Starting phenix.real_space_refine on Tue Aug 4 20:36:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8oif_16891/08_2026/8oif_16891.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oif_16891/08_2026/8oif_16891.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8oif_16891/08_2026/8oif_16891.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8oif_16891/08_2026/8oif_16891.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8oif_16891/08_2026/8oif_16891.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oif_16891/08_2026/8oif_16891.map" model { file = "/net/cci-nas-00/data/ceres_data/8oif_16891/08_2026/8oif_16891.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oif_16891/08_2026/8oif_16891.cif" } resolution = 3.5 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 20 5.16 5 C 4237 2.51 5 N 1166 2.21 5 O 1165 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6589 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 4939 Classifications: {'peptide': 704} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'PTRANS': 41, 'TRANS': 662} Chain breaks: 8 Unresolved non-hydrogen bonds: 509 Unresolved non-hydrogen angles: 631 Unresolved non-hydrogen dihedrals: 411 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLU:plan': 31, 'ASP:plan': 19, 'ARG:plan': 14, 'GLN:plan1': 20, 'PHE:plan': 2, 'HIS:plan': 5, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 384 Chain: "I" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 560 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 74} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 5, 'ARG:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 47 Chain: "L" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1067 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 132} Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 5, 'GLN:plan1': 2, 'ASN:plan1': 2, 'TYR:plan': 1, 'ARG:plan': 5, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 109 Chain: "I" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 1.54, per 1000 atoms: 0.23 Number of scatterers: 6589 At special positions: 0 Unit cell: (110.656, 118.317, 82.5664, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 P 1 15.00 O 1165 8.00 N 1166 7.00 C 4237 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 599 " - pdb=" SG CYS L 86 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.52 Conformation dependent library (CDL) restraints added in 476.2 milliseconds 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1748 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 8 sheets defined 37.9% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 42 through 55 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 86 through 100 removed outlier: 4.417A pdb=" N GLU A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LEU A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASN A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 119 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 266 through 271 Processing helix chain 'A' and resid 281 through 305 removed outlier: 4.411A pdb=" N HIS A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N HIS A 286 " --> pdb=" O GLN A 282 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A 287 " --> pdb=" O GLU A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 removed outlier: 3.579A pdb=" N ALA A 316 " --> pdb=" O ASP A 312 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 353 Processing helix chain 'A' and resid 357 through 375 Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 423 through 433 removed outlier: 3.507A pdb=" N GLN A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG A 432 " --> pdb=" O GLU A 428 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN A 433 " --> pdb=" O LYS A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 455 removed outlier: 3.723A pdb=" N GLU A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 480 removed outlier: 3.615A pdb=" N SER A 478 " --> pdb=" O SER A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 488 removed outlier: 3.741A pdb=" N VAL A 488 " --> pdb=" O SER A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 504 removed outlier: 3.638A pdb=" N VAL A 495 " --> pdb=" O PRO A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 532 removed outlier: 3.977A pdb=" N ARG A 531 " --> pdb=" O ASN A 527 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL A 532 " --> pdb=" O PHE A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 556 Processing helix chain 'A' and resid 585 through 592 removed outlier: 3.531A pdb=" N SER A 591 " --> pdb=" O SER A 587 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU A 592 " --> pdb=" O ALA A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 615 Processing helix chain 'A' and resid 853 through 872 removed outlier: 3.746A pdb=" N THR A 857 " --> pdb=" O ILE A 853 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS A 870 " --> pdb=" O LEU A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 891 No H-bonds generated for 'chain 'A' and resid 889 through 891' Processing helix chain 'A' and resid 927 through 939 Processing helix chain 'A' and resid 959 through 967 removed outlier: 3.609A pdb=" N HIS A 966 " --> pdb=" O LYS A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 979 Processing helix chain 'I' and resid 103 through 116 removed outlier: 3.680A pdb=" N LEU I 107 " --> pdb=" O THR I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 136 through 141 removed outlier: 4.384A pdb=" N TYR I 140 " --> pdb=" O PRO I 136 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY I 141 " --> pdb=" O LEU I 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 136 through 141' Processing helix chain 'L' and resid 4 through 17 removed outlier: 4.081A pdb=" N VAL L 8 " --> pdb=" O SER L 4 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU L 12 " --> pdb=" O VAL L 8 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP L 13 " --> pdb=" O LYS L 9 " (cutoff:3.500A) Processing helix chain 'L' and resid 100 through 114 removed outlier: 3.732A pdb=" N VAL L 104 " --> pdb=" O LYS L 100 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG L 114 " --> pdb=" O VAL L 110 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 132 removed outlier: 3.637A pdb=" N ASP L 127 " --> pdb=" O MET L 123 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU L 128 " --> pdb=" O ASP L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 147 removed outlier: 3.570A pdb=" N PHE L 136 " --> pdb=" O ASN L 132 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU L 141 " --> pdb=" O ARG L 137 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU L 142 " --> pdb=" O LYS L 138 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 106 removed outlier: 6.207A pdb=" N LEU A 59 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL A 35 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N HIS A 62 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL A 37 " --> pdb=" O HIS A 62 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ARG A 34 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N VAL A 123 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU A 36 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N THR A 125 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N SER A 38 " --> pdb=" O THR A 125 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 155 " --> pdb=" O ARG A 152 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 168 Processing sheet with id=AA3, first strand: chain 'A' and resid 178 through 179 removed outlier: 3.721A pdb=" N VAL A 209 " --> pdb=" O ARG A 226 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 509 through 512 removed outlier: 6.511A pdb=" N TYR A 435 " --> pdb=" O THR A 465 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N VAL A 467 " --> pdb=" O TYR A 435 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU A 437 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA A 562 " --> pdb=" O ALA A 537 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 904 through 906 Processing sheet with id=AA6, first strand: chain 'A' and resid 917 through 919 removed outlier: 6.543A pdb=" N LEU A 917 " --> pdb=" O HIS A1009 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLU A1011 " --> pdb=" O LEU A 917 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL A 919 " --> pdb=" O GLU A1011 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU A 946 " --> pdb=" O LEU A 953 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 93 through 98 Processing sheet with id=AA8, first strand: chain 'L' and resid 23 through 26 removed outlier: 4.248A pdb=" N LEU L 25 " --> pdb=" O HIS L 36 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N HIS L 36 " --> pdb=" O LEU L 25 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA L 37 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU L 53 " --> pdb=" O ALA L 37 " (cutoff:3.500A) 280 hydrogen bonds defined for protein. 759 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: 1.28 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2169 1.34 - 1.46: 1537 1.46 - 1.58: 3014 1.58 - 1.70: 1 1.70 - 1.82: 27 Bond restraints: 6748 Sorted by residual: bond pdb=" CG PRO A 382 " pdb=" CD PRO A 382 " ideal model delta sigma weight residual 1.503 1.549 -0.046 3.40e-02 8.65e+02 1.85e+00 bond pdb=" C LEU A 456 " pdb=" N GLY A 457 " ideal model delta sigma weight residual 1.331 1.311 0.020 1.46e-02 4.69e+03 1.82e+00 bond pdb=" C4 AMP I 201 " pdb=" C5 AMP I 201 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.43e+00 bond pdb=" CB PRO A 382 " pdb=" CG PRO A 382 " ideal model delta sigma weight residual 1.492 1.551 -0.059 5.00e-02 4.00e+02 1.41e+00 bond pdb=" CA GLU A 113 " pdb=" CB GLU A 113 " ideal model delta sigma weight residual 1.524 1.536 -0.012 1.31e-02 5.83e+03 8.95e-01 ... (remaining 6743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 9103 1.87 - 3.73: 144 3.73 - 5.60: 28 5.60 - 7.46: 4 7.46 - 9.33: 1 Bond angle restraints: 9280 Sorted by residual: angle pdb=" CA PRO A 382 " pdb=" N PRO A 382 " pdb=" CD PRO A 382 " ideal model delta sigma weight residual 112.00 106.39 5.61 1.40e+00 5.10e-01 1.61e+01 angle pdb=" N VAL A 102 " pdb=" CA VAL A 102 " pdb=" C VAL A 102 " ideal model delta sigma weight residual 113.71 109.95 3.76 9.50e-01 1.11e+00 1.57e+01 angle pdb=" CG1 ILE L 55 " pdb=" CB ILE L 55 " pdb=" CG2 ILE L 55 " ideal model delta sigma weight residual 110.70 101.37 9.33 3.00e+00 1.11e-01 9.67e+00 angle pdb=" N GLU A 113 " pdb=" CA GLU A 113 " pdb=" C GLU A 113 " ideal model delta sigma weight residual 111.81 107.53 4.28 1.44e+00 4.82e-01 8.84e+00 angle pdb=" CB MET A 54 " pdb=" CG MET A 54 " pdb=" SD MET A 54 " ideal model delta sigma weight residual 112.70 119.83 -7.13 3.00e+00 1.11e-01 5.64e+00 ... (remaining 9275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.94: 3753 23.94 - 47.87: 193 47.87 - 71.81: 10 71.81 - 95.75: 1 95.75 - 119.68: 1 Dihedral angle restraints: 3958 sinusoidal: 1265 harmonic: 2693 Sorted by residual: dihedral pdb=" C5' AMP I 201 " pdb=" O5' AMP I 201 " pdb=" P AMP I 201 " pdb=" O3P AMP I 201 " ideal model delta sinusoidal sigma weight residual -60.00 -179.68 119.68 1 2.00e+01 2.50e-03 3.59e+01 dihedral pdb=" CA HIS A 907 " pdb=" C HIS A 907 " pdb=" N HIS A 908 " pdb=" CA HIS A 908 " ideal model delta harmonic sigma weight residual 180.00 154.83 25.17 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA PHE A 906 " pdb=" C PHE A 906 " pdb=" N HIS A 907 " pdb=" CA HIS A 907 " ideal model delta harmonic sigma weight residual 180.00 -161.21 -18.79 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 3955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 870 0.042 - 0.085: 206 0.085 - 0.127: 55 0.127 - 0.169: 1 0.169 - 0.211: 2 Chirality restraints: 1134 Sorted by residual: chirality pdb=" CB ILE L 55 " pdb=" CA ILE L 55 " pdb=" CG1 ILE L 55 " pdb=" CG2 ILE L 55 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CB ILE L 68 " pdb=" CA ILE L 68 " pdb=" CG1 ILE L 68 " pdb=" CG2 ILE L 68 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA ILE L 55 " pdb=" N ILE L 55 " pdb=" C ILE L 55 " pdb=" CB ILE L 55 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 1131 not shown) Planarity restraints: 1191 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 381 " 0.078 5.00e-02 4.00e+02 1.15e-01 2.11e+01 pdb=" N PRO A 382 " -0.199 5.00e-02 4.00e+02 pdb=" CA PRO A 382 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 382 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 594 " 0.043 5.00e-02 4.00e+02 6.48e-02 6.73e+00 pdb=" N PRO A 595 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 595 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 595 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 395 " -0.037 5.00e-02 4.00e+02 5.59e-02 5.00e+00 pdb=" N PRO A 396 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 396 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 396 " -0.031 5.00e-02 4.00e+02 ... (remaining 1188 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1320 2.78 - 3.31: 5865 3.31 - 3.84: 10156 3.84 - 4.37: 10721 4.37 - 4.90: 20038 Nonbonded interactions: 48100 Sorted by model distance: nonbonded pdb=" OG1 THR I 125 " pdb=" OD1 ASN I 151 " model vdw 2.246 3.040 nonbonded pdb=" OH TYR L 46 " pdb=" O TYR L 75 " model vdw 2.252 3.040 nonbonded pdb=" O THR A 927 " pdb=" OG SER A 930 " model vdw 2.259 3.040 nonbonded pdb=" OG SER I 112 " pdb=" O VAL I 117 " model vdw 2.280 3.040 nonbonded pdb=" O ASN A 527 " pdb=" OG SER A 530 " model vdw 2.302 3.040 ... (remaining 48095 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 group one per residue 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: 1.380 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: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 7.980 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 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 : 0.004 0.247 6750 Z= 0.332 Angle : 0.595 9.327 9282 Z= 0.295 Chirality : 0.039 0.211 1134 Planarity : 0.006 0.115 1191 Dihedral : 13.828 119.684 2207 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 0.00 % Allowed : 12.11 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -0.42 (0.29), residues: 912 helix: 1.47 (0.31), residues: 316 sheet: -0.16 (0.45), residues: 137 loop : -1.65 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 85 TYR 0.008 0.001 TYR A 596 PHE 0.009 0.001 PHE A 483 TRP 0.007 0.001 TRP I 123 HIS 0.005 0.001 HIS A 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 6748) covalent geometry : angle 0.59552 / 0.30 ( 9280) SS BOND : bond 0.00002 / 0.00 ( 1) SS BOND : angle 0.32219 / 0.21 ( 2) hydrogen bonds : bond 0.15334 / 10.53 ( 280) hydrogen bonds : angle 5.30972 / 3.92 ( 759) Misc. bond : bond 0.24679 / 12.99 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.268 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0387 time to fit residues: 2.2676 Evaluate side-chains 32 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.0870 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1009 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.087555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.071533 restraints weight = 18812.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.072889 restraints weight = 11396.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.073807 restraints weight = 8314.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.074328 restraints weight = 6786.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.074767 restraints weight = 5995.176| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.0637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6750 Z= 0.157 Angle : 0.596 7.399 9282 Z= 0.289 Chirality : 0.040 0.172 1134 Planarity : 0.006 0.079 1191 Dihedral : 6.325 112.325 989 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 1.49 % Allowed : 15.42 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -0.49 (0.29), residues: 912 helix: 1.45 (0.31), residues: 314 sheet: -0.12 (0.49), residues: 121 loop : -1.68 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 258 TYR 0.009 0.001 TYR A 596 PHE 0.009 0.001 PHE A1005 TRP 0.009 0.001 TRP A 69 HIS 0.006 0.001 HIS A 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 6748) covalent geometry : angle 0.59645 / 0.29 ( 9280) SS BOND : bond 0.00024 / 0.01 ( 1) SS BOND : angle 0.37046 / 0.25 ( 2) hydrogen bonds : bond 0.03679 / 2.58 ( 280) hydrogen bonds : angle 4.45935 / 3.23 ( 759) Misc. bond : bond 0.00019 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.169 Fit side-chains REVERT: A 1005 PHE cc_start: 0.6597 (OUTLIER) cc_final: 0.5685 (t80) outliers start: 9 outliers final: 5 residues processed: 42 average time/residue: 0.0402 time to fit residues: 2.9272 Evaluate side-chains 37 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain L residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 1 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 90 optimal weight: 0.0970 chunk 58 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1009 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.089106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.073213 restraints weight = 18505.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.074608 restraints weight = 11105.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.075564 restraints weight = 8047.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.076175 restraints weight = 6524.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.076361 restraints weight = 5705.135| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.0808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6750 Z= 0.096 Angle : 0.545 9.871 9282 Z= 0.257 Chirality : 0.038 0.163 1134 Planarity : 0.005 0.070 1191 Dihedral : 5.630 92.540 989 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.66 % Allowed : 17.41 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -0.29 (0.29), residues: 912 helix: 1.63 (0.31), residues: 314 sheet: -0.08 (0.49), residues: 122 loop : -1.55 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 882 TYR 0.007 0.001 TYR A 603 PHE 0.007 0.001 PHE A 483 TRP 0.008 0.001 TRP A 614 HIS 0.004 0.001 HIS A 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 ( 6748) covalent geometry : angle 0.54470 / 0.26 ( 9280) SS BOND : bond 0.00047 / 0.02 ( 1) SS BOND : angle 0.34154 / 0.23 ( 2) hydrogen bonds : bond 0.02767 / 1.93 ( 280) hydrogen bonds : angle 4.05378 / 2.94 ( 759) Misc. bond : bond 0.00026 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.156 Fit side-chains REVERT: A 1005 PHE cc_start: 0.6526 (OUTLIER) cc_final: 0.5445 (t80) outliers start: 10 outliers final: 5 residues processed: 47 average time/residue: 0.0574 time to fit residues: 4.1689 Evaluate side-chains 40 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain L residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 18 optimal weight: 0.0470 chunk 36 optimal weight: 0.1980 chunk 78 optimal weight: 0.0040 chunk 7 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 22 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.4292 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1009 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.090293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.074241 restraints weight = 18520.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.075777 restraints weight = 10648.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.076795 restraints weight = 7486.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.077428 restraints weight = 5961.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.077838 restraints weight = 5176.029| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6750 Z= 0.085 Angle : 0.533 8.650 9282 Z= 0.248 Chirality : 0.038 0.170 1134 Planarity : 0.005 0.057 1191 Dihedral : 4.782 58.005 989 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.32 % Allowed : 17.74 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -0.07 (0.30), residues: 912 helix: 1.72 (0.31), residues: 314 sheet: 0.17 (0.45), residues: 146 loop : -1.48 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 551 TYR 0.006 0.001 TYR A 603 PHE 0.007 0.001 PHE A 483 TRP 0.008 0.001 TRP I 123 HIS 0.003 0.001 HIS A 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.08 ( 6748) covalent geometry : angle 0.53335 / 0.25 ( 9280) SS BOND : bond 0.00065 / 0.03 ( 1) SS BOND : angle 0.33997 / 0.23 ( 2) hydrogen bonds : bond 0.02375 / 1.64 ( 280) hydrogen bonds : angle 3.82335 / 2.77 ( 759) Misc. bond : bond 0.00022 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 36 time to evaluate : 0.163 Fit side-chains REVERT: A 1005 PHE cc_start: 0.6447 (OUTLIER) cc_final: 0.5570 (t80) outliers start: 14 outliers final: 9 residues processed: 50 average time/residue: 0.0508 time to fit residues: 4.0089 Evaluate side-chains 44 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain L residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 72 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.085648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.069320 restraints weight = 19226.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.070677 restraints weight = 11677.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.071586 restraints weight = 8519.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.072094 restraints weight = 6970.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.072364 restraints weight = 6188.576| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 6750 Z= 0.244 Angle : 0.685 9.625 9282 Z= 0.331 Chirality : 0.043 0.157 1134 Planarity : 0.006 0.066 1191 Dihedral : 5.242 45.807 989 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 3.15 % Allowed : 17.58 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -0.77 (0.28), residues: 912 helix: 1.26 (0.30), residues: 313 sheet: -0.33 (0.47), residues: 127 loop : -1.87 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 85 TYR 0.013 0.002 TYR A 596 PHE 0.012 0.002 PHE A 389 TRP 0.012 0.002 TRP A 386 HIS 0.008 0.002 HIS A 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.24 ( 6748) covalent geometry : angle 0.68486 / 0.33 ( 9280) SS BOND : bond 0.00087 / 0.05 ( 1) SS BOND : angle 0.32841 / 0.22 ( 2) hydrogen bonds : bond 0.04548 / 3.18 ( 280) hydrogen bonds : angle 4.58200 / 3.29 ( 759) Misc. bond : bond 0.00008 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 33 time to evaluate : 0.233 Fit side-chains REVERT: A 867 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7667 (mm-30) REVERT: A 1005 PHE cc_start: 0.7240 (OUTLIER) cc_final: 0.6103 (t80) REVERT: L 39 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7446 (pt) outliers start: 19 outliers final: 15 residues processed: 51 average time/residue: 0.0379 time to fit residues: 3.3570 Evaluate side-chains 48 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 31 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 85 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 88 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 43 optimal weight: 0.0010 chunk 55 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 overall best weight: 0.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.088156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.072045 restraints weight = 18839.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.073426 restraints weight = 11324.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.074356 restraints weight = 8195.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.074907 restraints weight = 6672.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.075333 restraints weight = 5881.652| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6750 Z= 0.104 Angle : 0.560 7.694 9282 Z= 0.266 Chirality : 0.039 0.166 1134 Planarity : 0.005 0.059 1191 Dihedral : 4.672 46.309 989 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.99 % Allowed : 18.57 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -0.45 (0.29), residues: 912 helix: 1.61 (0.31), residues: 313 sheet: -0.39 (0.46), residues: 128 loop : -1.68 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 263 TYR 0.006 0.001 TYR A 603 PHE 0.006 0.001 PHE A 159 TRP 0.009 0.001 TRP A 614 HIS 0.004 0.001 HIS A 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.10 ( 6748) covalent geometry : angle 0.56008 / 0.27 ( 9280) SS BOND : bond 0.00316 / 0.17 ( 1) SS BOND : angle 1.29850 / 0.87 ( 2) hydrogen bonds : bond 0.02840 / 1.99 ( 280) hydrogen bonds : angle 4.06281 / 2.95 ( 759) Misc. bond : bond 0.00021 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 34 time to evaluate : 0.157 Fit side-chains REVERT: A 867 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7439 (mm-30) REVERT: A 1005 PHE cc_start: 0.6972 (OUTLIER) cc_final: 0.5569 (t80) outliers start: 18 outliers final: 15 residues processed: 50 average time/residue: 0.0344 time to fit residues: 2.9211 Evaluate side-chains 48 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 32 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 85 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 89 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 78 optimal weight: 0.2980 chunk 66 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.088464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.072433 restraints weight = 18553.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.073783 restraints weight = 11180.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.074722 restraints weight = 8152.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.075322 restraints weight = 6634.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.075629 restraints weight = 5813.173| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6750 Z= 0.104 Angle : 0.551 7.847 9282 Z= 0.260 Chirality : 0.039 0.183 1134 Planarity : 0.005 0.058 1191 Dihedral : 4.529 46.520 989 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.48 % Allowed : 17.91 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -0.35 (0.29), residues: 912 helix: 1.67 (0.31), residues: 314 sheet: -0.33 (0.47), residues: 127 loop : -1.60 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 551 TYR 0.008 0.001 TYR A 603 PHE 0.006 0.001 PHE A 159 TRP 0.009 0.001 TRP I 123 HIS 0.004 0.001 HIS A 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.10 ( 6748) covalent geometry : angle 0.55072 / 0.26 ( 9280) SS BOND : bond 0.00328 / 0.17 ( 1) SS BOND : angle 1.04418 / 0.70 ( 2) hydrogen bonds : bond 0.02754 / 1.92 ( 280) hydrogen bonds : angle 3.96333 / 2.87 ( 759) Misc. bond : bond 0.00009 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 35 time to evaluate : 0.162 Fit side-chains REVERT: A 75 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8581 (tm-30) REVERT: A 456 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8490 (tp) REVERT: A 867 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7455 (mm-30) REVERT: A 1005 PHE cc_start: 0.6891 (OUTLIER) cc_final: 0.5552 (t80) outliers start: 21 outliers final: 15 residues processed: 54 average time/residue: 0.0407 time to fit residues: 3.6688 Evaluate side-chains 52 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 34 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 85 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 85 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 60 optimal weight: 0.1980 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.086982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.070725 restraints weight = 18829.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.072082 restraints weight = 11390.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.072925 restraints weight = 8299.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.073548 restraints weight = 6845.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.073812 restraints weight = 6011.622| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6750 Z= 0.158 Angle : 0.604 8.416 9282 Z= 0.290 Chirality : 0.040 0.174 1134 Planarity : 0.005 0.058 1191 Dihedral : 4.814 46.909 989 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.98 % Allowed : 17.41 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -0.50 (0.29), residues: 912 helix: 1.57 (0.31), residues: 313 sheet: -0.41 (0.46), residues: 127 loop : -1.71 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 85 TYR 0.008 0.001 TYR A 596 PHE 0.009 0.001 PHE A 389 TRP 0.008 0.001 TRP I 123 HIS 0.006 0.001 HIS A 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 ( 6748) covalent geometry : angle 0.60426 / 0.29 ( 9280) SS BOND : bond 0.00117 / 0.06 ( 1) SS BOND : angle 0.88733 / 0.59 ( 2) hydrogen bonds : bond 0.03528 / 2.46 ( 280) hydrogen bonds : angle 4.20527 / 3.04 ( 759) Misc. bond : bond 0.00018 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 33 time to evaluate : 0.174 Fit side-chains REVERT: A 75 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8524 (tm-30) REVERT: A 1005 PHE cc_start: 0.7095 (OUTLIER) cc_final: 0.5862 (t80) outliers start: 24 outliers final: 19 residues processed: 55 average time/residue: 0.0358 time to fit residues: 3.3440 Evaluate side-chains 52 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 31 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 85 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 66 optimal weight: 0.0060 chunk 51 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 887 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.088679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.072627 restraints weight = 18676.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.074023 restraints weight = 11188.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.074929 restraints weight = 8073.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.075529 restraints weight = 6593.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.075799 restraints weight = 5784.822| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6750 Z= 0.097 Angle : 0.554 7.845 9282 Z= 0.264 Chirality : 0.038 0.168 1134 Planarity : 0.005 0.069 1191 Dihedral : 4.553 47.194 989 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.65 % Allowed : 17.41 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -0.29 (0.29), residues: 912 helix: 1.72 (0.31), residues: 314 sheet: -0.35 (0.46), residues: 128 loop : -1.55 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 551 TYR 0.005 0.001 TYR A 547 PHE 0.006 0.001 PHE A 159 TRP 0.009 0.001 TRP I 123 HIS 0.004 0.001 HIS A 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 ( 6748) covalent geometry : angle 0.55355 / 0.26 ( 9280) SS BOND : bond 0.00195 / 0.10 ( 1) SS BOND : angle 0.54652 / 0.36 ( 2) hydrogen bonds : bond 0.02622 / 1.83 ( 280) hydrogen bonds : angle 3.93579 / 2.86 ( 759) Misc. bond : bond 0.00000 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 36 time to evaluate : 0.161 Fit side-chains REVERT: A 75 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8541 (tm-30) REVERT: A 456 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8494 (tp) REVERT: A 1005 PHE cc_start: 0.6878 (OUTLIER) cc_final: 0.5538 (t80) outliers start: 22 outliers final: 17 residues processed: 56 average time/residue: 0.0458 time to fit residues: 3.8989 Evaluate side-chains 53 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 33 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 85 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 55 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 43 optimal weight: 0.1980 chunk 45 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 75 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 76 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.089496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.073455 restraints weight = 18690.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.074872 restraints weight = 11221.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.075814 restraints weight = 8103.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.076371 restraints weight = 6582.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.076625 restraints weight = 5800.187| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6750 Z= 0.092 Angle : 0.545 8.000 9282 Z= 0.258 Chirality : 0.039 0.172 1134 Planarity : 0.005 0.058 1191 Dihedral : 4.380 47.204 989 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.99 % Allowed : 18.08 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -0.13 (0.29), residues: 912 helix: 1.76 (0.31), residues: 316 sheet: -0.04 (0.45), residues: 135 loop : -1.49 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 551 TYR 0.007 0.001 TYR A 603 PHE 0.006 0.001 PHE A 159 TRP 0.009 0.001 TRP I 123 HIS 0.004 0.001 HIS A 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.09 ( 6748) covalent geometry : angle 0.54461 / 0.26 ( 9280) SS BOND : bond 0.00072 / 0.04 ( 1) SS BOND : angle 0.55333 / 0.37 ( 2) hydrogen bonds : bond 0.02400 / 1.67 ( 280) hydrogen bonds : angle 3.80982 / 2.76 ( 759) Misc. bond : bond 0.00003 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 39 time to evaluate : 0.159 Fit side-chains REVERT: A 75 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8532 (tm-30) REVERT: A 456 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8481 (tp) REVERT: A 867 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7426 (mm-30) REVERT: A 1005 PHE cc_start: 0.6676 (OUTLIER) cc_final: 0.5467 (t80) outliers start: 18 outliers final: 15 residues processed: 55 average time/residue: 0.0429 time to fit residues: 3.6743 Evaluate side-chains 56 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 38 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 85 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 89 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 0.0970 chunk 20 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 84 optimal weight: 0.0370 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.089755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.073530 restraints weight = 18516.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.075029 restraints weight = 10695.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.076029 restraints weight = 7564.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.076657 restraints weight = 6058.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.076869 restraints weight = 5276.540| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6750 Z= 0.090 Angle : 0.540 7.753 9282 Z= 0.255 Chirality : 0.038 0.171 1134 Planarity : 0.005 0.058 1191 Dihedral : 4.312 47.456 989 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.32 % Allowed : 17.91 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -0.11 (0.29), residues: 912 helix: 1.81 (0.31), residues: 316 sheet: -0.19 (0.47), residues: 127 loop : -1.43 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 551 TYR 0.007 0.001 TYR A 603 PHE 0.006 0.001 PHE A 159 TRP 0.008 0.001 TRP I 123 HIS 0.004 0.001 HIS A 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.09 ( 6748) covalent geometry : angle 0.53985 / 0.25 ( 9280) SS BOND : bond 0.00058 / 0.03 ( 1) SS BOND : angle 0.46711 / 0.31 ( 2) hydrogen bonds : bond 0.02371 / 1.65 ( 280) hydrogen bonds : angle 3.77256 / 2.74 ( 759) Misc. bond : bond 0.00000 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1008.94 seconds wall clock time: 18 minutes 1.06 seconds (1081.06 seconds total)