Starting phenix.real_space_refine on Wed Jan 22 13:01:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gd3_51247/01_2025/9gd3_51247.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gd3_51247/01_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_51247/01_2025/9gd3_51247.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gd3_51247/01_2025/9gd3_51247.map" model { file = "/net/cci-nas-00/data/ceres_data/9gd3_51247/01_2025/9gd3_51247.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gd3_51247/01_2025/9gd3_51247.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 11.86, per 1000 atoms: 0.62 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: 4.61 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 9.05 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: 18.25 Time building geometry restraints manager: 5.36 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: 5.000 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: 0.010 Extract box with map and model: 0.820 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 56.130 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.100 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: 0.010 Load rotamer database and sin/cos tables:12.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.010 ------------------------------------------------------------------------------- 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 : 0.005 0.032 19955 Z= 0.279 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.016 0.004 TRP W 507 HIS 0.012 0.003 HIS D 46 PHE 0.024 0.002 PHE C 25 TYR 0.026 0.005 TYR W1192 ARG 0.023 0.003 ARG B 17 *********************** 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 : 1.756 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: 2.0034 time to fit residues: 613.2180 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 : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 0.7980 chunk 140 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 145 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 88 optimal weight: 10.0000 chunk 108 optimal weight: 0.9980 chunk 168 optimal weight: 20.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 B 75 HIS 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.111223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.071632 restraints weight = 47979.342| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.70 r_work: 0.2952 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19955 Z= 0.226 Angle : 0.618 7.376 28149 Z= 0.359 Chirality : 0.035 0.141 3150 Planarity : 0.004 0.033 2600 Dihedral : 27.548 177.085 4932 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.20), residues: 1600 helix: 1.73 (0.16), residues: 980 sheet: 0.34 (0.51), residues: 90 loop : 0.08 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP W 793 HIS 0.007 0.001 HIS B 75 PHE 0.020 0.002 PHE W1263 TYR 0.014 0.002 TYR F 88 ARG 0.007 0.001 ARG T 130 *********************** 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 206 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASP cc_start: 0.8221 (t0) cc_final: 0.7959 (t0) REVERT: C 92 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7955 (mt-10) REVERT: D 65 ASP cc_start: 0.8869 (t70) cc_final: 0.8401 (t0) REVERT: E 79 LYS cc_start: 0.6964 (tptt) cc_final: 0.6678 (tptm) REVERT: G 64 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8545 (tp30) REVERT: T 129 ASN cc_start: 0.8858 (m-40) cc_final: 0.7461 (t0) REVERT: W 270 MET cc_start: 0.8757 (mmp) cc_final: 0.8492 (mmp) REVERT: W 681 MET cc_start: 0.7457 (mpt) cc_final: 0.7228 (mpt) REVERT: W 1142 TYR cc_start: 0.9004 (t80) cc_final: 0.8758 (t80) REVERT: W 1192 TYR cc_start: 0.8202 (t80) cc_final: 0.7973 (t80) outliers start: 32 outliers final: 10 residues processed: 192 average time/residue: 1.5931 time to fit residues: 340.1040 Evaluate side-chains 153 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 1.689 ------------------------------------------------------------------------------- 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 127 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 160 optimal weight: 0.6980 chunk 51 optimal weight: 20.0000 chunk 105 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 73 ASN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 132 ASN ** W 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.110119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.068916 restraints weight = 47733.609| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.69 r_work: 0.2930 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19955 Z= 0.227 Angle : 0.578 8.104 28149 Z= 0.335 Chirality : 0.035 0.147 3150 Planarity : 0.004 0.055 2600 Dihedral : 27.314 153.324 4932 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.40 % Allowed : 13.27 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.21), residues: 1600 helix: 2.05 (0.16), residues: 986 sheet: 0.27 (0.51), residues: 90 loop : 0.07 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP W 386 HIS 0.003 0.001 HIS B 75 PHE 0.012 0.001 PHE W1263 TYR 0.033 0.002 TYR F 88 ARG 0.008 0.000 ARG T 130 *********************** 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 187 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASP cc_start: 0.8325 (t0) cc_final: 0.7913 (t0) REVERT: C 35 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.7942 (mpt-90) REVERT: C 61 GLU cc_start: 0.8046 (tt0) cc_final: 0.7674 (tt0) REVERT: C 64 GLU cc_start: 0.8884 (tp30) cc_final: 0.8658 (tp30) REVERT: D 65 ASP cc_start: 0.8902 (t70) cc_final: 0.8443 (t0) REVERT: E 79 LYS cc_start: 0.7080 (tptt) cc_final: 0.6682 (tptt) REVERT: E 94 GLU cc_start: 0.8767 (tp30) cc_final: 0.8558 (mm-30) REVERT: G 64 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8589 (tp30) REVERT: T 129 ASN cc_start: 0.8905 (m-40) cc_final: 0.7555 (t0) REVERT: W 538 MET cc_start: 0.8927 (tmm) cc_final: 0.8346 (ttt) REVERT: W 681 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7278 (mpt) REVERT: W 1056 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.8126 (mpp) REVERT: W 1192 TYR cc_start: 0.8122 (t80) cc_final: 0.7798 (t80) outliers start: 34 outliers final: 11 residues processed: 175 average time/residue: 1.7730 time to fit residues: 343.3131 Evaluate side-chains 156 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 1.780 ------------------------------------------------------------------------------- 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 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 267 ILE 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 97 optimal weight: 10.0000 chunk 176 optimal weight: 20.0000 chunk 119 optimal weight: 0.0170 chunk 144 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 170 optimal weight: 0.3980 chunk 70 optimal weight: 20.0000 chunk 179 optimal weight: 20.0000 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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 = 0.4037 r_free = 0.4037 target = 0.111615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.071666 restraints weight = 47914.838| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.66 r_work: 0.2987 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19955 Z= 0.171 Angle : 0.545 7.416 28149 Z= 0.313 Chirality : 0.033 0.126 3150 Planarity : 0.003 0.035 2600 Dihedral : 26.847 140.481 4932 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.19 % Allowed : 13.69 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.21), residues: 1600 helix: 2.32 (0.16), residues: 986 sheet: 0.30 (0.52), residues: 90 loop : 0.05 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP W 386 HIS 0.003 0.000 HIS C 31 PHE 0.010 0.001 PHE W 370 TYR 0.021 0.001 TYR F 88 ARG 0.011 0.000 ARG W 276 *********************** 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: 31 poor density : 171 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 GLU cc_start: 0.8902 (tp30) cc_final: 0.8688 (tp30) REVERT: C 77 ARG cc_start: 0.7904 (mtp85) cc_final: 0.7684 (mtt90) REVERT: D 65 ASP cc_start: 0.8889 (t70) cc_final: 0.8414 (t0) REVERT: E 79 LYS cc_start: 0.7023 (tptt) cc_final: 0.6682 (tptt) REVERT: E 94 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8523 (mm-30) REVERT: H 43 LYS cc_start: 0.8783 (mtpp) cc_final: 0.8533 (mttt) REVERT: T 129 ASN cc_start: 0.8867 (m-40) cc_final: 0.7525 (t0) REVERT: W 538 MET cc_start: 0.8810 (tmm) cc_final: 0.8347 (ttt) REVERT: W 681 MET cc_start: 0.7478 (OUTLIER) cc_final: 0.7252 (mpt) REVERT: W 837 MET cc_start: 0.9057 (tpt) cc_final: 0.8725 (tpp) REVERT: W 1056 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.8196 (mpp) REVERT: W 1192 TYR cc_start: 0.7899 (t80) cc_final: 0.7639 (t80) outliers start: 31 outliers final: 9 residues processed: 188 average time/residue: 1.6705 time to fit residues: 347.4349 Evaluate side-chains 160 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 2.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain H residue 115 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 781 MET Chi-restraints excluded: chain W residue 1056 MET 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 101 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 60 ASN H 60 ASN T 138 ASN W 206 ASN W 210 ASN ** W 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.109162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.067978 restraints weight = 48115.556| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.73 r_work: 0.2892 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 19955 Z= 0.272 Angle : 0.577 8.616 28149 Z= 0.328 Chirality : 0.036 0.141 3150 Planarity : 0.003 0.036 2600 Dihedral : 26.905 127.160 4932 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.33 % Allowed : 15.03 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.21), residues: 1600 helix: 2.28 (0.16), residues: 993 sheet: 0.07 (0.52), residues: 90 loop : 0.03 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP W 311 HIS 0.004 0.001 HIS W 428 PHE 0.012 0.001 PHE E 84 TYR 0.022 0.002 TYR W 841 ARG 0.006 0.000 ARG W 274 *********************** 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 188 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 155 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASP cc_start: 0.8432 (t0) cc_final: 0.8031 (t0) REVERT: C 64 GLU cc_start: 0.8956 (tp30) cc_final: 0.8741 (tp30) REVERT: D 65 ASP cc_start: 0.8993 (t70) cc_final: 0.8501 (t0) REVERT: E 79 LYS cc_start: 0.7427 (tptt) cc_final: 0.7199 (tptm) REVERT: F 59 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8329 (ttmt) REVERT: G 64 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8636 (tp30) REVERT: G 91 GLU cc_start: 0.8686 (tt0) cc_final: 0.8404 (tm-30) REVERT: H 31 LYS cc_start: 0.8481 (tppp) cc_final: 0.8197 (tppp) REVERT: H 43 LYS cc_start: 0.8798 (mtpp) cc_final: 0.8564 (mttt) REVERT: H 110 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8224 (mt-10) REVERT: W 274 ARG cc_start: 0.8819 (mmp80) cc_final: 0.8556 (mmp80) REVERT: W 681 MET cc_start: 0.7504 (mpt) cc_final: 0.7241 (mpt) REVERT: W 837 MET cc_start: 0.9071 (tpt) cc_final: 0.8736 (tpp) REVERT: W 1192 TYR cc_start: 0.7848 (t80) cc_final: 0.7595 (t80) outliers start: 33 outliers final: 14 residues processed: 176 average time/residue: 1.6591 time to fit residues: 323.3358 Evaluate side-chains 163 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain E residue 76 GLN 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 64 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain W residue 267 ILE Chi-restraints excluded: chain W residue 297 SER 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 43 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 172 optimal weight: 10.0000 chunk 141 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 chunk 161 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 84 optimal weight: 30.0000 chunk 110 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 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 G 110 ASN H 60 ASN H 81 ASN W 685 ASN ** W 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.107522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.066033 restraints weight = 47960.834| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.73 r_work: 0.2848 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 19955 Z= 0.356 Angle : 0.622 9.870 28149 Z= 0.349 Chirality : 0.039 0.212 3150 Planarity : 0.004 0.037 2600 Dihedral : 26.991 125.974 4932 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.26 % Allowed : 15.24 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.21), residues: 1600 helix: 2.11 (0.16), residues: 994 sheet: -0.12 (0.52), residues: 90 loop : -0.13 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP W 311 HIS 0.005 0.001 HIS B 75 PHE 0.013 0.001 PHE E 84 TYR 0.016 0.002 TYR B 88 ARG 0.003 0.000 ARG E 116 *********************** 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 187 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASP cc_start: 0.8493 (t0) cc_final: 0.8198 (t0) REVERT: G 64 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8627 (tp30) REVERT: H 31 LYS cc_start: 0.8561 (tppp) cc_final: 0.8263 (tppp) REVERT: H 43 LYS cc_start: 0.8842 (mtpp) cc_final: 0.8608 (mttt) REVERT: H 110 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8215 (mt-10) REVERT: W 681 MET cc_start: 0.7557 (mpt) cc_final: 0.7300 (mpt) REVERT: W 837 MET cc_start: 0.9084 (tpt) cc_final: 0.8810 (tpp) outliers start: 32 outliers final: 15 residues processed: 171 average time/residue: 1.6988 time to fit residues: 320.6818 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 : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain D residue 75 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 T residue 135 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 453 CYS 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 76 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 184 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3995 r_free = 0.3995 target = 0.109252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.068192 restraints weight = 47703.695| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.67 r_work: 0.2908 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19955 Z= 0.204 Angle : 0.579 9.574 28149 Z= 0.324 Chirality : 0.035 0.173 3150 Planarity : 0.003 0.039 2600 Dihedral : 26.747 120.358 4932 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.91 % Allowed : 16.37 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.21), residues: 1600 helix: 2.36 (0.16), residues: 990 sheet: -0.06 (0.51), residues: 90 loop : -0.09 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP W 447 HIS 0.004 0.001 HIS B 75 PHE 0.009 0.001 PHE E 67 TYR 0.022 0.001 TYR W 841 ARG 0.007 0.000 ARG W 276 *********************** 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 177 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 1.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASP cc_start: 0.8447 (t0) cc_final: 0.8066 (t0) REVERT: D 44 GLN cc_start: 0.9225 (tt0) cc_final: 0.8679 (tt0) REVERT: D 65 ASP cc_start: 0.8891 (t0) cc_final: 0.8627 (t0) REVERT: D 113 LYS cc_start: 0.9058 (ttmm) cc_final: 0.8771 (tttp) REVERT: E 94 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8574 (mm-30) REVERT: G 64 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8667 (tp30) REVERT: H 31 LYS cc_start: 0.8579 (tppp) cc_final: 0.8259 (tppp) REVERT: H 43 LYS cc_start: 0.8796 (mtpp) cc_final: 0.8566 (mttt) REVERT: H 110 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8219 (mt-10) REVERT: H 117 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8054 (tptt) REVERT: W 837 MET cc_start: 0.9061 (tpt) cc_final: 0.8716 (tpp) outliers start: 27 outliers final: 10 residues processed: 166 average time/residue: 1.6602 time to fit residues: 305.2494 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 : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 94 GLU 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 H residue 117 LYS Chi-restraints excluded: chain W residue 297 SER Chi-restraints excluded: chain W residue 616 VAL 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 62 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 19 optimal weight: 0.1980 chunk 166 optimal weight: 7.9990 chunk 145 optimal weight: 5.9990 chunk 169 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 139 optimal weight: 5.9990 chunk 124 optimal weight: 0.0060 chunk 57 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 overall best weight: 0.5196 ------------------------------------------------------------------------------- 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 = 0.4021 r_free = 0.4021 target = 0.110675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.070919 restraints weight = 48071.766| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.88 r_work: 0.2951 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19955 Z= 0.167 Angle : 0.571 12.353 28149 Z= 0.319 Chirality : 0.034 0.149 3150 Planarity : 0.003 0.035 2600 Dihedral : 26.517 113.470 4932 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.34 % Allowed : 16.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.21), residues: 1600 helix: 2.47 (0.16), residues: 989 sheet: 0.04 (0.51), residues: 90 loop : -0.04 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP W 447 HIS 0.002 0.000 HIS D 46 PHE 0.009 0.001 PHE E 67 TYR 0.030 0.001 TYR W 841 ARG 0.011 0.000 ARG W 274 *********************** 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 175 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 1.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASP cc_start: 0.8411 (t0) cc_final: 0.8020 (t0) REVERT: D 44 GLN cc_start: 0.9238 (tt0) cc_final: 0.8776 (tt0) REVERT: D 65 ASP cc_start: 0.8872 (t0) cc_final: 0.8618 (t0) REVERT: D 113 LYS cc_start: 0.9042 (ttmm) cc_final: 0.8783 (tttp) REVERT: E 59 GLU cc_start: 0.8297 (pm20) cc_final: 0.7952 (pm20) REVERT: E 90 MET cc_start: 0.9079 (tpp) cc_final: 0.8835 (mmm) REVERT: E 94 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8555 (mm-30) REVERT: H 31 LYS cc_start: 0.8597 (tppp) cc_final: 0.8273 (tppp) REVERT: H 43 LYS cc_start: 0.8785 (mtpp) cc_final: 0.8550 (mttt) REVERT: H 110 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8201 (mt-10) REVERT: H 117 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7961 (tptt) REVERT: W 270 MET cc_start: 0.8698 (mmp) cc_final: 0.7943 (tpt) REVERT: W 274 ARG cc_start: 0.8789 (mmp80) cc_final: 0.8387 (mmp80) REVERT: W 538 MET cc_start: 0.8925 (ttt) cc_final: 0.8687 (ttt) REVERT: W 837 MET cc_start: 0.9021 (tpt) cc_final: 0.8698 (tpp) outliers start: 19 outliers final: 7 residues processed: 166 average time/residue: 1.6396 time to fit residues: 302.1648 Evaluate side-chains 152 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain W residue 297 SER Chi-restraints excluded: chain W residue 616 VAL 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 160 optimal weight: 0.1980 chunk 99 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 178 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 184 optimal weight: 10.0000 chunk 136 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 = 0.108797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.068798 restraints weight = 48091.597| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.53 r_work: 0.2906 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 19955 Z= 0.287 Angle : 0.600 9.653 28149 Z= 0.334 Chirality : 0.036 0.172 3150 Planarity : 0.004 0.046 2600 Dihedral : 26.711 115.922 4932 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.48 % Allowed : 17.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.21), residues: 1600 helix: 2.38 (0.16), residues: 993 sheet: 0.10 (0.52), residues: 85 loop : -0.08 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP W 311 HIS 0.004 0.001 HIS B 75 PHE 0.010 0.001 PHE E 84 TYR 0.035 0.002 TYR W1142 ARG 0.007 0.000 ARG C 35 *********************** 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 165 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASP cc_start: 0.8424 (t0) cc_final: 0.8083 (t0) REVERT: D 44 GLN cc_start: 0.9238 (tt0) cc_final: 0.8731 (tt0) REVERT: D 65 ASP cc_start: 0.8910 (t0) cc_final: 0.8600 (t0) REVERT: E 59 GLU cc_start: 0.8471 (pm20) cc_final: 0.8087 (pm20) REVERT: E 90 MET cc_start: 0.9116 (tpp) cc_final: 0.8837 (mmp) REVERT: E 94 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8548 (mm-30) REVERT: H 43 LYS cc_start: 0.8812 (mtpp) cc_final: 0.8577 (mttt) REVERT: H 56 MET cc_start: 0.9301 (tpt) cc_final: 0.9082 (tpt) REVERT: H 110 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8206 (mt-10) REVERT: H 117 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8112 (tptt) REVERT: W 270 MET cc_start: 0.8769 (mmp) cc_final: 0.8154 (tpt) REVERT: W 538 MET cc_start: 0.8969 (ttt) cc_final: 0.8649 (ttt) REVERT: W 837 MET cc_start: 0.9040 (tpt) cc_final: 0.8780 (tpp) REVERT: W 1057 MET cc_start: 0.8560 (ppp) cc_final: 0.8326 (pmt) outliers start: 21 outliers final: 9 residues processed: 160 average time/residue: 1.6533 time to fit residues: 293.2645 Evaluate side-chains 152 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 25 PHE Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain W residue 297 SER Chi-restraints excluded: chain W residue 616 VAL 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: 0.7980 chunk 135 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 86 optimal weight: 20.0000 chunk 89 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 83 optimal weight: 30.0000 chunk 28 optimal weight: 1.9990 chunk 147 optimal weight: 0.4980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 132 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 = 0.109336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.069079 restraints weight = 47842.503| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.66 r_work: 0.2914 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19955 Z= 0.201 Angle : 0.597 11.091 28149 Z= 0.332 Chirality : 0.035 0.169 3150 Planarity : 0.004 0.087 2600 Dihedral : 26.709 114.339 4932 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.27 % Allowed : 17.64 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.21), residues: 1600 helix: 2.37 (0.16), residues: 993 sheet: -0.07 (0.50), residues: 95 loop : -0.03 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP W 447 HIS 0.004 0.001 HIS C 31 PHE 0.009 0.001 PHE W 379 TYR 0.039 0.002 TYR W1142 ARG 0.014 0.000 ARG W 274 ********************** 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 161 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 1.810 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: 0.8044 (t0) REVERT: B 74 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8452 (tm-30) REVERT: D 44 GLN cc_start: 0.9244 (tt0) cc_final: 0.8738 (tt0) REVERT: D 65 ASP cc_start: 0.8890 (t0) cc_final: 0.8586 (t0) REVERT: E 59 GLU cc_start: 0.8457 (pm20) cc_final: 0.8059 (pm20) REVERT: E 90 MET cc_start: 0.9101 (tpp) cc_final: 0.8828 (mmp) REVERT: E 94 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8553 (mm-30) REVERT: H 43 LYS cc_start: 0.8810 (mtpp) cc_final: 0.8574 (mttt) REVERT: H 56 MET cc_start: 0.9287 (tpt) cc_final: 0.9050 (tpt) REVERT: H 110 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8218 (mt-10) REVERT: H 117 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8107 (tptt) REVERT: W 270 MET cc_start: 0.8767 (mmp) cc_final: 0.7948 (tpt) REVERT: W 274 ARG cc_start: 0.8840 (mmp80) cc_final: 0.8331 (mmp80) REVERT: W 538 MET cc_start: 0.8953 (ttt) cc_final: 0.8624 (ttt) REVERT: W 837 MET cc_start: 0.9043 (tpt) cc_final: 0.8700 (tpp) REVERT: W 1057 MET cc_start: 0.8556 (ppp) cc_final: 0.8334 (pmt) outliers start: 18 outliers final: 11 residues processed: 154 average time/residue: 1.6554 time to fit residues: 282.3153 Evaluate side-chains 152 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 25 PHE Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain W residue 297 SER Chi-restraints excluded: chain W residue 616 VAL 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 67 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 82 optimal weight: 20.0000 chunk 75 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 118 optimal weight: 0.0570 chunk 88 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.7900 ------------------------------------------------------------------------------- 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 132 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 = 0.4005 r_free = 0.4005 target = 0.109844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.070078 restraints weight = 48174.415| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.65 r_work: 0.2929 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19955 Z= 0.187 Angle : 0.588 9.763 28149 Z= 0.326 Chirality : 0.035 0.154 3150 Planarity : 0.003 0.052 2600 Dihedral : 26.610 110.141 4932 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.06 % Allowed : 17.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.21), residues: 1600 helix: 2.44 (0.16), residues: 992 sheet: 0.04 (0.50), residues: 95 loop : -0.07 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP W 447 HIS 0.004 0.001 HIS C 31 PHE 0.009 0.001 PHE E 67 TYR 0.037 0.001 TYR W1142 ARG 0.012 0.000 ARG W 274 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14044.13 seconds wall clock time: 252 minutes 16.35 seconds (15136.35 seconds total)