27 1.10e+00 8.26e-01 3.25e+01 angle pdb=" C MET P 44 " pdb=" N VAL P 45 " pdb=" CA VAL P 45 " ideal model delta sigma weight residual 120.24 123.26 -3.02 6.30e-01 2.52e+00 2.30e+01 angle pdb=" C MET R 44 " pdb=" N VAL R 45 " pdb=" CA VAL R 45 " ideal model delta sigma weight residual 120.24 123.15 -2.91 6.30e-01 2.52e+00 2.13e+01 angle pdb=" C MET L 44 " pdb=" N VAL L 45 " pdb=" CA VAL L 45 " ideal model delta sigma weight residual 120.33 123.78 -3.45 8.00e-01 1.56e+00 1.86e+01 ... (remaining 12305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 4898 17.04 - 34.08: 252 34.08 - 51.13: 53 51.13 - 68.17: 9 68.17 - 85.21: 6 Dihedral angle restraints: 5218 sinusoidal: 1908 harmonic: 3310 Sorted by residual: dihedral pdb=" CA GLY R 81 " pdb=" C GLY R 81 " pdb=" N GLN R 82 " pdb=" CA GLN R 82 " ideal model delta harmonic sigma weight residual -180.00 -160.48 -19.52 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA LEU a 185 " pdb=" C LEU a 185 " pdb=" N HIS a 186 " pdb=" CA HIS a 186 " ideal model delta harmonic sigma weight residual -180.00 -162.10 -17.90 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA LEU N 59 " pdb=" C LEU N 59 " pdb=" N ASP N 60 " pdb=" CA ASP N 60 " ideal model delta harmonic sigma weight residual -180.00 -163.74 -16.26 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 5215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 851 0.024 - 0.048: 343 0.048 - 0.073: 219 0.073 - 0.097: 80 0.097 - 0.121: 25 Chirality restraints: 1518 Sorted by residual: chirality pdb=" CA HIS a 186 " pdb=" N HIS a 186 " pdb=" C HIS a 186 " pdb=" CB HIS a 186 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.66e-01 chirality pdb=" CA PRO M 46 " pdb=" N PRO M 46 " pdb=" C PRO M 46 " pdb=" CB PRO M 46 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.11 2.00e-01 2.50e+01 3.26e-01 chirality pdb=" CA PRO J 42 " pdb=" N PRO J 42 " pdb=" C PRO J 42 " pdb=" CB PRO J 42 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.21e-01 ... (remaining 1515 not shown) Planarity restraints: 1522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU L 18 " -0.018 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C LEU L 18 " 0.064 2.00e-02 2.50e+03 pdb=" O LEU L 18 " -0.024 2.00e-02 2.50e+03 pdb=" N GLY L 19 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY R 81 " 0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C GLY R 81 " -0.062 2.00e-02 2.50e+03 pdb=" O GLY R 81 " 0.023 2.00e-02 2.50e+03 pdb=" N GLN R 82 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO Y 27 " 0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO Y 28 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO Y 28 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO Y 28 " 0.020 5.00e-02 4.00e+02 ... (remaining 1519 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 5 2.40 - 3.03: 5554 3.03 - 3.65: 13390 3.65 - 4.28: 19732 4.28 - 4.90: 34460 Nonbonded interactions: 73141 Sorted by model distance: nonbonded pdb=" OE1 GLU a 182 " pdb="ZN ZN a 301 " model vdw 1.776 2.230 nonbonded pdb=" OE2 GLU a 182 " pdb="ZN ZN a 301 " model vdw 1.989 2.230 nonbonded pdb=" OD1 ASP a 287 " pdb="ZN ZN a 301 " model vdw 1.989 2.230 nonbonded pdb=" CD GLU a 182 " pdb="ZN ZN a 301 " model vdw 2.107 2.460 nonbonded pdb=" OE2 GLU a 182 " pdb=" OD1 ASP a 287 " model vdw 2.281 3.040 ... (remaining 73136 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'I' and (resid 1 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'J' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 82 or (resid 83 and (name N or name CA or name C or name O \ or name CB )))) selection = (chain 'L' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 82 or (resid 83 and (name N or name CA or name C or name O \ or name CB )))) selection = (chain 'M' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 82 or (resid 83 and (name N or name CA or name C or name O \ or name CB )))) selection = (chain 'N' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 82 or (resid 83 and (name N or name CA or name C or name O \ or name CB )))) selection = (chain 'O' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 82 or (resid 83 and (name N or name CA or name C or name O \ or name CB )))) selection = (chain 'P' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 83)) selection = (chain 'Q' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 82 or (resid 83 and (name N or name CA or name C or name O \ or name CB )))) selection = (chain 'R' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 82 or (resid 83 and (name N or name CA or name C or name O \ or name CB )))) selection = (chain 'S' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 82 or (resid 83 and (name N or name CA or name C or name O \ or name CB )))) } ncs_group { reference = chain 'X' selection = chain 'Y' } 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: 6.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.890 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:7.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 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 0.263 9082 Z= 0.193 Angle : 0.570 8.361 12310 Z= 0.331 Chirality : 0.037 0.121 1518 Planarity : 0.004 0.037 1522 Dihedral : 11.429 85.210 3110 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.22 % Allowed : 5.43 % Favored : 93.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.24), residues: 1184 helix: 2.03 (0.16), residues: 1030 sheet: None (None), residues: 0 loop : -1.49 (0.45), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG a 145 TYR 0.010 0.001 TYR a 9 PHE 0.011 0.001 PHE X 14 TRP 0.007 0.001 TRP X 26 HIS 0.002 0.001 HIS a 13 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9080) covalent geometry : angle 0.56951 (12310) hydrogen bonds : bond 0.12346 ( 818) hydrogen bonds : angle 4.58837 ( 2427) metal coordination : bond 0.24949 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 191 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: I 41 GLN cc_start: 0.7723 (mm-40) cc_final: 0.7519 (mm-40) REVERT: I 60 ASP cc_start: 0.8212 (p0) cc_final: 0.8006 (p0) REVERT: S 44 MET cc_start: 0.7859 (mmp) cc_final: 0.7618 (mmp) REVERT: X 23 LYS cc_start: 0.7939 (mtpt) cc_final: 0.7696 (mtmt) REVERT: a 231 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8525 (tt) outliers start: 11 outliers final: 2 residues processed: 199 average time/residue: 0.7757 time to fit residues: 161.8494 Evaluate side-chains 131 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 128 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain R residue 65 ILE Chi-restraints excluded: chain a residue 231 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 49 GLN I 82 GLN M 49 GLN N 82 GLN P 82 GLN X 4 ASN a 45 HIS a 225 ASN a 269 GLN a 285 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.075693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.057204 restraints weight = 16297.014| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 1.93 r_work: 0.2805 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9082 Z= 0.140 Angle : 0.560 7.829 12310 Z= 0.288 Chirality : 0.038 0.177 1518 Planarity : 0.004 0.037 1522 Dihedral : 4.282 54.818 1225 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.33 % Allowed : 14.63 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.74 (0.24), residues: 1184 helix: 2.28 (0.16), residues: 1032 sheet: None (None), residues: 0 loop : -1.61 (0.45), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 40 TYR 0.012 0.001 TYR a 9 PHE 0.012 0.001 PHE X 20 TRP 0.020 0.001 TRP a 27 HIS 0.005 0.001 HIS a 186 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9080) covalent geometry : angle 0.56042 (12310) hydrogen bonds : bond 0.05202 ( 818) hydrogen bonds : angle 4.00675 ( 2427) metal coordination : bond 0.00868 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: I 41 GLN cc_start: 0.8290 (mm-40) cc_final: 0.7670 (mm-40) REVERT: Q 44 MET cc_start: 0.8661 (mtm) cc_final: 0.8435 (mtp) REVERT: R 1 MET cc_start: 0.7170 (ptp) cc_final: 0.6939 (ptp) REVERT: S 43 GLU cc_start: 0.8247 (mp0) cc_final: 0.7947 (mp0) REVERT: S 80 VAL cc_start: 0.8519 (t) cc_final: 0.8243 (m) REVERT: X 23 LYS cc_start: 0.7824 (mtpt) cc_final: 0.7386 (mtmt) REVERT: X 34 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8250 (mt0) REVERT: a 127 ASP cc_start: 0.8641 (m-30) cc_final: 0.8112 (m-30) REVERT: a 207 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8124 (mm-30) REVERT: a 231 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8157 (tt) outliers start: 21 outliers final: 4 residues processed: 147 average time/residue: 0.7516 time to fit residues: 115.9141 Evaluate side-chains 138 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 132 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain X residue 34 GLN Chi-restraints excluded: chain a residue 231 LEU Chi-restraints excluded: chain a residue 283 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 81 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.073513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.055094 restraints weight = 16306.641| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 1.92 r_work: 0.2766 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9082 Z= 0.160 Angle : 0.576 8.724 12310 Z= 0.292 Chirality : 0.039 0.172 1518 Planarity : 0.004 0.038 1522 Dihedral : 4.186 53.553 1222 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.33 % Allowed : 14.86 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.82 (0.24), residues: 1184 helix: 2.32 (0.15), residues: 1033 sheet: None (None), residues: 0 loop : -1.55 (0.45), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 40 TYR 0.014 0.001 TYR a 9 PHE 0.012 0.001 PHE X 20 TRP 0.005 0.001 TRP a 42 HIS 0.003 0.001 HIS a 186 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 9080) covalent geometry : angle 0.57594 (12310) hydrogen bonds : bond 0.05565 ( 818) hydrogen bonds : angle 3.96615 ( 2427) metal coordination : bond 0.00516 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: I 44 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7716 (mmp) REVERT: J 40 ARG cc_start: 0.7642 (ttm-80) cc_final: 0.7146 (mtt90) REVERT: N 1 MET cc_start: 0.7710 (tpp) cc_final: 0.7502 (tpt) REVERT: O 1 MET cc_start: 0.5875 (tmm) cc_final: 0.5671 (tmm) REVERT: R 1 MET cc_start: 0.7194 (ptp) cc_final: 0.6912 (ptp) REVERT: S 43 GLU cc_start: 0.8278 (mp0) cc_final: 0.7981 (mp0) REVERT: S 80 VAL cc_start: 0.8542 (t) cc_final: 0.8329 (m) REVERT: X 1 MET cc_start: 0.7085 (OUTLIER) cc_final: 0.6518 (mmt) REVERT: X 23 LYS cc_start: 0.7773 (mtpt) cc_final: 0.7372 (mtmt) REVERT: X 34 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8258 (mt0) REVERT: X 37 GLN cc_start: 0.7595 (OUTLIER) cc_final: 0.7320 (mm-40) REVERT: Y 26 TRP cc_start: 0.7858 (t-100) cc_final: 0.7639 (t-100) REVERT: a 127 ASP cc_start: 0.8620 (m-30) cc_final: 0.8098 (m-30) REVERT: a 139 ASP cc_start: 0.7547 (t0) cc_final: 0.7110 (t0) REVERT: a 231 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8228 (tt) outliers start: 30 outliers final: 9 residues processed: 157 average time/residue: 0.6368 time to fit residues: 105.1524 Evaluate side-chains 147 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain R residue 65 ILE Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 19 LEU Chi-restraints excluded: chain X residue 30 ILE Chi-restraints excluded: chain X residue 34 GLN Chi-restraints excluded: chain X residue 37 GLN Chi-restraints excluded: chain a residue 137 THR Chi-restraints excluded: chain a residue 231 LEU Chi-restraints excluded: chain a residue 283 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 105 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 41 GLN R 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.073693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.055200 restraints weight = 16542.005| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 1.93 r_work: 0.2762 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9082 Z= 0.152 Angle : 0.563 8.314 12310 Z= 0.286 Chirality : 0.038 0.181 1518 Planarity : 0.004 0.039 1522 Dihedral : 4.171 53.218 1222 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.77 % Allowed : 15.63 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.94 (0.24), residues: 1184 helix: 2.42 (0.15), residues: 1032 sheet: None (None), residues: 0 loop : -1.55 (0.45), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG M 40 TYR 0.013 0.001 TYR a 9 PHE 0.012 0.001 PHE N 75 TRP 0.005 0.001 TRP a 42 HIS 0.003 0.000 HIS a 186 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 9080) covalent geometry : angle 0.56254 (12310) hydrogen bonds : bond 0.05317 ( 818) hydrogen bonds : angle 3.92518 ( 2427) metal coordination : bond 0.00429 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: J 40 ARG cc_start: 0.7769 (ttm-80) cc_final: 0.7206 (mtt90) REVERT: O 1 MET cc_start: 0.6082 (tmm) cc_final: 0.5457 (tmm) REVERT: R 1 MET cc_start: 0.7283 (ptp) cc_final: 0.7019 (ptp) REVERT: R 2 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7467 (mt-10) REVERT: S 43 GLU cc_start: 0.8265 (mp0) cc_final: 0.7965 (mp0) REVERT: X 1 MET cc_start: 0.7116 (OUTLIER) cc_final: 0.6467 (mmt) REVERT: X 23 LYS cc_start: 0.7844 (mtpt) cc_final: 0.7430 (mtmt) REVERT: Y 26 TRP cc_start: 0.7906 (t-100) cc_final: 0.7677 (t-100) REVERT: Y 35 GLU cc_start: 0.7404 (mt-10) cc_final: 0.6879 (tm-30) REVERT: a 127 ASP cc_start: 0.8585 (m-30) cc_final: 0.8079 (m-30) REVERT: a 139 ASP cc_start: 0.7703 (t0) cc_final: 0.7250 (t0) REVERT: a 191 LYS cc_start: 0.8284 (mptt) cc_final: 0.7609 (mtmp) REVERT: a 207 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8317 (mm-30) REVERT: a 231 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8275 (tt) outliers start: 25 outliers final: 12 residues processed: 155 average time/residue: 0.6587 time to fit residues: 107.0009 Evaluate side-chains 152 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain R residue 65 ILE Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 19 LEU Chi-restraints excluded: chain X residue 30 ILE Chi-restraints excluded: chain a residue 62 ILE Chi-restraints excluded: chain a residue 137 THR Chi-restraints excluded: chain a residue 231 LEU Chi-restraints excluded: chain a residue 283 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 76 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.072654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.054211 restraints weight = 16434.383| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 1.92 r_work: 0.2735 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9082 Z= 0.168 Angle : 0.580 8.772 12310 Z= 0.294 Chirality : 0.039 0.182 1518 Planarity : 0.004 0.040 1522 Dihedral : 4.201 52.836 1222 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.66 % Allowed : 16.08 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.91 (0.24), residues: 1184 helix: 2.40 (0.15), residues: 1032 sheet: None (None), residues: 0 loop : -1.55 (0.44), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG M 40 TYR 0.013 0.001 TYR a 9 PHE 0.012 0.001 PHE J 75 TRP 0.006 0.001 TRP a 42 HIS 0.003 0.001 HIS a 186 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 9080) covalent geometry : angle 0.57954 (12310) hydrogen bonds : bond 0.05617 ( 818) hydrogen bonds : angle 3.93653 ( 2427) metal coordination : bond 0.00471 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: J 40 ARG cc_start: 0.7839 (ttm-80) cc_final: 0.7279 (mtt90) REVERT: M 44 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7614 (mmm) REVERT: O 1 MET cc_start: 0.6244 (tmm) cc_final: 0.5459 (tmm) REVERT: Q 2 GLU cc_start: 0.8682 (mp0) cc_final: 0.8366 (mm-30) REVERT: R 1 MET cc_start: 0.7382 (ptp) cc_final: 0.7147 (ptp) REVERT: R 2 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7459 (mt-10) REVERT: R 43 GLU cc_start: 0.8722 (mp0) cc_final: 0.8427 (pt0) REVERT: X 1 MET cc_start: 0.7229 (OUTLIER) cc_final: 0.6547 (mmt) REVERT: X 23 LYS cc_start: 0.7850 (mtpt) cc_final: 0.7417 (mtmt) REVERT: X 34 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8292 (mt0) REVERT: Y 26 TRP cc_start: 0.7918 (t-100) cc_final: 0.7669 (t-100) REVERT: Y 35 GLU cc_start: 0.7435 (mt-10) cc_final: 0.6897 (tm-30) REVERT: Y 44 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7708 (mm) REVERT: a 127 ASP cc_start: 0.8628 (m-30) cc_final: 0.8258 (m-30) REVERT: a 139 ASP cc_start: 0.7695 (t0) cc_final: 0.7237 (t0) REVERT: a 191 LYS cc_start: 0.8294 (mptt) cc_final: 0.7640 (mtmp) REVERT: a 194 VAL cc_start: 0.8126 (OUTLIER) cc_final: 0.7859 (p) REVERT: a 207 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8259 (mm-30) REVERT: a 231 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8320 (tt) outliers start: 33 outliers final: 14 residues processed: 157 average time/residue: 0.6367 time to fit residues: 104.9989 Evaluate side-chains 155 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain M residue 44 MET Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain R residue 65 ILE Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 19 LEU Chi-restraints excluded: chain X residue 30 ILE Chi-restraints excluded: chain X residue 34 GLN Chi-restraints excluded: chain X residue 37 GLN Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain a residue 137 THR Chi-restraints excluded: chain a residue 194 VAL Chi-restraints excluded: chain a residue 231 LEU Chi-restraints excluded: chain a residue 283 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 3 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 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 41 GLN ** 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 = 0.3259 r_free = 0.3259 target = 0.074342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.056187 restraints weight = 16504.226| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 1.91 r_work: 0.2784 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9082 Z= 0.131 Angle : 0.531 8.342 12310 Z= 0.272 Chirality : 0.037 0.184 1518 Planarity : 0.004 0.039 1522 Dihedral : 4.095 52.869 1222 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.77 % Allowed : 16.96 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.18 (0.24), residues: 1184 helix: 2.58 (0.15), residues: 1033 sheet: None (None), residues: 0 loop : -1.49 (0.45), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 40 TYR 0.011 0.001 TYR a 9 PHE 0.012 0.001 PHE X 14 TRP 0.006 0.001 TRP a 42 HIS 0.002 0.000 HIS a 186 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 9080) covalent geometry : angle 0.53135 (12310) hydrogen bonds : bond 0.04853 ( 818) hydrogen bonds : angle 3.84256 ( 2427) metal coordination : bond 0.00272 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: N 2 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7822 (mt-10) REVERT: O 1 MET cc_start: 0.6217 (tmm) cc_final: 0.5422 (tmm) REVERT: R 1 MET cc_start: 0.7316 (ptp) cc_final: 0.7019 (ptp) REVERT: R 2 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7403 (mt-10) REVERT: X 1 MET cc_start: 0.7079 (OUTLIER) cc_final: 0.6373 (mmt) REVERT: X 23 LYS cc_start: 0.7806 (mtpt) cc_final: 0.7368 (mtmt) REVERT: X 34 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8341 (mt0) REVERT: Y 26 TRP cc_start: 0.7893 (t-100) cc_final: 0.7658 (t-100) REVERT: Y 35 GLU cc_start: 0.7435 (mt-10) cc_final: 0.6850 (tm-30) REVERT: Y 44 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7614 (mm) REVERT: a 127 ASP cc_start: 0.8538 (m-30) cc_final: 0.8035 (m-30) REVERT: a 139 ASP cc_start: 0.7739 (t0) cc_final: 0.7267 (t0) REVERT: a 191 LYS cc_start: 0.8300 (mptt) cc_final: 0.7637 (mtmp) REVERT: a 207 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8208 (mm-30) REVERT: a 231 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8246 (tt) outliers start: 25 outliers final: 10 residues processed: 152 average time/residue: 0.6602 time to fit residues: 105.3157 Evaluate side-chains 151 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain N residue 2 GLU Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain R residue 65 ILE Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 30 ILE Chi-restraints excluded: chain X residue 34 GLN Chi-restraints excluded: chain X residue 37 GLN Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain a residue 137 THR Chi-restraints excluded: chain a residue 231 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 74 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 77 ASN N 41 GLN R 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.072525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.054338 restraints weight = 16601.646| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 1.91 r_work: 0.2743 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9082 Z= 0.167 Angle : 0.579 8.895 12310 Z= 0.291 Chirality : 0.039 0.180 1518 Planarity : 0.004 0.040 1522 Dihedral : 4.147 52.752 1222 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.10 % Allowed : 17.29 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.04 (0.24), residues: 1184 helix: 2.47 (0.15), residues: 1032 sheet: None (None), residues: 0 loop : -1.45 (0.44), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 40 TYR 0.013 0.001 TYR a 9 PHE 0.012 0.001 PHE J 75 TRP 0.005 0.001 TRP a 42 HIS 0.003 0.001 HIS a 186 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 9080) covalent geometry : angle 0.57888 (12310) hydrogen bonds : bond 0.05504 ( 818) hydrogen bonds : angle 3.88032 ( 2427) metal coordination : bond 0.00433 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.244 Fit side-chains REVERT: J 40 ARG cc_start: 0.7783 (ttm170) cc_final: 0.7270 (mtt90) REVERT: M 44 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7594 (mmm) REVERT: N 2 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7903 (mt-10) REVERT: O 1 MET cc_start: 0.6207 (tmm) cc_final: 0.5412 (tmm) REVERT: R 1 MET cc_start: 0.7436 (ptp) cc_final: 0.7193 (ptp) REVERT: R 2 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7468 (mt-10) REVERT: R 43 GLU cc_start: 0.8721 (mp0) cc_final: 0.8408 (pt0) REVERT: S 60 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.8238 (m-30) REVERT: X 23 LYS cc_start: 0.7856 (mtpt) cc_final: 0.7411 (mtmt) REVERT: X 34 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8351 (mt0) REVERT: X 38 LYS cc_start: 0.8318 (tttp) cc_final: 0.7823 (tptp) REVERT: Y 26 TRP cc_start: 0.7919 (t-100) cc_final: 0.7683 (t-100) REVERT: Y 35 GLU cc_start: 0.7413 (mt-10) cc_final: 0.6875 (tm-30) REVERT: Y 44 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7618 (mm) REVERT: a 74 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.7963 (tt0) REVERT: a 127 ASP cc_start: 0.8565 (m-30) cc_final: 0.8088 (m-30) REVERT: a 139 ASP cc_start: 0.7671 (t0) cc_final: 0.7226 (t0) REVERT: a 191 LYS cc_start: 0.8285 (mptt) cc_final: 0.7657 (mtmp) REVERT: a 194 VAL cc_start: 0.8102 (OUTLIER) cc_final: 0.7827 (p) REVERT: a 207 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8179 (mm-30) REVERT: a 231 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8314 (tt) REVERT: a 283 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7999 (ptp) outliers start: 28 outliers final: 13 residues processed: 152 average time/residue: 0.7271 time to fit residues: 115.9037 Evaluate side-chains 156 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain M residue 44 MET Chi-restraints excluded: chain N residue 2 GLU Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain R residue 65 ILE Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain S residue 60 ASP Chi-restraints excluded: chain X residue 19 LEU Chi-restraints excluded: chain X residue 30 ILE Chi-restraints excluded: chain X residue 34 GLN Chi-restraints excluded: chain X residue 37 GLN Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain a residue 74 GLN Chi-restraints excluded: chain a residue 137 THR Chi-restraints excluded: chain a residue 194 VAL Chi-restraints excluded: chain a residue 231 LEU Chi-restraints excluded: chain a residue 283 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 105 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 90 optimal weight: 0.4980 chunk 86 optimal weight: 0.2980 chunk 93 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 41 GLN R 41 GLN a 16 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.075941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.057696 restraints weight = 16542.609| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.93 r_work: 0.2821 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 9082 Z= 0.121 Angle : 0.527 9.044 12310 Z= 0.268 Chirality : 0.037 0.186 1518 Planarity : 0.004 0.040 1522 Dihedral : 4.015 52.966 1222 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.00 % Allowed : 18.85 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.40 (0.24), residues: 1184 helix: 2.81 (0.16), residues: 1013 sheet: None (None), residues: 0 loop : -1.56 (0.40), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 40 TYR 0.009 0.001 TYR a 9 PHE 0.013 0.001 PHE X 14 TRP 0.006 0.001 TRP a 42 HIS 0.002 0.000 HIS a 186 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 9080) covalent geometry : angle 0.52690 (12310) hydrogen bonds : bond 0.04432 ( 818) hydrogen bonds : angle 3.77312 ( 2427) metal coordination : bond 0.00165 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: J 40 ARG cc_start: 0.7617 (ttm170) cc_final: 0.7136 (mtt90) REVERT: O 1 MET cc_start: 0.6207 (tmm) cc_final: 0.5402 (tmm) REVERT: R 1 MET cc_start: 0.7337 (ptp) cc_final: 0.7088 (ptp) REVERT: R 2 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7341 (mt-10) REVERT: R 43 GLU cc_start: 0.8718 (mp0) cc_final: 0.8276 (pt0) REVERT: S 43 GLU cc_start: 0.8251 (mp0) cc_final: 0.7970 (mp0) REVERT: X 23 LYS cc_start: 0.7770 (mtpt) cc_final: 0.7329 (mtmt) REVERT: Y 26 TRP cc_start: 0.7878 (t-100) cc_final: 0.7637 (t-100) REVERT: Y 35 GLU cc_start: 0.7472 (mt-10) cc_final: 0.6895 (tm-30) REVERT: a 74 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7962 (tt0) REVERT: a 127 ASP cc_start: 0.8504 (m-30) cc_final: 0.8040 (m-30) REVERT: a 139 ASP cc_start: 0.7686 (t0) cc_final: 0.7243 (t0) REVERT: a 191 LYS cc_start: 0.8296 (mptt) cc_final: 0.7670 (mtmp) REVERT: a 194 VAL cc_start: 0.8083 (OUTLIER) cc_final: 0.7810 (p) REVERT: a 207 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8053 (mm-30) REVERT: a 231 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8222 (tt) REVERT: a 244 MET cc_start: 0.6312 (mmp) cc_final: 0.6110 (mmm) outliers start: 18 outliers final: 8 residues processed: 149 average time/residue: 0.7312 time to fit residues: 114.2291 Evaluate side-chains 146 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain R residue 65 ILE Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain X residue 30 ILE Chi-restraints excluded: chain a residue 74 GLN Chi-restraints excluded: chain a residue 194 VAL Chi-restraints excluded: chain a residue 231 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 13 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 102 optimal weight: 0.0970 chunk 72 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 77 ASN N 41 GLN R 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.076372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.058138 restraints weight = 16463.640| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.93 r_work: 0.2828 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9082 Z= 0.120 Angle : 0.533 9.470 12310 Z= 0.267 Chirality : 0.037 0.187 1518 Planarity : 0.004 0.043 1522 Dihedral : 3.950 52.750 1222 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.88 % Allowed : 19.29 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.49 (0.24), residues: 1184 helix: 2.87 (0.15), residues: 1013 sheet: None (None), residues: 0 loop : -1.49 (0.40), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 40 TYR 0.009 0.001 TYR a 9 PHE 0.012 0.001 PHE X 14 TRP 0.005 0.001 TRP a 42 HIS 0.002 0.000 HIS a 186 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 9080) covalent geometry : angle 0.53251 (12310) hydrogen bonds : bond 0.04372 ( 818) hydrogen bonds : angle 3.71178 ( 2427) metal coordination : bond 0.00201 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: I 43 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7965 (pm20) REVERT: I 44 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8128 (mtp) REVERT: J 40 ARG cc_start: 0.7595 (ttm170) cc_final: 0.7121 (mtt90) REVERT: O 1 MET cc_start: 0.6214 (tmm) cc_final: 0.5940 (ttt) REVERT: R 1 MET cc_start: 0.7261 (ptp) cc_final: 0.7042 (ptp) REVERT: R 43 GLU cc_start: 0.8682 (mp0) cc_final: 0.8180 (pt0) REVERT: S 43 GLU cc_start: 0.8232 (mp0) cc_final: 0.7948 (mp0) REVERT: S 60 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.8118 (m-30) REVERT: X 23 LYS cc_start: 0.7743 (mtpt) cc_final: 0.7311 (mtmt) REVERT: Y 26 TRP cc_start: 0.7888 (t-100) cc_final: 0.7657 (t-100) REVERT: Y 35 GLU cc_start: 0.7517 (mt-10) cc_final: 0.6932 (tm-30) REVERT: a 74 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7669 (tm-30) REVERT: a 127 ASP cc_start: 0.8490 (m-30) cc_final: 0.7924 (m-30) REVERT: a 139 ASP cc_start: 0.7733 (t0) cc_final: 0.7267 (t0) REVERT: a 191 LYS cc_start: 0.8292 (mptt) cc_final: 0.7666 (mtmp) REVERT: a 194 VAL cc_start: 0.8103 (OUTLIER) cc_final: 0.7825 (p) REVERT: a 207 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8084 (mm-30) REVERT: a 231 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8247 (tt) REVERT: a 244 MET cc_start: 0.6258 (mmp) cc_final: 0.5981 (mmm) outliers start: 17 outliers final: 8 residues processed: 149 average time/residue: 0.6651 time to fit residues: 104.1190 Evaluate side-chains 148 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain R residue 65 ILE Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain S residue 60 ASP Chi-restraints excluded: chain X residue 30 ILE Chi-restraints excluded: chain a residue 74 GLN Chi-restraints excluded: chain a residue 194 VAL Chi-restraints excluded: chain a residue 231 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 85 optimal weight: 3.9990 chunk 86 optimal weight: 0.1980 chunk 55 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 77 ASN N 41 GLN R 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.073526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.055176 restraints weight = 16633.378| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 1.93 r_work: 0.2762 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9082 Z= 0.154 Angle : 0.591 9.500 12310 Z= 0.293 Chirality : 0.038 0.183 1518 Planarity : 0.004 0.046 1522 Dihedral : 4.073 52.903 1222 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.77 % Allowed : 19.84 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.29 (0.24), residues: 1184 helix: 2.63 (0.15), residues: 1033 sheet: None (None), residues: 0 loop : -1.27 (0.45), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 40 TYR 0.012 0.001 TYR a 9 PHE 0.011 0.001 PHE J 75 TRP 0.005 0.001 TRP a 42 HIS 0.003 0.001 HIS a 186 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 9080) covalent geometry : angle 0.59122 (12310) hydrogen bonds : bond 0.05182 ( 818) hydrogen bonds : angle 3.79095 ( 2427) metal coordination : bond 0.00389 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.353 Fit side-chains REVERT: I 43 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7979 (pm20) REVERT: I 44 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8098 (mtp) REVERT: J 40 ARG cc_start: 0.7735 (ttm170) cc_final: 0.7200 (mtt90) REVERT: O 1 MET cc_start: 0.6287 (tmm) cc_final: 0.5971 (tmm) REVERT: R 43 GLU cc_start: 0.8702 (mp0) cc_final: 0.8164 (pt0) REVERT: S 43 GLU cc_start: 0.8275 (mp0) cc_final: 0.7983 (mp0) REVERT: S 60 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.8219 (m-30) REVERT: X 23 LYS cc_start: 0.7773 (mtpt) cc_final: 0.7322 (mtmt) REVERT: X 38 LYS cc_start: 0.8314 (tttp) cc_final: 0.7814 (tptp) REVERT: Y 26 TRP cc_start: 0.7918 (t-100) cc_final: 0.7668 (t-100) REVERT: Y 35 GLU cc_start: 0.7536 (mt-10) cc_final: 0.6925 (tm-30) REVERT: a 74 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7968 (tt0) REVERT: a 127 ASP cc_start: 0.8574 (m-30) cc_final: 0.8026 (m-30) REVERT: a 139 ASP cc_start: 0.7703 (t0) cc_final: 0.7251 (t0) REVERT: a 191 LYS cc_start: 0.8315 (mptt) cc_final: 0.7693 (mtmp) REVERT: a 194 VAL cc_start: 0.8095 (OUTLIER) cc_final: 0.7811 (p) REVERT: a 207 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8147 (mm-30) REVERT: a 231 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8285 (tt) REVERT: a 244 MET cc_start: 0.6304 (mmp) cc_final: 0.6052 (mmm) outliers start: 16 outliers final: 9 residues processed: 144 average time/residue: 0.7232 time to fit residues: 109.5428 Evaluate side-chains 146 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain P residue 23 THR Chi-restraints excluded: chain R residue 65 ILE Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain S residue 60 ASP Chi-restraints excluded: chain X residue 30 ILE Chi-restraints excluded: chain Y residue 22 MET Chi-restraints excluded: chain a residue 74 GLN Chi-restraints excluded: chain a residue 194 VAL Chi-restraints excluded: chain a residue 231 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 110 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 17 optimal weight: 0.0970 chunk 65 optimal weight: 8.9990 chunk 60 optimal weight: 0.6980 chunk 54 optimal weight: 0.2980 chunk 70 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 0.0870 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 77 ASN N 41 GLN R 41 GLN a 13 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.077404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.059222 restraints weight = 16351.303| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 1.92 r_work: 0.2859 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9082 Z= 0.119 Angle : 0.527 8.848 12310 Z= 0.264 Chirality : 0.036 0.189 1518 Planarity : 0.004 0.051 1522 Dihedral : 3.941 53.070 1222 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.88 % Allowed : 20.07 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.63 (0.24), residues: 1184 helix: 2.97 (0.15), residues: 1013 sheet: None (None), residues: 0 loop : -1.47 (0.41), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 40 TYR 0.007 0.001 TYR a 9 PHE 0.013 0.001 PHE X 14 TRP 0.006 0.001 TRP a 42 HIS 0.002 0.000 HIS a 186 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 9080) covalent geometry : angle 0.52654 (12310) hydrogen bonds : bond 0.04127 ( 818) hydrogen bonds : angle 3.69544 ( 2427) metal coordination : bond 0.00126 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3430.59 seconds wall clock time: 58 minutes 59.34 seconds (3539.34 seconds total)