Starting phenix.real_space_refine on Fri Aug 22 18:06:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oif_16891/08_2025/8oif_16891.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oif_16891/08_2025/8oif_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8oif_16891/08_2025/8oif_16891.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oif_16891/08_2025/8oif_16891.map" model { file = "/net/cci-nas-00/data/ceres_data/8oif_16891/08_2025/8oif_16891.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oif_16891/08_2025/8oif_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 1.45, per 1000 atoms: 0.22 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: 0.49 Conformation dependent library (CDL) restraints added in 300.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.21 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: 0.79 Time building geometry restraints manager: 0.62 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=" O4' AMP I 201 " ideal model delta sigma weight residual 1.426 1.453 -0.027 2.00e-02 2.50e+03 1.77e+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 ... (remaining 6743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 9095 1.90 - 3.80: 148 3.80 - 5.69: 32 5.69 - 7.59: 2 7.59 - 9.49: 3 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=" C1' AMP I 201 " pdb=" C2' AMP I 201 " pdb=" C3' AMP I 201 " ideal model delta sigma weight residual 111.00 101.51 9.49 3.00e+00 1.11e-01 1.00e+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 ... (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 - 0.046: 904 0.046 - 0.093: 193 0.093 - 0.139: 34 0.139 - 0.186: 0 0.186 - 0.232: 3 Chirality restraints: 1134 Sorted by residual: chirality pdb=" C3' AMP I 201 " pdb=" C2' AMP I 201 " pdb=" C4' AMP I 201 " pdb=" O3' AMP I 201 " both_signs ideal model delta sigma weight residual False -2.51 -2.74 0.23 2.00e-01 2.50e+01 1.35e+00 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 ... (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: 1.620 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.540 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.247 6750 Z= 0.333 Angle : 0.618 9.489 9282 Z= 0.300 Chirality : 0.040 0.232 1134 Planarity : 0.006 0.115 1191 Dihedral : 13.815 119.684 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 aren 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 covalent geometry : bond 0.00336 ( 6748) covalent geometry : angle 0.61815 ( 9280) SS BOND : bond 0.00002 ( 1) SS BOND : angle 0.32219 ( 2) hydrogen bonds : bond 0.15334 ( 280) hydrogen bonds : angle 5.30972 ( 759) Misc. bond : bond 0.24679 ( 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 : 0.157 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0332 time to fit residues: 1.8789 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 : 0.184 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3465 r_free = 0.3465 target = 0.087551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.071441 restraints weight = 18845.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.072833 restraints weight = 11400.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.073755 restraints weight = 8286.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.074366 restraints weight = 6740.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.074545 restraints weight = 5901.011| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.0668 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= 0.158 Angle : 0.606 7.322 9282 Z= 0.291 Chirality : 0.041 0.168 1134 Planarity : 0.006 0.081 1191 Dihedral : 5.470 95.889 989 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.49 % Allowed : 15.92 % Favored : 82.59 % 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 aren not related in a simple way. whole: -0.50 (0.29), residues: 912 helix: 1.43 (0.31), residues: 314 sheet: -0.11 (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 616 TYR 0.009 0.001 TYR A1010 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 covalent geometry : bond 0.00378 ( 6748) covalent geometry : angle 0.60649 ( 9280) SS BOND : bond 0.00021 ( 1) SS BOND : angle 0.37341 ( 2) hydrogen bonds : bond 0.03736 ( 280) hydrogen bonds : angle 4.45363 ( 759) Misc. bond : bond 0.00023 ( 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 43 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.268 Fit side-chains REVERT: A 1005 PHE cc_start: 0.6616 (OUTLIER) cc_final: 0.5606 (t80) outliers start: 9 outliers final: 5 residues processed: 43 average time/residue: 0.0636 time to fit residues: 4.2762 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 : 0.318 ------------------------------------------------------------------------------- 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: 1.9990 chunk 66 optimal weight: 0.3980 chunk 8 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 73 optimal weight: 0.4980 chunk 90 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.087463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.071370 restraints weight = 18665.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.072737 restraints weight = 11332.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.073644 restraints weight = 8288.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.074216 restraints weight = 6778.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.074551 restraints weight = 5980.491| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6750 Z= 0.140 Angle : 0.593 11.526 9282 Z= 0.280 Chirality : 0.040 0.159 1134 Planarity : 0.005 0.074 1191 Dihedral : 4.548 43.720 989 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.49 % Allowed : 17.25 % Favored : 80.27 % 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 aren not related in a simple way. whole: -0.50 (0.29), residues: 912 helix: 1.48 (0.31), residues: 313 sheet: -0.13 (0.49), residues: 121 loop : -1.71 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 258 TYR 0.008 0.001 TYR A 596 PHE 0.008 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 covalent geometry : bond 0.00336 ( 6748) covalent geometry : angle 0.59306 ( 9280) SS BOND : bond 0.00013 ( 1) SS BOND : angle 0.34931 ( 2) hydrogen bonds : bond 0.03464 ( 280) hydrogen bonds : angle 4.26583 ( 759) Misc. bond : bond 0.00048 ( 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 48 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 33 time to evaluate : 0.253 Fit side-chains REVERT: A 867 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7528 (mm-30) REVERT: A 1005 PHE cc_start: 0.6843 (OUTLIER) cc_final: 0.5652 (t80) outliers start: 15 outliers final: 9 residues processed: 48 average time/residue: 0.0386 time to fit residues: 3.1872 Evaluate side-chains 42 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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 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 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: 0.0270 chunk 36 optimal weight: 5.9990 chunk 78 optimal weight: 0.0270 chunk 7 optimal weight: 0.0020 chunk 24 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 82 optimal weight: 0.6980 overall best weight: 0.3506 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1009 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.090133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.074058 restraints weight = 18553.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.075593 restraints weight = 10669.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.076602 restraints weight = 7519.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.077192 restraints weight = 6014.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.077637 restraints weight = 5249.943| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6750 Z= 0.084 Angle : 0.540 8.628 9282 Z= 0.251 Chirality : 0.038 0.147 1134 Planarity : 0.005 0.058 1191 Dihedral : 4.030 30.129 989 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.66 % Allowed : 18.08 % Favored : 80.27 % 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 aren not related in a simple way. whole: -0.18 (0.29), residues: 912 helix: 1.67 (0.31), residues: 313 sheet: 0.10 (0.47), residues: 131 loop : -1.51 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 882 TYR 0.006 0.001 TYR A 603 PHE 0.005 0.001 PHE A 300 TRP 0.008 0.001 TRP I 123 HIS 0.004 0.001 HIS A 554 Details of bonding type rmsd covalent geometry : bond 0.00196 ( 6748) covalent geometry : angle 0.53955 ( 9280) SS BOND : bond 0.00069 ( 1) SS BOND : angle 0.36115 ( 2) hydrogen bonds : bond 0.02322 ( 280) hydrogen bonds : angle 3.86484 ( 759) Misc. bond : bond 0.00025 ( 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 47 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.166 Fit side-chains REVERT: A 867 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7478 (mm-30) REVERT: A 1005 PHE cc_start: 0.6574 (OUTLIER) cc_final: 0.5547 (t80) outliers start: 10 outliers final: 7 residues processed: 47 average time/residue: 0.0512 time to fit residues: 3.7480 Evaluate side-chains 42 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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 395 LEU Chi-restraints excluded: chain A residue 467 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 72 optimal weight: 0.0670 chunk 20 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 76 optimal weight: 0.0470 chunk 88 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 74 optimal weight: 0.0370 chunk 18 optimal weight: 0.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.090300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.074367 restraints weight = 18734.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.075821 restraints weight = 11134.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.076787 restraints weight = 8002.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.077420 restraints weight = 6461.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.077780 restraints weight = 5639.334| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6750 Z= 0.084 Angle : 0.528 7.418 9282 Z= 0.246 Chirality : 0.038 0.142 1134 Planarity : 0.005 0.055 1191 Dihedral : 3.854 25.117 989 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.82 % Allowed : 19.07 % Favored : 79.10 % 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 aren not related in a simple way. whole: -0.07 (0.29), residues: 912 helix: 1.76 (0.31), residues: 314 sheet: 0.05 (0.45), residues: 147 loop : -1.45 (0.30), residues: 451 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 0.003 0.001 HIS A 554 Details of bonding type rmsd covalent geometry : bond 0.00199 ( 6748) covalent geometry : angle 0.52763 ( 9280) SS BOND : bond 0.00033 ( 1) SS BOND : angle 0.25222 ( 2) hydrogen bonds : bond 0.02336 ( 280) hydrogen bonds : angle 3.75680 ( 759) Misc. bond : bond 0.00021 ( 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 45 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.152 Fit side-chains REVERT: A 1005 PHE cc_start: 0.6545 (OUTLIER) cc_final: 0.5593 (t80) outliers start: 11 outliers final: 9 residues processed: 44 average time/residue: 0.0364 time to fit residues: 2.6838 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 : 0.147 ------------------------------------------------------------------------------- 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 395 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 L residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 88 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 81 optimal weight: 0.0870 chunk 43 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 32 optimal weight: 0.0170 chunk 2 optimal weight: 7.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.090325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.074182 restraints weight = 18716.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.075708 restraints weight = 10740.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.076725 restraints weight = 7561.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.077360 restraints weight = 6050.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.077816 restraints weight = 5263.237| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 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 0.034 6750 Z= 0.086 Angle : 0.529 8.050 9282 Z= 0.245 Chirality : 0.038 0.176 1134 Planarity : 0.005 0.055 1191 Dihedral : 3.788 24.626 989 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.16 % Allowed : 19.40 % 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 aren not related in a simple way. whole: -0.02 (0.29), residues: 912 helix: 1.80 (0.31), residues: 314 sheet: 0.07 (0.45), residues: 147 loop : -1.42 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 551 TYR 0.005 0.001 TYR A 603 PHE 0.006 0.001 PHE A 159 TRP 0.008 0.001 TRP I 123 HIS 0.003 0.001 HIS A 907 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 6748) covalent geometry : angle 0.52910 ( 9280) SS BOND : bond 0.00078 ( 1) SS BOND : angle 0.26479 ( 2) hydrogen bonds : bond 0.02337 ( 280) hydrogen bonds : angle 3.72895 ( 759) Misc. bond : bond 0.00018 ( 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 51 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.172 Fit side-chains REVERT: A 75 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8543 (tm-30) REVERT: A 867 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7363 (mm-30) REVERT: A 1005 PHE cc_start: 0.6470 (OUTLIER) cc_final: 0.5520 (t80) outliers start: 13 outliers final: 8 residues processed: 49 average time/residue: 0.0385 time to fit residues: 3.2479 Evaluate side-chains 48 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 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 167 THR Chi-restraints excluded: chain A residue 168 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 L residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 89 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 60 optimal weight: 0.7980 chunk 78 optimal weight: 0.0670 chunk 66 optimal weight: 0.0020 chunk 62 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 overall best weight: 0.9728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.089214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.073244 restraints weight = 18502.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.074655 restraints weight = 11144.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.075586 restraints weight = 8065.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.076191 restraints weight = 6560.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.076443 restraints weight = 5756.644| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6750 Z= 0.104 Angle : 0.542 7.835 9282 Z= 0.253 Chirality : 0.039 0.177 1134 Planarity : 0.005 0.054 1191 Dihedral : 3.895 25.048 989 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.82 % Allowed : 18.91 % Favored : 78.28 % 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 aren not related in a simple way. whole: -0.15 (0.29), residues: 912 helix: 1.78 (0.31), residues: 316 sheet: -0.13 (0.47), residues: 127 loop : -1.49 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 85 TYR 0.007 0.001 TYR A 603 PHE 0.006 0.001 PHE A 159 TRP 0.007 0.001 TRP I 123 HIS 0.004 0.001 HIS A 286 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 6748) covalent geometry : angle 0.54191 ( 9280) SS BOND : bond 0.00026 ( 1) SS BOND : angle 0.26621 ( 2) hydrogen bonds : bond 0.02718 ( 280) hydrogen bonds : angle 3.82383 ( 759) Misc. bond : bond 0.00011 ( 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 54 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 37 time to evaluate : 0.169 Fit side-chains REVERT: A 75 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8516 (tm-30) REVERT: A 867 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7526 (mm-30) REVERT: A 1005 PHE cc_start: 0.6644 (OUTLIER) cc_final: 0.5624 (t80) outliers start: 17 outliers final: 12 residues processed: 53 average time/residue: 0.0389 time to fit residues: 3.4991 Evaluate side-chains 51 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 37 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 464 LEU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain L residue 68 ILE Chi-restraints excluded: chain L residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 85 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 75 optimal weight: 0.0020 chunk 60 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 overall best weight: 0.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.089371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.073140 restraints weight = 18603.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.074639 restraints weight = 10801.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.075632 restraints weight = 7643.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.076221 restraints weight = 6145.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.076674 restraints weight = 5387.398| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6750 Z= 0.097 Angle : 0.539 7.758 9282 Z= 0.251 Chirality : 0.039 0.171 1134 Planarity : 0.005 0.055 1191 Dihedral : 3.851 24.931 989 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % 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 aren not related in a simple way. whole: -0.06 (0.29), residues: 912 helix: 1.90 (0.31), residues: 310 sheet: -0.20 (0.46), residues: 129 loop : -1.38 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 551 TYR 0.004 0.001 TYR A 603 PHE 0.006 0.001 PHE A 159 TRP 0.007 0.001 TRP I 123 HIS 0.003 0.001 HIS A 286 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 6748) covalent geometry : angle 0.53901 ( 9280) SS BOND : bond 0.00054 ( 1) SS BOND : angle 0.26672 ( 2) hydrogen bonds : bond 0.02584 ( 280) hydrogen bonds : angle 3.80405 ( 759) Misc. bond : bond 0.00005 ( 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 53 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 35 time to evaluate : 0.157 Fit side-chains REVERT: A 75 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8514 (tm-30) REVERT: A 1005 PHE cc_start: 0.6688 (OUTLIER) cc_final: 0.5689 (t80) outliers start: 18 outliers final: 13 residues processed: 52 average time/residue: 0.0363 time to fit residues: 3.1363 Evaluate side-chains 49 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 34 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 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 361 VAL 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 L residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 66 optimal weight: 0.1980 chunk 51 optimal weight: 0.0070 chunk 76 optimal weight: 0.0980 chunk 39 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 21 optimal weight: 0.0770 chunk 62 optimal weight: 0.6980 overall best weight: 0.1956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 887 HIS A 891 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.091163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.075153 restraints weight = 18491.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.076695 restraints weight = 10560.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.077713 restraints weight = 7409.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.078319 restraints weight = 5900.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.078803 restraints weight = 5134.214| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1422 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= 0.082 Angle : 0.534 8.940 9282 Z= 0.245 Chirality : 0.038 0.174 1134 Planarity : 0.005 0.054 1191 Dihedral : 3.627 24.383 989 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.65 % Allowed : 19.07 % Favored : 78.28 % 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 aren not related in a simple way. whole: 0.04 (0.30), residues: 912 helix: 1.92 (0.31), residues: 313 sheet: -0.03 (0.43), residues: 153 loop : -1.40 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 551 TYR 0.006 0.000 TYR A 603 PHE 0.005 0.001 PHE A 604 TRP 0.011 0.001 TRP A 568 HIS 0.003 0.001 HIS A 554 Details of bonding type rmsd covalent geometry : bond 0.00190 ( 6748) covalent geometry : angle 0.53420 ( 9280) SS BOND : bond 0.00039 ( 1) SS BOND : angle 0.17984 ( 2) hydrogen bonds : bond 0.02132 ( 280) hydrogen bonds : angle 3.61919 ( 759) Misc. bond : bond 0.00013 ( 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 55 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 0.165 Fit side-chains REVERT: A 1005 PHE cc_start: 0.6437 (OUTLIER) cc_final: 0.5571 (t80) outliers start: 16 outliers final: 13 residues processed: 53 average time/residue: 0.0483 time to fit residues: 3.9614 Evaluate side-chains 52 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 38 time to evaluate : 0.149 ------------------------------------------------------------------------------- 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 106 VAL 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 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 1005 PHE Chi-restraints excluded: chain L residue 68 ILE Chi-restraints excluded: chain L residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 55 optimal weight: 0.3980 chunk 35 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.089035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.072951 restraints weight = 18600.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.074372 restraints weight = 11151.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.075303 restraints weight = 8077.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.075847 restraints weight = 6573.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.076258 restraints weight = 5803.894| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6750 Z= 0.119 Angle : 0.572 7.785 9282 Z= 0.265 Chirality : 0.039 0.180 1134 Planarity : 0.005 0.055 1191 Dihedral : 3.900 25.116 989 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.65 % Allowed : 19.07 % Favored : 78.28 % 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 aren not related in a simple way. whole: -0.05 (0.29), residues: 912 helix: 1.92 (0.31), residues: 310 sheet: -0.17 (0.47), residues: 128 loop : -1.39 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 85 TYR 0.006 0.001 TYR A 603 PHE 0.007 0.001 PHE A 146 TRP 0.008 0.001 TRP I 123 HIS 0.004 0.001 HIS A 286 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 6748) covalent geometry : angle 0.57249 ( 9280) SS BOND : bond 0.00117 ( 1) SS BOND : angle 0.25692 ( 2) hydrogen bonds : bond 0.02886 ( 280) hydrogen bonds : angle 3.86957 ( 759) Misc. bond : bond 0.00017 ( 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 51 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 35 time to evaluate : 0.267 Fit side-chains REVERT: A 75 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8534 (tm-30) REVERT: A 1005 PHE cc_start: 0.6731 (OUTLIER) cc_final: 0.5751 (t80) outliers start: 16 outliers final: 14 residues processed: 50 average time/residue: 0.0449 time to fit residues: 3.8796 Evaluate side-chains 51 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 35 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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 361 VAL 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 L residue 68 ILE Chi-restraints excluded: chain L residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 89 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 84 optimal weight: 0.0570 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.089552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.073508 restraints weight = 18545.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.074944 restraints weight = 11107.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.075858 restraints weight = 8030.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.076488 restraints weight = 6544.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.076884 restraints weight = 5714.874| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6750 Z= 0.098 Angle : 0.557 8.129 9282 Z= 0.256 Chirality : 0.039 0.183 1134 Planarity : 0.005 0.055 1191 Dihedral : 3.846 24.942 989 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.82 % Allowed : 18.74 % 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 aren not related in a simple way. whole: -0.05 (0.29), residues: 912 helix: 1.99 (0.31), residues: 307 sheet: -0.22 (0.46), residues: 129 loop : -1.42 (0.29), residues: 476 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 0.003 0.001 HIS A 286 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 6748) covalent geometry : angle 0.55657 ( 9280) SS BOND : bond 0.00049 ( 1) SS BOND : angle 0.18058 ( 2) hydrogen bonds : bond 0.02580 ( 280) hydrogen bonds : angle 3.79703 ( 759) Misc. bond : bond 0.00011 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1093.14 seconds wall clock time: 19 minutes 25.05 seconds (1165.05 seconds total)