Starting phenix.real_space_refine on Fri Aug 7 01:36:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gd3_51247/08_2026/9gd3_51247.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gd3_51247/08_2026/9gd3_51247.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gd3_51247/08_2026/9gd3_51247.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gd3_51247/08_2026/9gd3_51247.map" model { file = "/net/cci-nas-00/data/ceres_data/9gd3_51247/08_2026/9gd3_51247.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gd3_51247/08_2026/9gd3_51247.cif" } resolution = 3.0 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= 0.001 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: 8 Type Number sf(0) Gaussians P 286 5.49 5 Mg 1 5.21 5 S 40 5.16 5 Be 1 3.05 5 C 11106 2.51 5 N 3466 2.21 5 O 4127 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s 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: 19030 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 774 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "B" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "C" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 750 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 780 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 800 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2892 Classifications: {'DNA': 142} Link IDs: {'rna3p': 141} Chain: "J" Number of atoms: 2930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2930 Classifications: {'DNA': 142} Link IDs: {'rna3p': 141} Chain: "T" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 203 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "W" Number of atoms: 7085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 864, 7085 Classifications: {'peptide': 864} Link IDs: {'PTRANS': 26, 'TRANS': 837} Chain breaks: 5 Chain: "W" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.03, per 1000 atoms: 0.21 Number of scatterers: 19030 At special positions: 0 Unit cell: (125.934, 133.44, 180.144, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 40 16.00 P 286 15.00 Mg 1 11.99 F 3 9.00 O 4127 8.00 N 3466 7.00 C 11106 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.81 Conformation dependent library (CDL) restraints added in 669.4 milliseconds 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3072 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 16 sheets defined 63.5% alpha, 7.0% beta 135 base pairs and 282 stacking pairs defined. Time for finding SS restraints: 2.74 Creating SS restraints... Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 115 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.590A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.533A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 120 removed outlier: 3.590A pdb=" N ALA D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.542A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.656A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.491A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.678A pdb=" N ALA H 104 " --> pdb=" O PRO H 100 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'W' and resid 204 through 210 Processing helix chain 'W' and resid 221 through 225 removed outlier: 3.508A pdb=" N ASN W 225 " --> pdb=" O HIS W 222 " (cutoff:3.500A) Processing helix chain 'W' and resid 229 through 234 Processing helix chain 'W' and resid 238 through 258 removed outlier: 3.579A pdb=" N LEU W 242 " --> pdb=" O GLY W 238 " (cutoff:3.500A) Processing helix chain 'W' and resid 263 through 282 removed outlier: 3.848A pdb=" N ARG W 274 " --> pdb=" O MET W 270 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU W 275 " --> pdb=" O ASP W 271 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU W 280 " --> pdb=" O ARG W 276 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE W 281 " --> pdb=" O ARG W 277 " (cutoff:3.500A) Processing helix chain 'W' and resid 324 through 331 removed outlier: 4.018A pdb=" N LYS W 329 " --> pdb=" O THR W 325 " (cutoff:3.500A) Processing helix chain 'W' and resid 331 through 343 Processing helix chain 'W' and resid 347 through 351 Processing helix chain 'W' and resid 377 through 394 Processing helix chain 'W' and resid 406 through 421 Processing helix chain 'W' and resid 433 through 435 No H-bonds generated for 'chain 'W' and resid 433 through 435' Processing helix chain 'W' and resid 436 through 448 Processing helix chain 'W' and resid 459 through 471 removed outlier: 3.531A pdb=" N PHE W 471 " --> pdb=" O ARG W 467 " (cutoff:3.500A) Processing helix chain 'W' and resid 492 through 498 Processing helix chain 'W' and resid 498 through 504 Processing helix chain 'W' and resid 514 through 520 removed outlier: 4.040A pdb=" N ASN W 520 " --> pdb=" O ARG W 517 " (cutoff:3.500A) Processing helix chain 'W' and resid 523 through 532 removed outlier: 3.526A pdb=" N PHE W 532 " --> pdb=" O SER W 528 " (cutoff:3.500A) Processing helix chain 'W' and resid 548 through 560 Processing helix chain 'W' and resid 576 through 591 Processing helix chain 'W' and resid 598 through 603 Processing helix chain 'W' and resid 619 through 631 Processing helix chain 'W' and resid 633 through 641 Processing helix chain 'W' and resid 650 through 661 Processing helix chain 'W' and resid 662 through 665 Processing helix chain 'W' and resid 669 through 674 Processing helix chain 'W' and resid 675 through 679 Processing helix chain 'W' and resid 682 through 693 Processing helix chain 'W' and resid 694 through 711 Processing helix chain 'W' and resid 720 through 734 Processing helix chain 'W' and resid 746 through 758 Processing helix chain 'W' and resid 794 through 806 removed outlier: 3.919A pdb=" N ASP W 798 " --> pdb=" O ASN W 794 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA W 805 " --> pdb=" O ALA W 801 " (cutoff:3.500A) Processing helix chain 'W' and resid 824 through 844 removed outlier: 4.011A pdb=" N GLU W 828 " --> pdb=" O THR W 824 " (cutoff:3.500A) Processing helix chain 'W' and resid 1011 through 1026 Processing helix chain 'W' and resid 1031 through 1038 Processing helix chain 'W' and resid 1045 through 1072 Processing helix chain 'W' and resid 1130 through 1152 Processing helix chain 'W' and resid 1154 through 1158 Processing helix chain 'W' and resid 1176 through 1191 Processing helix chain 'W' and resid 1194 through 1201 Processing helix chain 'W' and resid 1202 through 1209 removed outlier: 6.190A pdb=" N ILE W1206 " --> pdb=" O PHE W1203 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N THR W1207 " --> pdb=" O LEU W1204 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASP W1208 " --> pdb=" O GLY W1205 " (cutoff:3.500A) Processing helix chain 'W' and resid 1249 through 1266 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.732A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.919A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.767A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.490A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.075A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'W' and resid 179 through 187 removed outlier: 5.560A pdb=" N VAL W 182 " --> pdb=" O LYS W 216 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LYS W 216 " --> pdb=" O VAL W 182 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN W 184 " --> pdb=" O LEU W 214 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'W' and resid 287 through 297 removed outlier: 6.632A pdb=" N LEU W 308 " --> pdb=" O ILE W 291 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N SER W 293 " --> pdb=" O GLN W 306 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLN W 306 " --> pdb=" O SER W 293 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ARG W 295 " --> pdb=" O GLN W 304 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N GLN W 304 " --> pdb=" O ARG W 295 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'W' and resid 453 through 456 removed outlier: 4.380A pdb=" N THR W 491 " --> pdb=" O TYR W 456 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N MET W 510 " --> pdb=" O MET W 538 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ILE W 540 " --> pdb=" O MET W 510 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL W 512 " --> pdb=" O ILE W 540 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY W 397 " --> pdb=" O ARG W 537 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE W 398 " --> pdb=" O LEU W 595 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'W' and resid 472 through 473 removed outlier: 4.877A pdb=" N THR W 482 " --> pdb=" O THR W 473 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'W' and resid 609 through 616 removed outlier: 6.489A pdb=" N VAL W 786 " --> pdb=" O TYR W 817 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N LEU W 819 " --> pdb=" O VAL W 786 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ILE W 788 " --> pdb=" O LEU W 819 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N SER W 821 " --> pdb=" O ILE W 788 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL W 714 " --> pdb=" O PHE W 767 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LEU W 769 " --> pdb=" O VAL W 714 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE W 716 " --> pdb=" O LEU W 769 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLN W 739 " --> pdb=" O LEU W 768 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N SER W 770 " --> pdb=" O GLN W 739 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU W 741 " --> pdb=" O SER W 770 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'W' and resid 1119 through 1122 removed outlier: 6.339A pdb=" N PHE W1122 " --> pdb=" O LYS W1126 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LYS W1126 " --> pdb=" O PHE W1122 " (cutoff:3.500A) 763 hydrogen bonds defined for protein. 2229 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 343 hydrogen bonds 686 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 282 stacking parallelities Total time for adding SS restraints: 6.99 Time building geometry restraints manager: 2.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5162 1.34 - 1.45: 4606 1.45 - 1.57: 9545 1.57 - 1.69: 569 1.69 - 1.81: 73 Bond restraints: 19955 Sorted by residual: bond pdb=" N LYS E 56 " pdb=" CA LYS E 56 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.23e-02 6.61e+03 6.89e+00 bond pdb=" O3' DG J -70 " pdb=" P DG J -69 " ideal model delta sigma weight residual 1.607 1.578 0.029 1.20e-02 6.94e+03 5.79e+00 bond pdb=" O3' DG J 8 " pdb=" P DT J 9 " ideal model delta sigma weight residual 1.607 1.582 0.025 1.20e-02 6.94e+03 4.42e+00 bond pdb=" O3' DA I 16 " pdb=" P DA I 17 " ideal model delta sigma weight residual 1.607 1.587 0.020 1.20e-02 6.94e+03 2.72e+00 bond pdb=" O3' DT I 14 " pdb=" P DT I 15 " ideal model delta sigma weight residual 1.607 1.588 0.019 1.20e-02 6.94e+03 2.44e+00 ... (remaining 19950 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 27925 2.90 - 5.80: 217 5.80 - 8.70: 3 8.70 - 11.60: 1 11.60 - 14.49: 3 Bond angle restraints: 28149 Sorted by residual: angle pdb=" F2 BEF W1502 " pdb="BE BEF W1502 " pdb=" F3 BEF W1502 " ideal model delta sigma weight residual 119.96 105.47 14.49 3.00e+00 1.11e-01 2.33e+01 angle pdb=" F1 BEF W1502 " pdb="BE BEF W1502 " pdb=" F3 BEF W1502 " ideal model delta sigma weight residual 120.12 105.89 14.23 3.00e+00 1.11e-01 2.25e+01 angle pdb=" F1 BEF W1502 " pdb="BE BEF W1502 " pdb=" F2 BEF W1502 " ideal model delta sigma weight residual 119.91 106.70 13.21 3.00e+00 1.11e-01 1.94e+01 angle pdb=" C4' DG J 21 " pdb=" O4' DG J 21 " pdb=" C1' DG J 21 " ideal model delta sigma weight residual 110.10 106.49 3.61 1.00e+00 1.00e+00 1.30e+01 angle pdb=" C4' DA I 50 " pdb=" O4' DA I 50 " pdb=" C1' DA I 50 " ideal model delta sigma weight residual 110.10 106.53 3.57 1.00e+00 1.00e+00 1.27e+01 ... (remaining 28144 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 9740 35.97 - 71.93: 1563 71.93 - 107.90: 15 107.90 - 143.87: 1 143.87 - 179.83: 2 Dihedral angle restraints: 11321 sinusoidal: 6570 harmonic: 4751 Sorted by residual: dihedral pdb=" O1B ADP W1501 " pdb=" O3A ADP W1501 " pdb=" PB ADP W1501 " pdb=" PA ADP W1501 " ideal model delta sinusoidal sigma weight residual -60.00 119.83 -179.83 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP W1501 " pdb=" O5' ADP W1501 " pdb=" PA ADP W1501 " pdb=" O2A ADP W1501 " ideal model delta sinusoidal sigma weight residual -60.00 102.16 -162.16 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" CA ASN W 547 " pdb=" C ASN W 547 " pdb=" N ASN W 548 " pdb=" CA ASN W 548 " ideal model delta harmonic sigma weight residual 180.00 151.10 28.90 0 5.00e+00 4.00e-02 3.34e+01 ... (remaining 11318 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1945 0.038 - 0.077: 816 0.077 - 0.115: 343 0.115 - 0.153: 39 0.153 - 0.192: 7 Chirality restraints: 3150 Sorted by residual: chirality pdb=" C3' DG J -70 " pdb=" C4' DG J -70 " pdb=" O3' DG J -70 " pdb=" C2' DG J -70 " both_signs ideal model delta sigma weight residual False -2.73 -2.92 0.19 2.00e-01 2.50e+01 9.19e-01 chirality pdb=" CA ARG W 422 " pdb=" N ARG W 422 " pdb=" C ARG W 422 " pdb=" CB ARG W 422 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.60e-01 chirality pdb=" CA PRO W 348 " pdb=" N PRO W 348 " pdb=" C PRO W 348 " pdb=" CB PRO W 348 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.17 2.00e-01 2.50e+01 7.55e-01 ... (remaining 3147 not shown) Planarity restraints: 2600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU W 418 " 0.019 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C LEU W 418 " -0.065 2.00e-02 2.50e+03 pdb=" O LEU W 418 " 0.024 2.00e-02 2.50e+03 pdb=" N ILE W 419 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 49 " 0.016 2.00e-02 2.50e+03 3.23e-02 1.05e+01 pdb=" C ARG E 49 " -0.056 2.00e-02 2.50e+03 pdb=" O ARG E 49 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU E 50 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU W 441 " 0.016 2.00e-02 2.50e+03 3.16e-02 1.00e+01 pdb=" C LEU W 441 " -0.055 2.00e-02 2.50e+03 pdb=" O LEU W 441 " 0.020 2.00e-02 2.50e+03 pdb=" N ASP W 442 " 0.018 2.00e-02 2.50e+03 ... (remaining 2597 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1097 2.72 - 3.27: 17444 3.27 - 3.81: 33164 3.81 - 4.36: 44355 4.36 - 4.90: 66328 Nonbonded interactions: 162388 Sorted by model distance: nonbonded pdb=" OE2 GLU W 514 " pdb="MG MG W1503 " model vdw 2.176 2.170 nonbonded pdb=" OD1 ASP W 513 " pdb="MG MG W1503 " model vdw 2.176 2.170 nonbonded pdb=" O THR B 82 " pdb=" OD1 ASP B 85 " model vdw 2.235 3.040 nonbonded pdb=" OE2 GLU W 611 " pdb=" NH1 ARG W 818 " model vdw 2.280 3.120 nonbonded pdb=" N GLY W 406 " pdb=" O2A ADP W1501 " model vdw 2.322 3.120 ... (remaining 162383 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 41 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 15 through 111) } ncs_group { reference = (chain 'D' and resid 29 through 121) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 23.620 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 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 0.416 19956 Z= 0.387 Angle : 0.767 14.495 28149 Z= 0.522 Chirality : 0.047 0.192 3150 Planarity : 0.010 0.116 2600 Dihedral : 24.310 179.833 8249 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 1.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.07 % Allowed : 4.59 % Favored : 95.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.19), residues: 1600 helix: 0.23 (0.15), residues: 968 sheet: 0.34 (0.50), residues: 91 loop : -0.37 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.003 ARG B 17 TYR 0.026 0.005 TYR W1192 PHE 0.024 0.002 PHE C 25 TRP 0.016 0.004 TRP W 507 HIS 0.012 0.003 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.25 (19955) covalent geometry : angle 0.76682 / 0.52 (28149) hydrogen bonds : bond 0.12740 / 8.81 ( 1106) hydrogen bonds : angle 5.36984 / 3.84 ( 2915) Misc. bond : bond 0.41591 / 21.89 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 279 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 1028 LEU cc_start: 0.8298 (pp) cc_final: 0.8069 (pp) outliers start: 1 outliers final: 0 residues processed: 279 average time/residue: 0.8639 time to fit residues: 263.0624 Evaluate side-chains 149 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.0670 chunk 66 optimal weight: 0.0870 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.9898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 76 GLN B 75 HIS C 73 ASN D 106 HIS F 75 HIS G 110 ASN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W1150 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.111187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.071501 restraints weight = 48085.661| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.72 r_work: 0.2938 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 19956 Z= 0.166 Angle : 0.754 8.318 28149 Z= 0.409 Chirality : 0.048 0.197 3150 Planarity : 0.004 0.042 2600 Dihedral : 28.194 177.292 4932 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.05 % Allowed : 12.35 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.20), residues: 1600 helix: 1.45 (0.16), residues: 984 sheet: 0.27 (0.50), residues: 92 loop : 0.02 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG T 130 TYR 0.018 0.002 TYR F 88 PHE 0.017 0.002 PHE W1263 TRP 0.007 0.001 TRP W 793 HIS 0.005 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.17 (19955) covalent geometry : angle 0.75412 / 0.41 (28149) hydrogen bonds : bond 0.05167 / 3.49 ( 1106) hydrogen bonds : angle 3.97760 / 2.85 ( 2915) Misc. bond : bond 0.00687 / 0.36 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 166 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASP cc_start: 0.8217 (t0) cc_final: 0.7974 (t0) REVERT: C 35 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.7965 (mpt-90) REVERT: D 65 ASP cc_start: 0.8911 (t70) cc_final: 0.8386 (t0) REVERT: E 79 LYS cc_start: 0.6985 (tptt) cc_final: 0.6722 (tmtm) REVERT: E 133 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7950 (mt-10) REVERT: G 64 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8514 (tp30) REVERT: T 129 ASN cc_start: 0.8968 (m-40) cc_final: 0.7472 (t0) REVERT: W 681 MET cc_start: 0.7435 (mpt) cc_final: 0.7225 (mpt) REVERT: W 1192 TYR cc_start: 0.8185 (t80) cc_final: 0.7901 (t80) outliers start: 29 outliers final: 4 residues processed: 185 average time/residue: 0.7588 time to fit residues: 155.0628 Evaluate side-chains 147 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 141 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain W residue 694 SER Chi-restraints excluded: chain W residue 781 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 34 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 78 optimal weight: 20.0000 chunk 182 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 168 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 144 optimal weight: 0.2980 chunk 14 optimal weight: 0.8980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 73 ASN D 106 HIS H 44 GLN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.110253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.068822 restraints weight = 48144.289| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.77 r_work: 0.2921 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19956 Z= 0.160 Angle : 0.662 8.481 28149 Z= 0.367 Chirality : 0.045 0.195 3150 Planarity : 0.004 0.039 2600 Dihedral : 28.044 171.598 4932 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.26 % Allowed : 13.27 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.21), residues: 1600 helix: 1.81 (0.16), residues: 987 sheet: 0.21 (0.53), residues: 90 loop : 0.02 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG W 274 TYR 0.014 0.002 TYR W1142 PHE 0.016 0.001 PHE W1263 TRP 0.006 0.001 TRP W1175 HIS 0.004 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 (19955) covalent geometry : angle 0.66196 / 0.37 (28149) hydrogen bonds : bond 0.04549 / 3.08 ( 1106) hydrogen bonds : angle 3.69108 / 2.65 ( 2915) Misc. bond : bond 0.00312 / 0.16 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8249 (mt-10) cc_final: 0.8030 (mt-10) REVERT: B 24 ASP cc_start: 0.8272 (t0) cc_final: 0.7958 (t0) REVERT: C 64 GLU cc_start: 0.8859 (tp30) cc_final: 0.8647 (tp30) REVERT: D 65 ASP cc_start: 0.8922 (t70) cc_final: 0.8444 (t0) REVERT: E 133 GLU cc_start: 0.8269 (mt-10) cc_final: 0.8062 (mt-10) REVERT: G 64 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8542 (tp30) REVERT: T 129 ASN cc_start: 0.8958 (m-40) cc_final: 0.7604 (t0) REVERT: W 538 MET cc_start: 0.8946 (tmm) cc_final: 0.8330 (ttt) REVERT: W 681 MET cc_start: 0.7484 (OUTLIER) cc_final: 0.7254 (mpt) REVERT: W 720 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8495 (mtt) REVERT: W 751 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.8617 (ttt180) REVERT: W 1192 TYR cc_start: 0.8217 (t80) cc_final: 0.7976 (t80) outliers start: 32 outliers final: 11 residues processed: 176 average time/residue: 0.7593 time to fit residues: 148.3361 Evaluate side-chains 155 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain W residue 399 LEU Chi-restraints excluded: chain W residue 645 HIS Chi-restraints excluded: chain W residue 681 MET Chi-restraints excluded: chain W residue 694 SER Chi-restraints excluded: chain W residue 720 MET Chi-restraints excluded: chain W residue 751 ARG Chi-restraints excluded: chain W residue 781 MET Chi-restraints excluded: chain W residue 1207 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 78 optimal weight: 20.0000 chunk 138 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 2 optimal weight: 0.0980 chunk 129 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 175 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 89 optimal weight: 20.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 64 ASN H 44 GLN H 60 ASN W 132 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.110508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.070991 restraints weight = 48247.782| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.74 r_work: 0.2930 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19956 Z= 0.142 Angle : 0.630 9.325 28149 Z= 0.349 Chirality : 0.042 0.197 3150 Planarity : 0.004 0.046 2600 Dihedral : 27.846 156.538 4932 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.96 % Allowed : 12.99 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.21), residues: 1600 helix: 2.04 (0.16), residues: 986 sheet: 0.05 (0.52), residues: 90 loop : -0.02 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG W 274 TYR 0.028 0.002 TYR W1142 PHE 0.013 0.001 PHE W1263 TRP 0.008 0.001 TRP W1175 HIS 0.005 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.14 (19955) covalent geometry : angle 0.63029 / 0.35 (28149) hydrogen bonds : bond 0.04086 / 2.78 ( 1106) hydrogen bonds : angle 3.49916 / 2.52 ( 2915) Misc. bond : bond 0.00146 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 154 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASP cc_start: 0.8304 (t0) cc_final: 0.7941 (t0) REVERT: D 65 ASP cc_start: 0.8941 (t70) cc_final: 0.8399 (t0) REVERT: D 84 SER cc_start: 0.9247 (OUTLIER) cc_final: 0.9000 (p) REVERT: E 94 GLU cc_start: 0.8833 (tp30) cc_final: 0.8615 (mm-30) REVERT: E 133 GLU cc_start: 0.8293 (mt-10) cc_final: 0.8092 (mt-10) REVERT: F 59 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8277 (ttmt) REVERT: G 64 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8597 (tp30) REVERT: G 104 GLN cc_start: 0.8885 (mm-40) cc_final: 0.8668 (mm110) REVERT: H 117 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7936 (tptt) REVERT: T 129 ASN cc_start: 0.8934 (m-40) cc_final: 0.7589 (t0) REVERT: W 276 ARG cc_start: 0.8934 (mmp80) cc_final: 0.8424 (mmp80) REVERT: W 538 MET cc_start: 0.8989 (tmm) cc_final: 0.8434 (ttt) REVERT: W 837 MET cc_start: 0.9033 (tpt) cc_final: 0.8701 (tpp) REVERT: W 1056 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8250 (mpp) REVERT: W 1192 TYR cc_start: 0.8155 (t80) cc_final: 0.7815 (t80) outliers start: 42 outliers final: 12 residues processed: 180 average time/residue: 0.7677 time to fit residues: 153.3204 Evaluate side-chains 156 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain W residue 399 LEU Chi-restraints excluded: chain W residue 432 VAL Chi-restraints excluded: chain W residue 645 HIS Chi-restraints excluded: chain W residue 694 SER Chi-restraints excluded: chain W residue 781 MET Chi-restraints excluded: chain W residue 1007 MET Chi-restraints excluded: chain W residue 1056 MET Chi-restraints excluded: chain W residue 1184 LEU Chi-restraints excluded: chain W residue 1207 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 56 optimal weight: 0.6980 chunk 154 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 96 optimal weight: 20.0000 chunk 86 optimal weight: 50.0000 chunk 51 optimal weight: 20.0000 chunk 43 optimal weight: 0.9980 chunk 131 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 102 optimal weight: 10.0000 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN G 110 ASN H 60 ASN T 138 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.108607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.066981 restraints weight = 48350.623| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.71 r_work: 0.2866 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19956 Z= 0.229 Angle : 0.676 8.966 28149 Z= 0.366 Chirality : 0.044 0.218 3150 Planarity : 0.004 0.038 2600 Dihedral : 27.877 140.644 4932 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.26 % Allowed : 14.33 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.21), residues: 1600 helix: 1.95 (0.16), residues: 987 sheet: -0.13 (0.51), residues: 90 loop : -0.17 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG G 17 TYR 0.024 0.002 TYR W1142 PHE 0.013 0.001 PHE E 84 TRP 0.012 0.001 TRP W1175 HIS 0.007 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.23 (19955) covalent geometry : angle 0.67606 / 0.37 (28149) hydrogen bonds : bond 0.04790 / 3.25 ( 1106) hydrogen bonds : angle 3.59346 / 2.58 ( 2915) Misc. bond : bond 0.00054 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASP cc_start: 0.8399 (t0) cc_final: 0.8078 (t0) REVERT: D 65 ASP cc_start: 0.8999 (t70) cc_final: 0.8475 (t0) REVERT: D 84 SER cc_start: 0.9354 (OUTLIER) cc_final: 0.9095 (p) REVERT: E 90 MET cc_start: 0.9207 (tpp) cc_final: 0.8995 (mmm) REVERT: E 133 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8162 (mt-10) REVERT: G 64 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8616 (tp30) REVERT: H 31 LYS cc_start: 0.8331 (tppp) cc_final: 0.8069 (tppp) REVERT: H 43 LYS cc_start: 0.8818 (mtpp) cc_final: 0.8586 (mttt) REVERT: T 129 ASN cc_start: 0.9022 (m-40) cc_final: 0.7748 (t0) REVERT: W 272 MET cc_start: 0.8878 (ppp) cc_final: 0.8638 (ppp) REVERT: W 276 ARG cc_start: 0.8896 (mmp80) cc_final: 0.8446 (mmp80) REVERT: W 390 LEU cc_start: 0.9578 (OUTLIER) cc_final: 0.9309 (tp) REVERT: W 538 MET cc_start: 0.8984 (tmm) cc_final: 0.8619 (ttt) REVERT: W 837 MET cc_start: 0.9033 (tpt) cc_final: 0.8795 (tpp) REVERT: W 1192 TYR cc_start: 0.8153 (t80) cc_final: 0.7752 (t80) outliers start: 32 outliers final: 14 residues processed: 167 average time/residue: 0.6486 time to fit residues: 120.4534 Evaluate side-chains 159 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain W residue 390 LEU Chi-restraints excluded: chain W residue 399 LEU Chi-restraints excluded: chain W residue 495 ILE Chi-restraints excluded: chain W residue 645 HIS Chi-restraints excluded: chain W residue 694 SER Chi-restraints excluded: chain W residue 781 MET Chi-restraints excluded: chain W residue 1007 MET Chi-restraints excluded: chain W residue 1207 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 120 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 148 optimal weight: 6.9990 chunk 58 optimal weight: 0.5980 chunk 106 optimal weight: 8.9990 chunk 38 optimal weight: 0.4980 chunk 29 optimal weight: 0.7980 chunk 169 optimal weight: 5.9990 chunk 173 optimal weight: 4.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN H 60 ASN W 424 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.108544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.066938 restraints weight = 47643.533| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.73 r_work: 0.2876 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19956 Z= 0.200 Angle : 0.660 8.907 28149 Z= 0.357 Chirality : 0.043 0.235 3150 Planarity : 0.004 0.033 2600 Dihedral : 27.794 136.045 4932 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.61 % Allowed : 14.68 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.21), residues: 1600 helix: 1.95 (0.16), residues: 992 sheet: -0.20 (0.51), residues: 90 loop : -0.23 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 35 TYR 0.026 0.002 TYR W 841 PHE 0.009 0.001 PHE W 379 TRP 0.007 0.001 TRP W 440 HIS 0.007 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.20 (19955) covalent geometry : angle 0.65960 / 0.36 (28149) hydrogen bonds : bond 0.04451 / 3.02 ( 1106) hydrogen bonds : angle 3.55492 / 2.54 ( 2915) Misc. bond : bond 0.00042 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 152 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASP cc_start: 0.8428 (t0) cc_final: 0.8101 (t0) REVERT: D 65 ASP cc_start: 0.8985 (t70) cc_final: 0.8464 (t0) REVERT: D 84 SER cc_start: 0.9335 (OUTLIER) cc_final: 0.9064 (p) REVERT: E 90 MET cc_start: 0.9187 (tpp) cc_final: 0.8972 (mmm) REVERT: E 133 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8156 (mt-10) REVERT: F 59 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8380 (ttmt) REVERT: G 64 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8624 (tp30) REVERT: G 91 GLU cc_start: 0.8674 (tt0) cc_final: 0.8429 (tm-30) REVERT: H 31 LYS cc_start: 0.8313 (tppp) cc_final: 0.8051 (tppp) REVERT: T 129 ASN cc_start: 0.8990 (m-40) cc_final: 0.7546 (t0) REVERT: W 276 ARG cc_start: 0.8916 (mmp80) cc_final: 0.8495 (mmp80) REVERT: W 434 LEU cc_start: 0.9659 (OUTLIER) cc_final: 0.9290 (tp) REVERT: W 538 MET cc_start: 0.8975 (tmm) cc_final: 0.8553 (ttt) REVERT: W 837 MET cc_start: 0.9043 (tpt) cc_final: 0.8770 (tpp) REVERT: W 1192 TYR cc_start: 0.8064 (t80) cc_final: 0.7608 (t80) outliers start: 37 outliers final: 15 residues processed: 176 average time/residue: 0.6654 time to fit residues: 129.9671 Evaluate side-chains 165 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain W residue 297 SER Chi-restraints excluded: chain W residue 355 THR Chi-restraints excluded: chain W residue 399 LEU Chi-restraints excluded: chain W residue 434 LEU Chi-restraints excluded: chain W residue 645 HIS Chi-restraints excluded: chain W residue 694 SER Chi-restraints excluded: chain W residue 1007 MET Chi-restraints excluded: chain W residue 1207 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 102 optimal weight: 10.0000 chunk 40 optimal weight: 0.6980 chunk 169 optimal weight: 6.9990 chunk 118 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 134 optimal weight: 0.7980 chunk 179 optimal weight: 0.0670 chunk 142 optimal weight: 4.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN H 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.109751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.068443 restraints weight = 48047.483| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.73 r_work: 0.2918 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 19956 Z= 0.131 Angle : 0.618 8.960 28149 Z= 0.341 Chirality : 0.041 0.227 3150 Planarity : 0.003 0.041 2600 Dihedral : 27.573 134.376 4932 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.19 % Allowed : 15.46 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.21), residues: 1600 helix: 2.14 (0.16), residues: 991 sheet: -0.12 (0.52), residues: 90 loop : -0.11 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 35 TYR 0.025 0.001 TYR W1142 PHE 0.009 0.001 PHE W 370 TRP 0.020 0.001 TRP W 386 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.13 (19955) covalent geometry : angle 0.61830 / 0.34 (28149) hydrogen bonds : bond 0.03891 / 2.65 ( 1106) hydrogen bonds : angle 3.43247 / 2.47 ( 2915) Misc. bond : bond 0.00021 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASP cc_start: 0.8386 (t0) cc_final: 0.8036 (t0) REVERT: D 65 ASP cc_start: 0.8964 (t70) cc_final: 0.8453 (t0) REVERT: D 84 SER cc_start: 0.9261 (OUTLIER) cc_final: 0.9007 (p) REVERT: E 59 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7456 (pm20) REVERT: E 90 MET cc_start: 0.9146 (tpp) cc_final: 0.8915 (mmm) REVERT: E 94 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8615 (mm-30) REVERT: E 133 GLU cc_start: 0.8296 (mt-10) cc_final: 0.8088 (mt-10) REVERT: F 59 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8313 (ttmt) REVERT: G 91 GLU cc_start: 0.8665 (tt0) cc_final: 0.8394 (tm-30) REVERT: H 31 LYS cc_start: 0.8357 (tppp) cc_final: 0.8106 (tppp) REVERT: H 43 LYS cc_start: 0.8798 (mtpp) cc_final: 0.8546 (mttt) REVERT: H 117 LYS cc_start: 0.8281 (tptt) cc_final: 0.7716 (tptt) REVERT: H 118 TYR cc_start: 0.8669 (t80) cc_final: 0.8431 (t80) REVERT: T 129 ASN cc_start: 0.8979 (m-40) cc_final: 0.7701 (t0) REVERT: W 272 MET cc_start: 0.8809 (ppp) cc_final: 0.8489 (ppp) REVERT: W 276 ARG cc_start: 0.8851 (mmp80) cc_final: 0.8363 (mmp80) REVERT: W 538 MET cc_start: 0.8966 (tmm) cc_final: 0.8607 (ttt) REVERT: W 837 MET cc_start: 0.9017 (tpt) cc_final: 0.8743 (tpp) REVERT: W 1192 TYR cc_start: 0.7988 (t80) cc_final: 0.7704 (t80) outliers start: 31 outliers final: 10 residues processed: 177 average time/residue: 0.6346 time to fit residues: 124.8700 Evaluate side-chains 162 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain W residue 297 SER Chi-restraints excluded: chain W residue 355 THR Chi-restraints excluded: chain W residue 694 SER Chi-restraints excluded: chain W residue 1207 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 185 optimal weight: 7.9990 chunk 153 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 82 optimal weight: 50.0000 chunk 113 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 87 optimal weight: 50.0000 chunk 173 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 chunk 17 optimal weight: 10.0000 chunk 37 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN H 60 ASN T 138 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.109201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.067770 restraints weight = 47908.204| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.73 r_work: 0.2900 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19956 Z= 0.160 Angle : 0.638 10.501 28149 Z= 0.346 Chirality : 0.041 0.231 3150 Planarity : 0.004 0.036 2600 Dihedral : 27.496 129.421 4932 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.41 % Allowed : 16.65 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.21), residues: 1600 helix: 2.16 (0.16), residues: 990 sheet: -0.01 (0.51), residues: 90 loop : -0.05 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 35 TYR 0.023 0.001 TYR W1142 PHE 0.009 0.001 PHE W 379 TRP 0.015 0.001 TRP W 386 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 (19955) covalent geometry : angle 0.63784 / 0.35 (28149) hydrogen bonds : bond 0.04066 / 2.77 ( 1106) hydrogen bonds : angle 3.44402 / 2.47 ( 2915) Misc. bond : bond 0.00075 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASP cc_start: 0.8414 (t0) cc_final: 0.8093 (t0) REVERT: D 44 GLN cc_start: 0.9194 (tt0) cc_final: 0.8699 (tt0) REVERT: D 65 ASP cc_start: 0.8985 (t70) cc_final: 0.8493 (t0) REVERT: D 84 SER cc_start: 0.9295 (OUTLIER) cc_final: 0.9037 (p) REVERT: E 59 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7513 (pm20) REVERT: E 90 MET cc_start: 0.9179 (tpp) cc_final: 0.8951 (mmm) REVERT: E 94 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8569 (mm-30) REVERT: F 59 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8342 (ttmt) REVERT: G 91 GLU cc_start: 0.8689 (tt0) cc_final: 0.8411 (tm-30) REVERT: H 31 LYS cc_start: 0.8347 (tppp) cc_final: 0.8093 (tppp) REVERT: H 43 LYS cc_start: 0.8808 (mtpp) cc_final: 0.8555 (mttt) REVERT: H 117 LYS cc_start: 0.8315 (tptt) cc_final: 0.7751 (tptt) REVERT: H 118 TYR cc_start: 0.8695 (t80) cc_final: 0.8464 (t80) REVERT: T 129 ASN cc_start: 0.8996 (m-40) cc_final: 0.7707 (t0) REVERT: W 272 MET cc_start: 0.8851 (ppp) cc_final: 0.8616 (ppp) REVERT: W 538 MET cc_start: 0.8984 (tmm) cc_final: 0.8557 (ttt) REVERT: W 837 MET cc_start: 0.9013 (tpt) cc_final: 0.8737 (tpp) REVERT: W 1192 TYR cc_start: 0.7954 (t80) cc_final: 0.7692 (t80) outliers start: 20 outliers final: 11 residues processed: 166 average time/residue: 0.7077 time to fit residues: 130.2267 Evaluate side-chains 161 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain W residue 297 SER Chi-restraints excluded: chain W residue 355 THR Chi-restraints excluded: chain W residue 694 SER Chi-restraints excluded: chain W residue 1207 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 156 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 97 optimal weight: 40.0000 chunk 17 optimal weight: 10.0000 chunk 146 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 167 optimal weight: 0.8980 chunk 96 optimal weight: 20.0000 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN H 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.109653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.068458 restraints weight = 47865.648| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.73 r_work: 0.2913 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19956 Z= 0.139 Angle : 0.629 9.900 28149 Z= 0.343 Chirality : 0.040 0.230 3150 Planarity : 0.003 0.036 2600 Dihedral : 27.374 125.769 4932 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.62 % Allowed : 16.58 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.21), residues: 1600 helix: 2.22 (0.16), residues: 990 sheet: 0.01 (0.51), residues: 90 loop : -0.02 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG W 274 TYR 0.028 0.001 TYR W1142 PHE 0.009 0.001 PHE W 370 TRP 0.016 0.001 TRP W 386 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 (19955) covalent geometry : angle 0.62893 / 0.34 (28149) hydrogen bonds : bond 0.03855 / 2.62 ( 1106) hydrogen bonds : angle 3.39702 / 2.44 ( 2915) Misc. bond : bond 0.00011 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASP cc_start: 0.8395 (t0) cc_final: 0.8085 (t0) REVERT: D 44 GLN cc_start: 0.9169 (tt0) cc_final: 0.8678 (tt0) REVERT: D 65 ASP cc_start: 0.8969 (t70) cc_final: 0.8503 (t0) REVERT: D 84 SER cc_start: 0.9274 (OUTLIER) cc_final: 0.9025 (p) REVERT: E 59 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7539 (pm20) REVERT: E 90 MET cc_start: 0.9151 (tpp) cc_final: 0.8944 (mmm) REVERT: E 94 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8582 (mm-30) REVERT: F 59 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8324 (ttmt) REVERT: G 91 GLU cc_start: 0.8716 (tt0) cc_final: 0.8436 (tm-30) REVERT: H 43 LYS cc_start: 0.8789 (mtpp) cc_final: 0.8538 (mttt) REVERT: T 129 ASN cc_start: 0.9007 (m-40) cc_final: 0.7735 (t0) REVERT: W 181 ILE cc_start: 0.9216 (mt) cc_final: 0.8972 (mm) REVERT: W 272 MET cc_start: 0.8891 (ppp) cc_final: 0.8643 (ppp) REVERT: W 274 ARG cc_start: 0.8757 (mmp80) cc_final: 0.8520 (mmp80) REVERT: W 538 MET cc_start: 0.8945 (tmm) cc_final: 0.8527 (ttt) REVERT: W 837 MET cc_start: 0.9004 (tpt) cc_final: 0.8726 (tpp) REVERT: W 1192 TYR cc_start: 0.7965 (t80) cc_final: 0.7681 (t80) outliers start: 23 outliers final: 9 residues processed: 165 average time/residue: 0.6824 time to fit residues: 124.9395 Evaluate side-chains 159 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain W residue 355 THR Chi-restraints excluded: chain W residue 471 PHE Chi-restraints excluded: chain W residue 694 SER Chi-restraints excluded: chain W residue 1207 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 72 optimal weight: 9.9990 chunk 84 optimal weight: 50.0000 chunk 35 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 97 optimal weight: 40.0000 chunk 168 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN H 60 ASN ** W1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.109424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.068233 restraints weight = 47852.787| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.71 r_work: 0.2900 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19956 Z= 0.153 Angle : 0.643 12.154 28149 Z= 0.348 Chirality : 0.040 0.239 3150 Planarity : 0.004 0.049 2600 Dihedral : 27.314 123.227 4932 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.41 % Allowed : 17.36 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.21), residues: 1600 helix: 2.28 (0.16), residues: 987 sheet: 0.01 (0.51), residues: 90 loop : -0.07 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG W 274 TYR 0.024 0.001 TYR W1142 PHE 0.010 0.001 PHE W 789 TRP 0.012 0.001 TRP W 386 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 (19955) covalent geometry : angle 0.64256 / 0.35 (28149) hydrogen bonds : bond 0.03978 / 2.70 ( 1106) hydrogen bonds : angle 3.40772 / 2.44 ( 2915) Misc. bond : bond 0.00035 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASP cc_start: 0.8397 (t0) cc_final: 0.8099 (t0) REVERT: D 44 GLN cc_start: 0.9181 (tt0) cc_final: 0.8720 (tt0) REVERT: D 65 ASP cc_start: 0.8951 (t70) cc_final: 0.8456 (t0) REVERT: D 84 SER cc_start: 0.9291 (OUTLIER) cc_final: 0.9056 (p) REVERT: E 59 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7580 (pm20) REVERT: E 94 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8579 (mm-30) REVERT: F 59 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8342 (ttmt) REVERT: G 91 GLU cc_start: 0.8739 (tt0) cc_final: 0.8445 (tm-30) REVERT: H 31 LYS cc_start: 0.8459 (tppp) cc_final: 0.8188 (tppp) REVERT: H 43 LYS cc_start: 0.8835 (mtpp) cc_final: 0.8584 (mttt) REVERT: T 129 ASN cc_start: 0.9014 (m-40) cc_final: 0.7748 (t0) REVERT: W 272 MET cc_start: 0.8851 (ppp) cc_final: 0.8605 (ppp) REVERT: W 538 MET cc_start: 0.8969 (tmm) cc_final: 0.8542 (ttt) REVERT: W 837 MET cc_start: 0.9018 (tpt) cc_final: 0.8742 (tpp) REVERT: W 1192 TYR cc_start: 0.7964 (t80) cc_final: 0.7681 (t80) outliers start: 20 outliers final: 8 residues processed: 163 average time/residue: 0.7671 time to fit residues: 138.3716 Evaluate side-chains 155 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain W residue 355 THR Chi-restraints excluded: chain W residue 471 PHE Chi-restraints excluded: chain W residue 694 SER Chi-restraints excluded: chain W residue 1207 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 133 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 112 optimal weight: 0.0770 chunk 19 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 125 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 153 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN H 60 ASN ** W1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.109980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.069764 restraints weight = 47903.243| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.82 r_work: 0.2920 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19956 Z= 0.134 Angle : 0.622 10.225 28149 Z= 0.340 Chirality : 0.040 0.338 3150 Planarity : 0.004 0.046 2600 Dihedral : 27.228 120.586 4932 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.13 % Allowed : 17.36 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.21), residues: 1600 helix: 2.28 (0.16), residues: 990 sheet: 0.01 (0.51), residues: 90 loop : -0.02 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG W 274 TYR 0.030 0.002 TYR W1142 PHE 0.009 0.001 PHE W1122 TRP 0.015 0.001 TRP W 386 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (19955) covalent geometry : angle 0.62198 / 0.34 (28149) hydrogen bonds : bond 0.03789 / 2.57 ( 1106) hydrogen bonds : angle 3.34781 / 2.40 ( 2915) Misc. bond : bond 0.00004 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6741.88 seconds wall clock time: 115 minutes 24.63 seconds (6924.63 seconds total)