Starting phenix.real_space_refine on Thu Sep 18 17:08:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gd3_51247/09_2025/9gd3_51247.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gd3_51247/09_2025/9gd3_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_51247/09_2025/9gd3_51247.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gd3_51247/09_2025/9gd3_51247.map" model { file = "/net/cci-nas-00/data/ceres_data/9gd3_51247/09_2025/9gd3_51247.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gd3_51247/09_2025/9gd3_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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: 4.65, per 1000 atoms: 0.24 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: 1.73 Conformation dependent library (CDL) restraints added in 587.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 3.01 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: 6.70 Time building geometry restraints manager: 2.26 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 1.50e-02 4.44e+03 3.70e+00 bond pdb=" O3' DG J 8 " pdb=" P DT J 9 " ideal model delta sigma weight residual 1.607 1.582 0.025 1.50e-02 4.44e+03 2.83e+00 bond pdb=" C4 ADP W1501 " pdb=" C5 ADP W1501 " ideal model delta sigma weight residual 1.490 1.463 0.027 2.00e-02 2.50e+03 1.80e+00 bond pdb=" O3' DA I 16 " pdb=" P DA I 17 " ideal model delta sigma weight residual 1.607 1.587 0.020 1.50e-02 4.44e+03 1.74e+00 ... (remaining 19950 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 27752 2.90 - 5.80: 384 5.80 - 8.70: 9 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=" O3' DG J 8 " pdb=" C3' DG J 8 " pdb=" C2' DG J 8 " ideal model delta sigma weight residual 111.50 104.56 6.94 1.50e+00 4.44e-01 2.14e+01 angle pdb=" O3' DG J -70 " pdb=" C3' DG J -70 " pdb=" C2' DG J -70 " ideal model delta sigma weight residual 111.50 104.81 6.69 1.50e+00 4.44e-01 1.99e+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 ... (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 - 0.052: 2230 0.052 - 0.105: 658 0.105 - 0.157: 198 0.157 - 0.210: 60 0.210 - 0.262: 4 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 -2.66 -2.92 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" C3' DG J 8 " pdb=" C4' DG J 8 " pdb=" O3' DG J 8 " pdb=" C2' DG J 8 " both_signs ideal model delta sigma weight residual False -2.66 -2.89 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" C3' DG J 27 " pdb=" C4' DG J 27 " pdb=" O3' DG J 27 " pdb=" C2' DG J 27 " both_signs ideal model delta sigma weight residual False -2.66 -2.87 0.21 2.00e-01 2.50e+01 1.11e+00 ... (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: 3.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 23.290 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 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:8.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 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 : 0.006 0.416 19956 Z= 0.375 Angle : 0.850 14.495 28149 Z= 0.531 Chirality : 0.057 0.262 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 aren 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 covalent geometry : bond 0.00509 (19955) covalent geometry : angle 0.85033 (28149) hydrogen bonds : bond 0.12740 ( 1106) hydrogen bonds : angle 5.36984 ( 2915) Misc. bond : bond 0.41591 ( 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 : 0.766 Fit side-chains revert: symmetry clash 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: 0.9080 time to fit residues: 275.1533 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 : 0.626 ------------------------------------------------------------------------------- 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: 0.0170 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: 5.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 76 GLN C 73 ASN F 75 HIS G 110 ASN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 667 ASN ** W 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W1150 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.111045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.070341 restraints weight = 48185.314| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.63 r_work: 0.2964 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19956 Z= 0.180 Angle : 0.614 7.664 28149 Z= 0.357 Chirality : 0.036 0.155 3150 Planarity : 0.004 0.033 2600 Dihedral : 27.546 175.739 4932 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.26 % Allowed : 12.00 % Favored : 85.74 % 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 aren not related in a simple way. whole: 1.61 (0.20), residues: 1600 helix: 1.73 (0.16), residues: 980 sheet: 0.33 (0.51), residues: 90 loop : 0.06 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG T 130 TYR 0.017 0.002 TYR H 80 PHE 0.020 0.002 PHE W 676 TRP 0.005 0.001 TRP W 386 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00392 (19955) covalent geometry : angle 0.61445 (28149) hydrogen bonds : bond 0.04503 ( 1106) hydrogen bonds : angle 3.73443 ( 2915) Misc. bond : bond 0.00288 ( 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 204 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASP cc_start: 0.8206 (t0) cc_final: 0.7962 (t0) REVERT: C 92 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7964 (mt-10) REVERT: D 65 ASP cc_start: 0.8867 (t70) cc_final: 0.8394 (t0) REVERT: E 79 LYS cc_start: 0.6963 (tptt) cc_final: 0.6687 (tptm) REVERT: G 64 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8567 (tp30) REVERT: T 129 ASN cc_start: 0.8884 (m-40) cc_final: 0.7523 (t0) REVERT: W 270 MET cc_start: 0.8755 (mmp) cc_final: 0.8479 (mmp) REVERT: W 681 MET cc_start: 0.7443 (mpt) cc_final: 0.7220 (mpt) REVERT: W 1142 TYR cc_start: 0.8993 (t80) cc_final: 0.8749 (t80) REVERT: W 1192 TYR cc_start: 0.8227 (t80) cc_final: 0.8014 (t80) outliers start: 32 outliers final: 10 residues processed: 189 average time/residue: 0.7033 time to fit residues: 146.9639 Evaluate side-chains 151 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain C residue 92 GLU 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 W residue 297 SER Chi-restraints excluded: chain W residue 453 CYS 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=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: 5.9990 chunk 182 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 168 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 164 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 144 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 75 HIS C 73 ASN G 110 ASN H 60 ASN W 132 ASN W 685 ASN ** W 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.107938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.067186 restraints weight = 48064.812| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.58 r_work: 0.2861 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 19956 Z= 0.266 Angle : 0.639 8.041 28149 Z= 0.364 Chirality : 0.039 0.151 3150 Planarity : 0.004 0.041 2600 Dihedral : 27.518 140.485 4932 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.96 % Allowed : 13.27 % Favored : 83.77 % 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 aren not related in a simple way. whole: 1.59 (0.20), residues: 1600 helix: 1.79 (0.16), residues: 992 sheet: 0.20 (0.52), residues: 90 loop : -0.14 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG W 274 TYR 0.033 0.002 TYR F 88 PHE 0.016 0.002 PHE W 379 TRP 0.007 0.001 TRP W 793 HIS 0.005 0.001 HIS W 428 Details of bonding type rmsd covalent geometry : bond 0.00616 (19955) covalent geometry : angle 0.63873 (28149) hydrogen bonds : bond 0.04913 ( 1106) hydrogen bonds : angle 3.68063 ( 2915) Misc. bond : bond 0.00060 ( 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 193 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 151 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASP cc_start: 0.8376 (t0) cc_final: 0.7986 (t0) REVERT: C 35 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.7974 (mpt-90) REVERT: D 65 ASP cc_start: 0.8999 (t70) cc_final: 0.8499 (t0) REVERT: D 102 GLU cc_start: 0.7909 (pp20) cc_final: 0.7562 (pp20) REVERT: E 79 LYS cc_start: 0.7537 (tptt) cc_final: 0.7159 (tptt) REVERT: E 133 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8181 (mt-10) REVERT: G 64 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8604 (tp30) REVERT: G 91 GLU cc_start: 0.8693 (tt0) cc_final: 0.8479 (tm-30) REVERT: H 117 LYS cc_start: 0.8362 (tptt) cc_final: 0.8055 (tptt) REVERT: T 129 ASN cc_start: 0.8927 (m-40) cc_final: 0.7587 (t0) REVERT: W 538 MET cc_start: 0.8943 (tmm) cc_final: 0.8500 (ttt) REVERT: W 681 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.7287 (mpt) REVERT: W 1056 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8254 (mpp) REVERT: W 1192 TYR cc_start: 0.8162 (t80) cc_final: 0.7823 (t80) outliers start: 42 outliers final: 15 residues processed: 177 average time/residue: 0.7552 time to fit residues: 147.4046 Evaluate side-chains 160 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU 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 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 249 PHE Chi-restraints excluded: chain W residue 267 ILE Chi-restraints excluded: chain W residue 297 SER 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 781 MET Chi-restraints excluded: chain W residue 1007 MET Chi-restraints excluded: chain W residue 1056 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: 6.9990 chunk 138 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 129 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 175 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3998 r_free = 0.3998 target = 0.109394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.068651 restraints weight = 47671.830| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.73 r_work: 0.2904 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 19956 Z= 0.158 Angle : 0.567 7.678 28149 Z= 0.324 Chirality : 0.034 0.141 3150 Planarity : 0.003 0.034 2600 Dihedral : 27.142 136.880 4932 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.82 % Allowed : 13.41 % Favored : 83.77 % 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 aren not related in a simple way. whole: 1.94 (0.21), residues: 1600 helix: 2.11 (0.16), residues: 994 sheet: 0.19 (0.53), residues: 90 loop : -0.09 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG W 274 TYR 0.024 0.001 TYR F 88 PHE 0.009 0.001 PHE W 370 TRP 0.004 0.001 TRP W 391 HIS 0.003 0.000 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00350 (19955) covalent geometry : angle 0.56681 (28149) hydrogen bonds : bond 0.03834 ( 1106) hydrogen bonds : angle 3.39503 ( 2915) Misc. bond : bond 0.00012 ( 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 202 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 162 time to evaluate : 0.554 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: 0.8367 (t0) cc_final: 0.8006 (t0) REVERT: D 65 ASP cc_start: 0.8968 (t70) cc_final: 0.8467 (t0) REVERT: E 79 LYS cc_start: 0.7231 (tptt) cc_final: 0.6952 (tptm) REVERT: E 90 MET cc_start: 0.9119 (tpp) cc_final: 0.8907 (mmp) REVERT: E 94 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8618 (mm-30) REVERT: F 59 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8349 (ttmt) REVERT: G 91 GLU cc_start: 0.8664 (tt0) cc_final: 0.8445 (tm-30) REVERT: H 43 LYS cc_start: 0.8835 (mtpp) cc_final: 0.8581 (mttt) REVERT: H 117 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7935 (tptt) REVERT: T 129 ASN cc_start: 0.8903 (m-40) cc_final: 0.7583 (t0) REVERT: W 538 MET cc_start: 0.8896 (tmm) cc_final: 0.8479 (ttt) REVERT: W 681 MET cc_start: 0.7507 (OUTLIER) cc_final: 0.7281 (mpt) REVERT: W 691 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8930 (mt) REVERT: W 837 MET cc_start: 0.9089 (tpt) cc_final: 0.8731 (tpp) REVERT: W 1192 TYR cc_start: 0.8081 (t80) cc_final: 0.7819 (t80) outliers start: 40 outliers final: 9 residues processed: 182 average time/residue: 0.8222 time to fit residues: 164.6409 Evaluate side-chains 161 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain D residue 75 SER 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 H residue 117 LYS Chi-restraints excluded: chain W residue 267 ILE Chi-restraints excluded: chain W residue 681 MET Chi-restraints excluded: chain W residue 691 ILE Chi-restraints excluded: chain W residue 694 SER 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: 7.9990 chunk 44 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 86 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 chunk 43 optimal weight: 0.9980 chunk 131 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN H 60 ASN W 206 ASN W 210 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.108353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.067020 restraints weight = 47928.191| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.69 r_work: 0.2874 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 19956 Z= 0.205 Angle : 0.595 8.715 28149 Z= 0.335 Chirality : 0.036 0.190 3150 Planarity : 0.004 0.037 2600 Dihedral : 27.040 125.763 4932 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.03 % Allowed : 13.76 % Favored : 83.20 % 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 aren not related in a simple way. whole: 1.93 (0.21), residues: 1600 helix: 2.10 (0.16), residues: 995 sheet: 0.09 (0.52), residues: 90 loop : -0.09 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG W 274 TYR 0.028 0.002 TYR W1142 PHE 0.011 0.001 PHE W 379 TRP 0.013 0.001 TRP W 386 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00469 (19955) covalent geometry : angle 0.59518 (28149) hydrogen bonds : bond 0.04213 ( 1106) hydrogen bonds : angle 3.44556 ( 2915) Misc. bond : bond 0.00062 ( 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 205 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 162 time to evaluate : 0.570 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: 0.8451 (t0) cc_final: 0.8105 (t0) REVERT: D 65 ASP cc_start: 0.8992 (t70) cc_final: 0.8781 (t0) REVERT: D 68 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8231 (mp0) REVERT: E 59 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7612 (pm20) REVERT: F 59 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8359 (ttmt) REVERT: G 64 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.8719 (tp30) REVERT: G 91 GLU cc_start: 0.8699 (tt0) cc_final: 0.8491 (tm-30) REVERT: H 43 LYS cc_start: 0.8827 (mtpp) cc_final: 0.8591 (mttt) REVERT: H 110 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8210 (mt-10) REVERT: H 117 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8024 (tptt) REVERT: T 129 ASN cc_start: 0.8906 (m-40) cc_final: 0.7595 (t0) REVERT: W 538 MET cc_start: 0.8931 (tmm) cc_final: 0.8607 (ttt) REVERT: W 681 MET cc_start: 0.7500 (OUTLIER) cc_final: 0.7258 (mpt) REVERT: W 837 MET cc_start: 0.9054 (tpt) cc_final: 0.8749 (tpp) REVERT: W 1192 TYR cc_start: 0.7960 (t80) cc_final: 0.7752 (t80) outliers start: 43 outliers final: 15 residues processed: 187 average time/residue: 0.7105 time to fit residues: 146.4693 Evaluate side-chains 168 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain T residue 135 VAL Chi-restraints excluded: chain W residue 267 ILE Chi-restraints excluded: chain W residue 297 SER Chi-restraints excluded: chain W residue 681 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 120 optimal weight: 5.9990 chunk 9 optimal weight: 0.0570 chunk 73 optimal weight: 2.9990 chunk 109 optimal weight: 9.9990 chunk 148 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 106 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 173 optimal weight: 5.9990 overall best weight: 1.3304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3992 r_free = 0.3992 target = 0.109095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.068049 restraints weight = 47431.487| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.75 r_work: 0.2898 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19956 Z= 0.164 Angle : 0.568 8.875 28149 Z= 0.320 Chirality : 0.035 0.174 3150 Planarity : 0.003 0.034 2600 Dihedral : 26.838 122.643 4932 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.33 % Allowed : 15.46 % Favored : 82.22 % 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 aren not related in a simple way. whole: 2.08 (0.21), residues: 1600 helix: 2.25 (0.16), residues: 990 sheet: 0.04 (0.51), residues: 90 loop : -0.03 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG W 274 TYR 0.027 0.001 TYR W1142 PHE 0.009 0.001 PHE W 370 TRP 0.017 0.001 TRP W 386 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00372 (19955) covalent geometry : angle 0.56794 (28149) hydrogen bonds : bond 0.03746 ( 1106) hydrogen bonds : angle 3.32214 ( 2915) Misc. bond : bond 0.00028 ( 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 188 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 155 time to evaluate : 0.671 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: 0.8431 (t0) cc_final: 0.8067 (t0) REVERT: D 65 ASP cc_start: 0.8982 (t70) cc_final: 0.8480 (t0) REVERT: E 59 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7620 (pm20) REVERT: E 94 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8565 (mm-30) REVERT: F 59 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8358 (ttmt) REVERT: G 64 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8701 (tp30) REVERT: G 91 GLU cc_start: 0.8709 (tt0) cc_final: 0.8487 (tm-30) REVERT: H 43 LYS cc_start: 0.8785 (mtpp) cc_final: 0.8549 (mttt) REVERT: H 110 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8204 (mt-10) REVERT: H 117 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.8010 (tptt) REVERT: T 129 ASN cc_start: 0.8952 (m-40) cc_final: 0.7595 (t0) REVERT: W 538 MET cc_start: 0.8913 (tmm) cc_final: 0.8615 (ttt) REVERT: W 837 MET cc_start: 0.9055 (tpt) cc_final: 0.8759 (tpp) outliers start: 33 outliers final: 11 residues processed: 173 average time/residue: 0.7827 time to fit residues: 148.5731 Evaluate side-chains 161 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 86 SER 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 64 GLU Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain W residue 297 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 102 optimal weight: 9.9990 chunk 40 optimal weight: 0.8980 chunk 169 optimal weight: 5.9990 chunk 118 optimal weight: 0.2980 chunk 11 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 chunk 179 optimal weight: 20.0000 chunk 142 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN H 60 ASN W1027 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.109027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.067966 restraints weight = 47868.198| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.76 r_work: 0.2887 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 19956 Z= 0.171 Angle : 0.573 8.691 28149 Z= 0.322 Chirality : 0.035 0.162 3150 Planarity : 0.003 0.037 2600 Dihedral : 26.784 120.659 4932 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.26 % Allowed : 16.44 % Favored : 81.30 % 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 aren not related in a simple way. whole: 2.16 (0.21), residues: 1600 helix: 2.33 (0.16), residues: 991 sheet: 0.06 (0.52), residues: 90 loop : -0.04 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG W 274 TYR 0.031 0.002 TYR F 88 PHE 0.009 0.001 PHE W 370 TRP 0.012 0.001 TRP W 386 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00388 (19955) covalent geometry : angle 0.57296 (28149) hydrogen bonds : bond 0.03791 ( 1106) hydrogen bonds : angle 3.31046 ( 2915) Misc. bond : bond 0.00038 ( 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 190 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 0.643 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: 0.8459 (t0) cc_final: 0.8084 (t0) REVERT: C 61 GLU cc_start: 0.8050 (tt0) cc_final: 0.7475 (tt0) REVERT: C 90 ASP cc_start: 0.8699 (t0) cc_final: 0.8421 (t0) REVERT: D 44 GLN cc_start: 0.9200 (tt0) cc_final: 0.8709 (tt0) REVERT: D 65 ASP cc_start: 0.8985 (t70) cc_final: 0.8470 (t0) REVERT: E 59 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7653 (pm20) REVERT: E 94 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8604 (mm-30) REVERT: F 59 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8603 (ttmt) REVERT: G 64 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8723 (tp30) REVERT: G 91 GLU cc_start: 0.8734 (tt0) cc_final: 0.8396 (tm-30) REVERT: H 43 LYS cc_start: 0.8788 (mtpp) cc_final: 0.8554 (mttt) REVERT: H 110 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8206 (mt-10) REVERT: H 117 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.7981 (tptt) REVERT: T 129 ASN cc_start: 0.8953 (m-40) cc_final: 0.7574 (t0) REVERT: W 538 MET cc_start: 0.8942 (tmm) cc_final: 0.8574 (ttt) REVERT: W 837 MET cc_start: 0.9049 (tpt) cc_final: 0.8713 (tpp) outliers start: 32 outliers final: 10 residues processed: 179 average time/residue: 0.8081 time to fit residues: 158.9726 Evaluate side-chains 159 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 115 VAL 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 64 GLU Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain W residue 297 SER 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: 20.0000 chunk 153 optimal weight: 0.3980 chunk 57 optimal weight: 0.8980 chunk 82 optimal weight: 20.0000 chunk 113 optimal weight: 0.5980 chunk 154 optimal weight: 0.5980 chunk 87 optimal weight: 20.0000 chunk 173 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 17 optimal weight: 9.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN H 60 ASN H 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.110152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.070715 restraints weight = 47849.744| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.80 r_work: 0.2937 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19956 Z= 0.137 Angle : 0.570 9.962 28149 Z= 0.318 Chirality : 0.034 0.148 3150 Planarity : 0.004 0.049 2600 Dihedral : 26.621 115.007 4932 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.48 % Allowed : 16.87 % Favored : 81.65 % 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 aren not related in a simple way. whole: 2.27 (0.21), residues: 1600 helix: 2.43 (0.16), residues: 989 sheet: 0.09 (0.52), residues: 90 loop : -0.01 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG W 274 TYR 0.032 0.001 TYR W1142 PHE 0.009 0.001 PHE W 370 TRP 0.014 0.001 TRP W 386 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00300 (19955) covalent geometry : angle 0.57014 (28149) hydrogen bonds : bond 0.03430 ( 1106) hydrogen bonds : angle 3.21504 ( 2915) Misc. bond : bond 0.00008 ( 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 178 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASP cc_start: 0.8418 (t0) cc_final: 0.8045 (t0) REVERT: C 24 GLN cc_start: 0.8820 (mm-40) cc_final: 0.8616 (mp10) REVERT: C 61 GLU cc_start: 0.8084 (tt0) cc_final: 0.7852 (tt0) REVERT: D 44 GLN cc_start: 0.9203 (tt0) cc_final: 0.8766 (tt0) REVERT: D 65 ASP cc_start: 0.8944 (t70) cc_final: 0.8465 (t0) REVERT: D 113 LYS cc_start: 0.9009 (ttmm) cc_final: 0.8743 (tttp) REVERT: E 59 GLU cc_start: 0.8150 (pt0) cc_final: 0.7640 (pm20) REVERT: E 94 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8568 (mm-30) REVERT: F 59 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8317 (ttmt) REVERT: G 91 GLU cc_start: 0.8694 (tt0) cc_final: 0.8346 (tm-30) REVERT: H 43 LYS cc_start: 0.8764 (mtpp) cc_final: 0.8528 (mttt) REVERT: H 83 ARG cc_start: 0.8977 (mmt90) cc_final: 0.8770 (mmt90) REVERT: H 110 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8195 (mt-10) REVERT: H 117 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7962 (tptt) REVERT: W 272 MET cc_start: 0.8884 (ppp) cc_final: 0.8561 (ppp) REVERT: W 538 MET cc_start: 0.8907 (tmm) cc_final: 0.8569 (ttt) REVERT: W 837 MET cc_start: 0.9040 (tpt) cc_final: 0.8737 (tpp) outliers start: 21 outliers final: 8 residues processed: 169 average time/residue: 0.7509 time to fit residues: 139.8177 Evaluate side-chains 158 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 25 PHE Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain W residue 694 SER Chi-restraints excluded: chain W residue 1207 THR Chi-restraints excluded: chain W residue 1261 LEU 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: 9.9990 chunk 38 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 146 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 131 optimal weight: 0.0020 chunk 62 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 overall best weight: 1.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3987 r_free = 0.3987 target = 0.108890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.067757 restraints weight = 47774.388| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.72 r_work: 0.2889 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19956 Z= 0.193 Angle : 0.601 9.148 28149 Z= 0.334 Chirality : 0.036 0.155 3150 Planarity : 0.004 0.041 2600 Dihedral : 26.724 116.434 4932 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.62 % Allowed : 17.50 % Favored : 80.88 % 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 aren not related in a simple way. whole: 2.19 (0.21), residues: 1600 helix: 2.36 (0.16), residues: 988 sheet: -0.02 (0.50), residues: 95 loop : -0.03 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG W 274 TYR 0.039 0.002 TYR W1142 PHE 0.010 0.001 PHE E 84 TRP 0.009 0.001 TRP W 386 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00442 (19955) covalent geometry : angle 0.60055 (28149) hydrogen bonds : bond 0.04009 ( 1106) hydrogen bonds : angle 3.35042 ( 2915) Misc. bond : bond 0.00054 ( 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 167 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASP cc_start: 0.8426 (t0) cc_final: 0.8072 (t0) REVERT: D 44 GLN cc_start: 0.9222 (tt0) cc_final: 0.8691 (tt0) REVERT: D 65 ASP cc_start: 0.8986 (t70) cc_final: 0.8472 (t0) REVERT: D 113 LYS cc_start: 0.9038 (ttmm) cc_final: 0.8753 (tttp) REVERT: E 59 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7729 (pm20) REVERT: E 94 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8595 (mm-30) REVERT: F 59 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8594 (ttmt) REVERT: G 91 GLU cc_start: 0.8717 (tt0) cc_final: 0.8396 (tm-30) REVERT: H 43 LYS cc_start: 0.8824 (mtpp) cc_final: 0.8593 (mttt) REVERT: H 110 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8199 (mt-10) REVERT: H 117 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8008 (tptt) REVERT: W 272 MET cc_start: 0.8986 (ppp) cc_final: 0.8710 (ppp) REVERT: W 274 ARG cc_start: 0.8848 (mmp80) cc_final: 0.8597 (mmp80) REVERT: W 837 MET cc_start: 0.9049 (tpt) cc_final: 0.8717 (tpp) outliers start: 23 outliers final: 7 residues processed: 155 average time/residue: 0.7097 time to fit residues: 121.2840 Evaluate side-chains 151 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 140 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 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 H residue 117 LYS Chi-restraints excluded: chain W residue 297 SER 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: 4.9990 chunk 84 optimal weight: 40.0000 chunk 35 optimal weight: 10.0000 chunk 23 optimal weight: 0.0570 chunk 175 optimal weight: 0.0970 chunk 19 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 168 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4008 r_free = 0.4008 target = 0.110046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.070120 restraints weight = 47960.119| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.79 r_work: 0.2932 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19956 Z= 0.139 Angle : 0.605 13.560 28149 Z= 0.333 Chirality : 0.035 0.236 3150 Planarity : 0.003 0.043 2600 Dihedral : 26.666 112.202 4932 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.20 % Allowed : 18.00 % Favored : 80.80 % 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 aren not related in a simple way. whole: 2.27 (0.21), residues: 1600 helix: 2.42 (0.16), residues: 988 sheet: 0.07 (0.50), residues: 95 loop : 0.00 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG W 274 TYR 0.038 0.001 TYR W1142 PHE 0.008 0.001 PHE W 370 TRP 0.012 0.001 TRP W 386 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00303 (19955) covalent geometry : angle 0.60519 (28149) hydrogen bonds : bond 0.03567 ( 1106) hydrogen bonds : angle 3.28850 ( 2915) Misc. bond : bond 0.00026 ( 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 164 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASP cc_start: 0.8386 (t0) cc_final: 0.8085 (t0) REVERT: D 44 GLN cc_start: 0.9212 (tt0) cc_final: 0.8739 (tt0) REVERT: D 65 ASP cc_start: 0.8944 (t70) cc_final: 0.8457 (t0) REVERT: D 113 LYS cc_start: 0.9004 (ttmm) cc_final: 0.8731 (tttp) REVERT: E 59 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7686 (pm20) REVERT: E 94 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8601 (mm-30) REVERT: F 59 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8334 (ttmt) REVERT: G 91 GLU cc_start: 0.8685 (tt0) cc_final: 0.8352 (tm-30) REVERT: H 43 LYS cc_start: 0.8790 (mtpp) cc_final: 0.8549 (mttt) REVERT: H 110 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8207 (mt-10) REVERT: H 117 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.7954 (tptt) REVERT: W 270 MET cc_start: 0.8688 (mmp) cc_final: 0.8156 (tpt) REVERT: W 272 MET cc_start: 0.8974 (ppp) cc_final: 0.8697 (ppp) REVERT: W 538 MET cc_start: 0.8888 (ttt) cc_final: 0.8479 (ttt) REVERT: W 723 MET cc_start: 0.8506 (tpp) cc_final: 0.8277 (tpt) REVERT: W 837 MET cc_start: 0.9024 (tpt) cc_final: 0.8711 (tpp) outliers start: 17 outliers final: 6 residues processed: 156 average time/residue: 0.7270 time to fit residues: 124.9902 Evaluate side-chains 153 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 143 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 59 GLU 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 H residue 117 LYS Chi-restraints excluded: chain W residue 297 SER 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: 0.9980 chunk 137 optimal weight: 1.9990 chunk 112 optimal weight: 0.1980 chunk 19 optimal weight: 0.0370 chunk 134 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 overall best weight: 1.0462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4003 r_free = 0.4003 target = 0.109749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.070430 restraints weight = 47899.153| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.68 r_work: 0.2923 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.4099 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= 0.154 Angle : 0.605 13.360 28149 Z= 0.333 Chirality : 0.035 0.278 3150 Planarity : 0.004 0.054 2600 Dihedral : 26.607 107.292 4932 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.99 % Allowed : 18.35 % Favored : 80.66 % 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 aren not related in a simple way. whole: 2.24 (0.21), residues: 1600 helix: 2.43 (0.16), residues: 987 sheet: 0.10 (0.50), residues: 95 loop : -0.08 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG W 274 TYR 0.041 0.001 TYR W1142 PHE 0.009 0.001 PHE W 370 TRP 0.012 0.001 TRP W 386 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00345 (19955) covalent geometry : angle 0.60530 (28149) hydrogen bonds : bond 0.03642 ( 1106) hydrogen bonds : angle 3.30459 ( 2915) Misc. bond : bond 0.00015 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7154.55 seconds wall clock time: 122 minutes 11.56 seconds (7331.56 seconds total)