Starting phenix.real_space_refine on Tue Mar 3 18:01:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wu2_32817/03_2026/7wu2_32817.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wu2_32817/03_2026/7wu2_32817.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wu2_32817/03_2026/7wu2_32817.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wu2_32817/03_2026/7wu2_32817.map" model { file = "/net/cci-nas-00/data/ceres_data/7wu2_32817/03_2026/7wu2_32817.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wu2_32817/03_2026/7wu2_32817.cif" } resolution = 2.8 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= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 4968 2.51 5 N 1361 2.21 5 O 1450 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7829 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1734 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2586 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 423 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 971 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2115 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 269} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 1.58, per 1000 atoms: 0.20 Number of scatterers: 7829 At special positions: 0 Unit cell: (106.029, 118.881, 83.538, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 1450 8.00 N 1361 7.00 C 4968 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 632 " - pdb=" SG CYS R 704 " distance=2.03 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: 0.88 Conformation dependent library (CDL) restraints added in 337.0 milliseconds 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1892 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 10 sheets defined 40.5% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 26 through 40 Processing helix chain 'A' and resid 53 through 57 removed outlier: 3.904A pdb=" N VAL A 57 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.675A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.520A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.196A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.860A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.613A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.733A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 25 removed outlier: 4.305A pdb=" N ILE C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.532A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 48 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.606A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.503A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 559 through 591 Processing helix chain 'R' and resid 592 through 594 No H-bonds generated for 'chain 'R' and resid 592 through 594' Processing helix chain 'R' and resid 601 through 623 Processing helix chain 'R' and resid 629 through 662 removed outlier: 4.006A pdb=" N VAL R 637 " --> pdb=" O GLN R 633 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA R 646 " --> pdb=" O PHE R 642 " (cutoff:3.500A) Processing helix chain 'R' and resid 671 through 680 Processing helix chain 'R' and resid 680 through 694 removed outlier: 3.706A pdb=" N LEU R 684 " --> pdb=" O TRP R 680 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE R 693 " --> pdb=" O ILE R 689 " (cutoff:3.500A) Processing helix chain 'R' and resid 713 through 737 Proline residue: R 719 - end of helix Processing helix chain 'R' and resid 738 through 745 Processing helix chain 'R' and resid 745 through 750 removed outlier: 4.002A pdb=" N HIS R 749 " --> pdb=" O ASN R 745 " (cutoff:3.500A) Processing helix chain 'R' and resid 752 through 764 removed outlier: 3.967A pdb=" N LYS R 756 " --> pdb=" O PRO R 752 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU R 757 " --> pdb=" O SER R 753 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR R 758 " --> pdb=" O ALA R 754 " (cutoff:3.500A) Processing helix chain 'R' and resid 764 through 770 removed outlier: 4.572A pdb=" N ILE R 768 " --> pdb=" O VAL R 764 " (cutoff:3.500A) Processing helix chain 'R' and resid 773 through 778 removed outlier: 3.822A pdb=" N VAL R 777 " --> pdb=" O TRP R 773 " (cutoff:3.500A) Processing helix chain 'R' and resid 779 through 781 No H-bonds generated for 'chain 'R' and resid 779 through 781' Processing helix chain 'R' and resid 783 through 797 removed outlier: 3.647A pdb=" N PHE R 787 " --> pdb=" O CYS R 783 " (cutoff:3.500A) Processing helix chain 'R' and resid 797 through 807 Processing helix chain 'R' and resid 810 through 821 Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214 removed outlier: 6.251A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.759A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.714A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 removed outlier: 6.393A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.556A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.047A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.448A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.046A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 8 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.017A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 384 hydrogen bonds defined for protein. 1104 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: 1.35 Time building geometry restraints manager: 1.12 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: 2552 1.34 - 1.46: 1364 1.46 - 1.58: 4006 1.58 - 1.70: 0 1.70 - 1.82: 70 Bond restraints: 7992 Sorted by residual: bond pdb=" N ARG A 265 " pdb=" CA ARG A 265 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.35e-02 5.49e+03 5.23e+00 bond pdb=" N ASN A 254 " pdb=" CA ASN A 254 " ideal model delta sigma weight residual 1.460 1.487 -0.027 1.22e-02 6.72e+03 5.05e+00 bond pdb=" N TYR A 253 " pdb=" CA TYR A 253 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.42e-02 4.96e+03 4.84e+00 bond pdb=" N ASN A 50 " pdb=" CA ASN A 50 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 1.03e+00 bond pdb=" CA ASN A 50 " pdb=" CB ASN A 50 " ideal model delta sigma weight residual 1.530 1.547 -0.017 1.69e-02 3.50e+03 1.02e+00 ... (remaining 7987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 10714 1.89 - 3.78: 109 3.78 - 5.66: 16 5.66 - 7.55: 3 7.55 - 9.44: 3 Bond angle restraints: 10845 Sorted by residual: angle pdb=" C ASP A 49 " pdb=" N ASN A 50 " pdb=" CA ASN A 50 " ideal model delta sigma weight residual 121.54 130.98 -9.44 1.91e+00 2.74e-01 2.44e+01 angle pdb=" CB ARG B 8 " pdb=" CG ARG B 8 " pdb=" CD ARG B 8 " ideal model delta sigma weight residual 111.30 119.21 -7.91 2.30e+00 1.89e-01 1.18e+01 angle pdb=" C ASN R 546 " pdb=" N PHE R 547 " pdb=" CA PHE R 547 " ideal model delta sigma weight residual 121.54 127.92 -6.38 1.91e+00 2.74e-01 1.12e+01 angle pdb=" N GLU A 299 " pdb=" CA GLU A 299 " pdb=" CB GLU A 299 " ideal model delta sigma weight residual 110.28 114.62 -4.34 1.55e+00 4.16e-01 7.84e+00 angle pdb=" N ASN A 50 " pdb=" CA ASN A 50 " pdb=" CB ASN A 50 " ideal model delta sigma weight residual 110.49 115.04 -4.55 1.69e+00 3.50e-01 7.25e+00 ... (remaining 10840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 4345 17.88 - 35.75: 321 35.75 - 53.63: 47 53.63 - 71.51: 9 71.51 - 89.38: 7 Dihedral angle restraints: 4729 sinusoidal: 1800 harmonic: 2929 Sorted by residual: dihedral pdb=" CB CYS R 632 " pdb=" SG CYS R 632 " pdb=" SG CYS R 704 " pdb=" CB CYS R 704 " ideal model delta sinusoidal sigma weight residual -86.00 -132.06 46.06 1 1.00e+01 1.00e-02 2.94e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -42.57 -43.43 1 1.00e+01 1.00e-02 2.63e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual 180.00 -160.12 -19.88 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 4726 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 876 0.037 - 0.075: 263 0.075 - 0.112: 73 0.112 - 0.149: 22 0.149 - 0.186: 2 Chirality restraints: 1236 Sorted by residual: chirality pdb=" CA ASN A 50 " pdb=" N ASN A 50 " pdb=" C ASN A 50 " pdb=" CB ASN A 50 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.68e-01 chirality pdb=" CB VAL N 110 " pdb=" CA VAL N 110 " pdb=" CG1 VAL N 110 " pdb=" CG2 VAL N 110 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.18e-01 chirality pdb=" CA THR R 630 " pdb=" N THR R 630 " pdb=" C THR R 630 " pdb=" CB THR R 630 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.44e-01 ... (remaining 1233 not shown) Planarity restraints: 1385 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 49 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.94e+00 pdb=" C ASP A 49 " 0.034 2.00e-02 2.50e+03 pdb=" O ASP A 49 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN A 50 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 252 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.06e+00 pdb=" C ASP A 252 " -0.030 2.00e-02 2.50e+03 pdb=" O ASP A 252 " 0.011 2.00e-02 2.50e+03 pdb=" N TYR A 253 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG R 598 " 0.007 2.00e-02 2.50e+03 1.40e-02 1.95e+00 pdb=" C ARG R 598 " -0.024 2.00e-02 2.50e+03 pdb=" O ARG R 598 " 0.009 2.00e-02 2.50e+03 pdb=" N ASN R 599 " 0.008 2.00e-02 2.50e+03 ... (remaining 1382 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 516 2.74 - 3.28: 7936 3.28 - 3.82: 13282 3.82 - 4.36: 15829 4.36 - 4.90: 27202 Nonbonded interactions: 64765 Sorted by model distance: nonbonded pdb=" O THR R 596 " pdb=" ND2 ASN R 599 " model vdw 2.200 3.120 nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.217 3.040 nonbonded pdb=" O ASP R 696 " pdb=" OG1 THR R 700 " model vdw 2.262 3.040 nonbonded pdb=" NE2 GLN B 220 " pdb=" OD1 ASP B 258 " model vdw 2.307 3.120 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.314 3.040 ... (remaining 64760 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.660 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.230 Find NCS groups from input model: 0.030 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:7.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 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 : 0.002 0.031 7995 Z= 0.111 Angle : 0.515 9.441 10851 Z= 0.276 Chirality : 0.041 0.186 1236 Planarity : 0.003 0.040 1385 Dihedral : 12.858 89.384 2828 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.79 (0.27), residues: 998 helix: 1.38 (0.29), residues: 369 sheet: 0.65 (0.34), residues: 224 loop : -0.27 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 8 TYR 0.013 0.001 TYR R 789 PHE 0.010 0.001 PHE N 29 TRP 0.014 0.001 TRP B 169 HIS 0.009 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00202 ( 7992) covalent geometry : angle 0.51252 (10845) SS BOND : bond 0.00493 ( 3) SS BOND : angle 2.01796 ( 6) hydrogen bonds : bond 0.13208 ( 384) hydrogen bonds : angle 5.84025 ( 1104) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.290 Fit side-chains REVERT: A 55 THR cc_start: 0.7759 (m) cc_final: 0.7467 (p) REVERT: A 307 LYS cc_start: 0.7889 (mmtt) cc_final: 0.7655 (mmmt) REVERT: A 343 ASP cc_start: 0.6462 (m-30) cc_final: 0.6038 (m-30) REVERT: R 804 LEU cc_start: 0.8517 (tt) cc_final: 0.8243 (tp) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.5107 time to fit residues: 84.1616 Evaluate side-chains 122 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.1980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 371 ASN B 32 GLN B 175 GLN B 266 HIS B 340 ASN N 31 ASN R 562 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.167520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.131647 restraints weight = 8142.910| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.67 r_work: 0.3353 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 7995 Z= 0.221 Angle : 0.647 8.717 10851 Z= 0.343 Chirality : 0.045 0.162 1236 Planarity : 0.004 0.045 1385 Dihedral : 4.564 30.323 1095 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.82 % Allowed : 10.02 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 0.94 (0.27), residues: 998 helix: 1.79 (0.28), residues: 356 sheet: 0.42 (0.34), residues: 216 loop : -0.19 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 8 TYR 0.026 0.002 TYR B 59 PHE 0.018 0.002 PHE R 665 TRP 0.012 0.002 TRP B 339 HIS 0.014 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00517 ( 7992) covalent geometry : angle 0.63904 (10845) SS BOND : bond 0.01014 ( 3) SS BOND : angle 4.32590 ( 6) hydrogen bonds : bond 0.04783 ( 384) hydrogen bonds : angle 4.64820 ( 1104) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 0.240 Fit side-chains REVERT: A 38 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.6962 (mtt180) REVERT: B 156 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8566 (pt0) REVERT: N 31 ASN cc_start: 0.8439 (m-40) cc_final: 0.8135 (m-40) REVERT: R 551 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8414 (mmm) REVERT: R 635 MET cc_start: 0.6092 (tmt) cc_final: 0.5796 (tmt) outliers start: 32 outliers final: 14 residues processed: 133 average time/residue: 0.4947 time to fit residues: 70.0840 Evaluate side-chains 124 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 551 MET Chi-restraints excluded: chain R residue 586 VAL Chi-restraints excluded: chain R residue 660 MET Chi-restraints excluded: chain R residue 700 THR Chi-restraints excluded: chain R residue 771 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 57 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 75 optimal weight: 0.1980 chunk 11 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 75 GLN B 175 GLN B 266 HIS R 562 HIS R 600 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.168874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.132132 restraints weight = 8142.877| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.74 r_work: 0.3377 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7995 Z= 0.136 Angle : 0.531 8.259 10851 Z= 0.284 Chirality : 0.041 0.151 1236 Planarity : 0.003 0.041 1385 Dihedral : 4.312 31.299 1095 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.82 % Allowed : 15.39 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 0.97 (0.27), residues: 998 helix: 1.95 (0.28), residues: 357 sheet: 0.43 (0.33), residues: 214 loop : -0.31 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 317 TYR 0.011 0.001 TYR N 95 PHE 0.011 0.001 PHE A 212 TRP 0.015 0.002 TRP B 169 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 7992) covalent geometry : angle 0.52343 (10845) SS BOND : bond 0.00351 ( 3) SS BOND : angle 3.80505 ( 6) hydrogen bonds : bond 0.03813 ( 384) hydrogen bonds : angle 4.35657 ( 1104) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 0.288 Fit side-chains REVERT: A 229 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.7483 (p0) REVERT: A 314 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7453 (mm-30) REVERT: B 156 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8388 (pt0) REVERT: N 43 LYS cc_start: 0.7384 (mtpp) cc_final: 0.6607 (mmtp) REVERT: N 57 SER cc_start: 0.7727 (t) cc_final: 0.7397 (m) REVERT: N 77 ASN cc_start: 0.7987 (m-40) cc_final: 0.7617 (m-40) REVERT: R 635 MET cc_start: 0.5989 (OUTLIER) cc_final: 0.5679 (tmt) outliers start: 32 outliers final: 13 residues processed: 126 average time/residue: 0.5289 time to fit residues: 70.8728 Evaluate side-chains 121 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 635 MET Chi-restraints excluded: chain R residue 692 SER Chi-restraints excluded: chain R residue 700 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 67 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 266 HIS R 562 HIS R 600 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.163338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.125854 restraints weight = 8224.882| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.80 r_work: 0.3275 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 7995 Z= 0.237 Angle : 0.647 11.685 10851 Z= 0.344 Chirality : 0.046 0.188 1236 Planarity : 0.005 0.070 1385 Dihedral : 4.755 31.839 1095 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 5.01 % Allowed : 16.59 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 0.65 (0.26), residues: 998 helix: 1.60 (0.28), residues: 360 sheet: 0.51 (0.34), residues: 210 loop : -0.58 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG N 72 TYR 0.017 0.002 TYR N 95 PHE 0.015 0.002 PHE A 208 TRP 0.016 0.002 TRP B 82 HIS 0.009 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00561 ( 7992) covalent geometry : angle 0.63945 (10845) SS BOND : bond 0.00735 ( 3) SS BOND : angle 4.15365 ( 6) hydrogen bonds : bond 0.04781 ( 384) hydrogen bonds : angle 4.61222 ( 1104) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 100 time to evaluate : 0.238 Fit side-chains REVERT: A 229 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7595 (p0) REVERT: A 268 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7407 (tt0) REVERT: A 314 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7546 (mm-30) REVERT: N 77 ASN cc_start: 0.8053 (m-40) cc_final: 0.7796 (m-40) REVERT: R 635 MET cc_start: 0.6170 (OUTLIER) cc_final: 0.5935 (tmt) REVERT: R 735 THR cc_start: 0.7804 (m) cc_final: 0.7530 (p) outliers start: 42 outliers final: 21 residues processed: 125 average time/residue: 0.5080 time to fit residues: 67.6839 Evaluate side-chains 121 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 586 VAL Chi-restraints excluded: chain R residue 635 MET Chi-restraints excluded: chain R residue 660 MET Chi-restraints excluded: chain R residue 692 SER Chi-restraints excluded: chain R residue 700 THR Chi-restraints excluded: chain R residue 771 THR Chi-restraints excluded: chain R residue 777 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN R 562 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.165623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.128538 restraints weight = 8108.245| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.80 r_work: 0.3301 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7995 Z= 0.161 Angle : 0.559 10.687 10851 Z= 0.299 Chirality : 0.042 0.149 1236 Planarity : 0.003 0.041 1385 Dihedral : 4.484 31.784 1095 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.89 % Allowed : 17.06 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 0.69 (0.26), residues: 998 helix: 1.70 (0.28), residues: 362 sheet: 0.42 (0.34), residues: 212 loop : -0.58 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 317 TYR 0.013 0.001 TYR N 95 PHE 0.012 0.002 PHE B 199 TRP 0.017 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 7992) covalent geometry : angle 0.55197 (10845) SS BOND : bond 0.00394 ( 3) SS BOND : angle 3.87529 ( 6) hydrogen bonds : bond 0.04068 ( 384) hydrogen bonds : angle 4.41567 ( 1104) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 101 time to evaluate : 0.280 Fit side-chains REVERT: A 229 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7650 (p0) REVERT: A 268 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7390 (tt0) REVERT: A 314 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7986 (mm-30) REVERT: B 156 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8321 (pt0) REVERT: N 43 LYS cc_start: 0.7685 (mtpp) cc_final: 0.6891 (mmtp) REVERT: N 77 ASN cc_start: 0.8060 (m-40) cc_final: 0.7792 (m-40) REVERT: R 635 MET cc_start: 0.6105 (OUTLIER) cc_final: 0.5832 (tmt) REVERT: R 735 THR cc_start: 0.7730 (m) cc_final: 0.7476 (p) outliers start: 41 outliers final: 17 residues processed: 125 average time/residue: 0.4960 time to fit residues: 66.1431 Evaluate side-chains 116 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 576 LEU Chi-restraints excluded: chain R residue 586 VAL Chi-restraints excluded: chain R residue 635 MET Chi-restraints excluded: chain R residue 692 SER Chi-restraints excluded: chain R residue 700 THR Chi-restraints excluded: chain R residue 757 LEU Chi-restraints excluded: chain R residue 777 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 65 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 79 optimal weight: 0.2980 chunk 21 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 29 optimal weight: 0.0970 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 175 GLN B 340 ASN R 562 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.167596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.130899 restraints weight = 8091.740| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.78 r_work: 0.3329 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7995 Z= 0.124 Angle : 0.515 7.504 10851 Z= 0.276 Chirality : 0.041 0.148 1236 Planarity : 0.003 0.039 1385 Dihedral : 4.301 35.080 1095 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.46 % Allowed : 19.57 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 0.82 (0.27), residues: 998 helix: 1.92 (0.28), residues: 362 sheet: 0.35 (0.34), residues: 214 loop : -0.53 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 317 TYR 0.009 0.001 TYR N 95 PHE 0.012 0.001 PHE B 199 TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 7992) covalent geometry : angle 0.50935 (10845) SS BOND : bond 0.00320 ( 3) SS BOND : angle 3.17816 ( 6) hydrogen bonds : bond 0.03683 ( 384) hydrogen bonds : angle 4.28435 ( 1104) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.324 Fit side-chains REVERT: A 268 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7369 (tt0) REVERT: A 314 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.8000 (mm-30) REVERT: B 134 ARG cc_start: 0.6651 (OUTLIER) cc_final: 0.6406 (ttp80) REVERT: N 43 LYS cc_start: 0.7657 (mtpp) cc_final: 0.6914 (mmtp) REVERT: N 77 ASN cc_start: 0.8049 (m-40) cc_final: 0.7786 (m-40) REVERT: R 635 MET cc_start: 0.6070 (OUTLIER) cc_final: 0.5827 (tmt) REVERT: R 735 THR cc_start: 0.7933 (m) cc_final: 0.7669 (p) outliers start: 29 outliers final: 15 residues processed: 122 average time/residue: 0.4996 time to fit residues: 65.0314 Evaluate side-chains 116 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 566 LEU Chi-restraints excluded: chain R residue 635 MET Chi-restraints excluded: chain R residue 692 SER Chi-restraints excluded: chain R residue 700 THR Chi-restraints excluded: chain R residue 757 LEU Chi-restraints excluded: chain R residue 777 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 50 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 22 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 66 optimal weight: 0.3980 chunk 59 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN R 562 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.166582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.129097 restraints weight = 8098.284| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.78 r_work: 0.3343 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7995 Z= 0.142 Angle : 0.534 7.457 10851 Z= 0.286 Chirality : 0.042 0.154 1236 Planarity : 0.003 0.039 1385 Dihedral : 4.419 36.721 1095 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.70 % Allowed : 19.21 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 0.82 (0.27), residues: 998 helix: 1.93 (0.28), residues: 362 sheet: 0.32 (0.34), residues: 214 loop : -0.52 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 317 TYR 0.011 0.001 TYR N 95 PHE 0.013 0.001 PHE B 199 TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 7992) covalent geometry : angle 0.52834 (10845) SS BOND : bond 0.00378 ( 3) SS BOND : angle 3.39765 ( 6) hydrogen bonds : bond 0.03816 ( 384) hydrogen bonds : angle 4.29484 ( 1104) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.339 Fit side-chains REVERT: A 268 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7362 (tt0) REVERT: A 314 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7989 (mm-30) REVERT: N 43 LYS cc_start: 0.7641 (mtpp) cc_final: 0.6918 (mmtp) REVERT: N 77 ASN cc_start: 0.8023 (m-40) cc_final: 0.7771 (m-40) REVERT: R 635 MET cc_start: 0.6091 (OUTLIER) cc_final: 0.5815 (tmt) REVERT: R 735 THR cc_start: 0.7990 (m) cc_final: 0.7717 (p) outliers start: 31 outliers final: 16 residues processed: 118 average time/residue: 0.5160 time to fit residues: 64.8008 Evaluate side-chains 112 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 566 LEU Chi-restraints excluded: chain R residue 576 LEU Chi-restraints excluded: chain R residue 635 MET Chi-restraints excluded: chain R residue 692 SER Chi-restraints excluded: chain R residue 695 MET Chi-restraints excluded: chain R residue 700 THR Chi-restraints excluded: chain R residue 757 LEU Chi-restraints excluded: chain R residue 777 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 92 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 79 optimal weight: 0.0000 chunk 32 optimal weight: 0.8980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN R 562 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.167594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.130104 restraints weight = 8046.583| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.76 r_work: 0.3348 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7995 Z= 0.131 Angle : 0.523 8.905 10851 Z= 0.279 Chirality : 0.041 0.158 1236 Planarity : 0.003 0.039 1385 Dihedral : 4.327 35.984 1095 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.98 % Allowed : 20.64 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 0.86 (0.27), residues: 998 helix: 1.99 (0.28), residues: 362 sheet: 0.27 (0.34), residues: 215 loop : -0.49 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 317 TYR 0.010 0.001 TYR N 95 PHE 0.012 0.001 PHE B 199 TRP 0.015 0.002 TRP B 169 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 7992) covalent geometry : angle 0.51785 (10845) SS BOND : bond 0.00277 ( 3) SS BOND : angle 3.07993 ( 6) hydrogen bonds : bond 0.03683 ( 384) hydrogen bonds : angle 4.23876 ( 1104) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.303 Fit side-chains REVERT: A 268 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7356 (tt0) REVERT: A 314 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7996 (mm-30) REVERT: N 43 LYS cc_start: 0.7644 (mtpp) cc_final: 0.6955 (mmtp) REVERT: N 77 ASN cc_start: 0.8008 (m-40) cc_final: 0.7783 (m-40) REVERT: R 635 MET cc_start: 0.6089 (OUTLIER) cc_final: 0.5832 (tmt) REVERT: R 735 THR cc_start: 0.7990 (m) cc_final: 0.7733 (p) outliers start: 25 outliers final: 18 residues processed: 115 average time/residue: 0.5301 time to fit residues: 64.8854 Evaluate side-chains 117 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 566 LEU Chi-restraints excluded: chain R residue 576 LEU Chi-restraints excluded: chain R residue 635 MET Chi-restraints excluded: chain R residue 692 SER Chi-restraints excluded: chain R residue 695 MET Chi-restraints excluded: chain R residue 700 THR Chi-restraints excluded: chain R residue 757 LEU Chi-restraints excluded: chain R residue 766 LEU Chi-restraints excluded: chain R residue 777 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 0.4980 chunk 89 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN R 562 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.166300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.129021 restraints weight = 8111.419| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.81 r_work: 0.3342 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7995 Z= 0.148 Angle : 0.542 8.641 10851 Z= 0.289 Chirality : 0.042 0.164 1236 Planarity : 0.003 0.039 1385 Dihedral : 4.415 35.775 1095 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.74 % Allowed : 21.12 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 0.80 (0.27), residues: 998 helix: 1.92 (0.28), residues: 362 sheet: 0.24 (0.33), residues: 220 loop : -0.51 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 317 TYR 0.012 0.001 TYR N 95 PHE 0.012 0.002 PHE B 199 TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 7992) covalent geometry : angle 0.53702 (10845) SS BOND : bond 0.00310 ( 3) SS BOND : angle 3.14850 ( 6) hydrogen bonds : bond 0.03867 ( 384) hydrogen bonds : angle 4.30346 ( 1104) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.309 Fit side-chains REVERT: A 268 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7305 (tt0) REVERT: A 314 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7505 (mm-30) REVERT: N 43 LYS cc_start: 0.7609 (mtpp) cc_final: 0.6886 (mmtp) REVERT: N 67 ARG cc_start: 0.6824 (ttm170) cc_final: 0.6604 (ttm170) REVERT: N 77 ASN cc_start: 0.8030 (m-40) cc_final: 0.7780 (m-40) REVERT: R 635 MET cc_start: 0.6103 (OUTLIER) cc_final: 0.5822 (tmt) REVERT: R 735 THR cc_start: 0.8014 (m) cc_final: 0.7730 (p) outliers start: 23 outliers final: 18 residues processed: 118 average time/residue: 0.5260 time to fit residues: 66.1422 Evaluate side-chains 120 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 566 LEU Chi-restraints excluded: chain R residue 576 LEU Chi-restraints excluded: chain R residue 635 MET Chi-restraints excluded: chain R residue 692 SER Chi-restraints excluded: chain R residue 700 THR Chi-restraints excluded: chain R residue 757 LEU Chi-restraints excluded: chain R residue 766 LEU Chi-restraints excluded: chain R residue 777 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 50 optimal weight: 0.7980 chunk 86 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN R 562 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.166418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.128948 restraints weight = 8052.126| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.75 r_work: 0.3337 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7995 Z= 0.145 Angle : 0.536 8.413 10851 Z= 0.287 Chirality : 0.042 0.173 1236 Planarity : 0.003 0.037 1385 Dihedral : 4.403 35.889 1095 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.74 % Allowed : 21.36 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 0.80 (0.27), residues: 998 helix: 1.91 (0.28), residues: 362 sheet: 0.22 (0.33), residues: 221 loop : -0.49 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 317 TYR 0.011 0.001 TYR A 253 PHE 0.012 0.001 PHE B 199 TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 7992) covalent geometry : angle 0.53147 (10845) SS BOND : bond 0.00302 ( 3) SS BOND : angle 3.08192 ( 6) hydrogen bonds : bond 0.03798 ( 384) hydrogen bonds : angle 4.27762 ( 1104) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.318 Fit side-chains REVERT: A 268 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7359 (tt0) REVERT: A 314 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7547 (mm-30) REVERT: N 43 LYS cc_start: 0.7592 (mtpp) cc_final: 0.6901 (mmtp) REVERT: N 67 ARG cc_start: 0.6860 (ttm170) cc_final: 0.6634 (ttm170) REVERT: N 77 ASN cc_start: 0.8031 (m-40) cc_final: 0.7796 (m-40) REVERT: R 635 MET cc_start: 0.6128 (OUTLIER) cc_final: 0.5845 (tmt) REVERT: R 735 THR cc_start: 0.8031 (m) cc_final: 0.7770 (p) outliers start: 23 outliers final: 19 residues processed: 115 average time/residue: 0.5270 time to fit residues: 64.6365 Evaluate side-chains 119 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 566 LEU Chi-restraints excluded: chain R residue 576 LEU Chi-restraints excluded: chain R residue 635 MET Chi-restraints excluded: chain R residue 692 SER Chi-restraints excluded: chain R residue 695 MET Chi-restraints excluded: chain R residue 700 THR Chi-restraints excluded: chain R residue 757 LEU Chi-restraints excluded: chain R residue 766 LEU Chi-restraints excluded: chain R residue 777 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 70 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 79 optimal weight: 10.0000 chunk 90 optimal weight: 0.1980 chunk 19 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN R 562 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.167955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.130860 restraints weight = 8080.403| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.73 r_work: 0.3333 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7995 Z= 0.146 Angle : 0.539 8.103 10851 Z= 0.288 Chirality : 0.042 0.163 1236 Planarity : 0.003 0.038 1385 Dihedral : 4.405 35.785 1095 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.98 % Allowed : 20.88 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 0.81 (0.27), residues: 998 helix: 1.91 (0.28), residues: 362 sheet: 0.25 (0.33), residues: 220 loop : -0.50 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 317 TYR 0.012 0.001 TYR N 95 PHE 0.012 0.001 PHE B 199 TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 7992) covalent geometry : angle 0.53426 (10845) SS BOND : bond 0.00293 ( 3) SS BOND : angle 3.05662 ( 6) hydrogen bonds : bond 0.03816 ( 384) hydrogen bonds : angle 4.29250 ( 1104) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3076.48 seconds wall clock time: 52 minutes 57.58 seconds (3177.58 seconds total)