Starting phenix.real_space_refine on Fri Oct 23 19:50:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wd0_65880/10_2026/9wd0_65880_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wd0_65880/10_2026/9wd0_65880.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wd0_65880/10_2026/9wd0_65880.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wd0_65880/10_2026/9wd0_65880.map" model { file = "/net/cci-nas-00/data/ceres_data/9wd0_65880/10_2026/9wd0_65880_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wd0_65880/10_2026/9wd0_65880_neut.cif" } resolution = 3.33 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 52 5.16 5 C 6784 2.51 5 N 1828 2.21 5 O 2009 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10674 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1009, 7948 Classifications: {'peptide': 1009} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 53, 'TRANS': 955} Chain: "B" Number of atoms: 2101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2101 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 17, 'TRANS': 244} Chain breaks: 1 Chain: "C" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 2.36, per 1000 atoms: 0.22 Number of scatterers: 10674 At special positions: 0 Unit cell: (89.424, 99.144, 131.544, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 P 1 15.00 O 2009 8.00 N 1828 7.00 C 6784 6.00 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=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 380.3 milliseconds 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2516 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 9 sheets defined 47.4% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 51 through 63 removed outlier: 3.510A pdb=" N TYR A 55 " --> pdb=" O ASP A 51 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ARG A 57 " --> pdb=" O GLY A 53 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N GLN A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL A 61 " --> pdb=" O ARG A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 71 Processing helix chain 'A' and resid 83 through 95 Processing helix chain 'A' and resid 110 through 114 Processing helix chain 'A' and resid 126 through 136 Proline residue: A 133 - end of helix Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 168 through 183 Processing helix chain 'A' and resid 305 through 312 Processing helix chain 'A' and resid 319 through 323 removed outlier: 3.728A pdb=" N PHE A 323 " --> pdb=" O PHE A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 344 removed outlier: 4.150A pdb=" N GLN A 328 " --> pdb=" O SER A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 369 Processing helix chain 'A' and resid 379 through 390 Processing helix chain 'A' and resid 394 through 415 Processing helix chain 'A' and resid 429 through 432 Processing helix chain 'A' and resid 440 through 445 Processing helix chain 'A' and resid 451 through 468 removed outlier: 4.273A pdb=" N VAL A 457 " --> pdb=" O GLY A 453 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N SER A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 9.086A pdb=" N ASP A 461 " --> pdb=" O VAL A 457 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU A 462 " --> pdb=" O PHE A 458 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN A 463 " --> pdb=" O GLY A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 491 Processing helix chain 'A' and resid 509 through 514 removed outlier: 3.868A pdb=" N ASN A 514 " --> pdb=" O SER A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 524 removed outlier: 4.168A pdb=" N VAL A 524 " --> pdb=" O PRO A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 540 Processing helix chain 'A' and resid 554 through 558 removed outlier: 3.612A pdb=" N GLU A 557 " --> pdb=" O PRO A 554 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ARG A 558 " --> pdb=" O ASP A 555 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 554 through 558' Processing helix chain 'A' and resid 561 through 568 Processing helix chain 'A' and resid 577 through 592 Processing helix chain 'A' and resid 617 through 621 removed outlier: 3.549A pdb=" N SER A 620 " --> pdb=" O SER A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 636 Processing helix chain 'A' and resid 640 through 657 Processing helix chain 'A' and resid 657 through 669 Processing helix chain 'A' and resid 670 through 678 removed outlier: 4.060A pdb=" N GLU A 674 " --> pdb=" O PRO A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 696 Processing helix chain 'A' and resid 702 through 719 removed outlier: 3.695A pdb=" N CYS A 706 " --> pdb=" O THR A 702 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL A 707 " --> pdb=" O TRP A 703 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR A 716 " --> pdb=" O HIS A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 729 removed outlier: 3.557A pdb=" N ARG A 723 " --> pdb=" O SER A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 762 Processing helix chain 'A' and resid 763 through 777 removed outlier: 3.662A pdb=" N TYR A 776 " --> pdb=" O PHE A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 792 removed outlier: 4.038A pdb=" N VAL A 787 " --> pdb=" O ASP A 783 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA A 788 " --> pdb=" O ARG A 784 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN A 792 " --> pdb=" O ALA A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 817 Processing helix chain 'A' and resid 822 through 833 Processing helix chain 'A' and resid 835 through 839 Processing helix chain 'A' and resid 857 through 873 Processing helix chain 'A' and resid 879 through 888 Processing helix chain 'A' and resid 894 through 915 removed outlier: 3.759A pdb=" N LYS A 911 " --> pdb=" O LEU A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 922 Processing helix chain 'A' and resid 971 through 983 Processing helix chain 'A' and resid 1003 through 1011 removed outlier: 3.514A pdb=" N LEU A1007 " --> pdb=" O PRO A1003 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLU A1009 " --> pdb=" O ALA A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1024 Processing helix chain 'B' and resid 939 through 944 Processing helix chain 'B' and resid 950 through 969 removed outlier: 3.518A pdb=" N PHE B 954 " --> pdb=" O GLU B 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 1060 through 1072 removed outlier: 3.582A pdb=" N ILE B1072 " --> pdb=" O ILE B1068 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1088 removed outlier: 4.009A pdb=" N ARG B1088 " --> pdb=" O ASP B1085 " (cutoff:3.500A) Processing helix chain 'B' and resid 1090 through 1118 Processing helix chain 'B' and resid 1123 through 1151 removed outlier: 4.250A pdb=" N ARG B1128 " --> pdb=" O GLU B1124 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR B1133 " --> pdb=" O GLN B1129 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY B1135 " --> pdb=" O PHE B1131 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N TRP B1136 " --> pdb=" O SER B1132 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU B1143 " --> pdb=" O VAL B1139 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N SER B1144 " --> pdb=" O ASN B1140 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU B1146 " --> pdb=" O ILE B1142 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU B1147 " --> pdb=" O GLU B1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 1262 through 1282 removed outlier: 3.794A pdb=" N LYS B1267 " --> pdb=" O LYS B1263 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 35 Processing helix chain 'C' and resid 55 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 144 through 147 removed outlier: 6.724A pdb=" N VAL A 99 " --> pdb=" O THR A 145 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N TYR A 147 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU A 101 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N SER A 74 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N VAL A 163 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU A 76 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N THR A 165 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N SER A 78 " --> pdb=" O THR A 165 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 206 through 208 Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 266 Processing sheet with id=AA4, first strand: chain 'A' and resid 545 through 548 removed outlier: 6.319A pdb=" N ILE A 500 " --> pdb=" O THR A 546 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N HIS A 548 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL A 502 " --> pdb=" O HIS A 548 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TYR A 471 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N THR A 503 " --> pdb=" O TYR A 471 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU A 473 " --> pdb=" O THR A 503 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LYS A 470 " --> pdb=" O GLY A 570 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N ALA A 572 " --> pdb=" O LYS A 470 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N PHE A 472 " --> pdb=" O ALA A 572 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N SER A 598 " --> pdb=" O ASN A 573 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 945 through 947 Processing sheet with id=AA6, first strand: chain 'A' and resid 958 through 961 removed outlier: 6.605A pdb=" N PHE A 958 " --> pdb=" O ARG A1054 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N THR A1056 " --> pdb=" O PHE A 958 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL A 960 " --> pdb=" O THR A1056 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N VAL A1035 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N GLN A 992 " --> pdb=" O VAL A1035 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLU A1037 " --> pdb=" O LEU A 990 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU A 990 " --> pdb=" O GLU A1037 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N CYS A1039 " --> pdb=" O THR A 988 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR A 998 " --> pdb=" O LEU A 990 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLN A 992 " --> pdb=" O MET A 996 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N MET A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 958 through 961 removed outlier: 6.605A pdb=" N PHE A 958 " --> pdb=" O ARG A1054 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N THR A1056 " --> pdb=" O PHE A 958 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL A 960 " --> pdb=" O THR A1056 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N CYS A1040 " --> pdb=" O VAL A1048 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 930 through 932 removed outlier: 4.548A pdb=" N PHE B 978 " --> pdb=" O LEU B 984 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N LEU B 984 " --> pdb=" O PHE B 978 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 12 through 16 removed outlier: 3.846A pdb=" N VAL C 70 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG C 42 " --> pdb=" O VAL C 70 " (cutoff:3.500A) 502 hydrogen bonds defined for protein. 1374 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.23 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3550 1.35 - 1.46: 2425 1.46 - 1.58: 4855 1.58 - 1.70: 1 1.70 - 1.82: 81 Bond restraints: 10912 Sorted by residual: bond pdb=" CG1 ILE A 50 " pdb=" CD1 ILE A 50 " ideal model delta sigma weight residual 1.513 1.465 0.048 3.90e-02 6.57e+02 1.53e+00 bond pdb=" CG ARG B1137 " pdb=" CD ARG B1137 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.38e+00 bond pdb=" C4 AMP A1101 " pdb=" C5 AMP A1101 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.34e+00 bond pdb=" CG LYS A 68 " pdb=" CD LYS A 68 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.29e+00 bond pdb=" CB GLN C 62 " pdb=" CG GLN C 62 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.29e+00 ... (remaining 10907 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 14528 2.10 - 4.20: 223 4.20 - 6.29: 37 6.29 - 8.39: 5 8.39 - 10.49: 3 Bond angle restraints: 14796 Sorted by residual: angle pdb=" N PHE B1084 " pdb=" CA PHE B1084 " pdb=" C PHE B1084 " ideal model delta sigma weight residual 114.56 109.68 4.88 1.27e+00 6.20e-01 1.48e+01 angle pdb=" C GLU B1102 " pdb=" N MET B1103 " pdb=" CA MET B1103 " ideal model delta sigma weight residual 121.58 114.25 7.33 1.95e+00 2.63e-01 1.41e+01 angle pdb=" CB MET A 410 " pdb=" CG MET A 410 " pdb=" SD MET A 410 " ideal model delta sigma weight residual 112.70 123.19 -10.49 3.00e+00 1.11e-01 1.22e+01 angle pdb=" N VAL A 130 " pdb=" CA VAL A 130 " pdb=" C VAL A 130 " ideal model delta sigma weight residual 113.42 109.49 3.93 1.17e+00 7.31e-01 1.13e+01 angle pdb=" CB MET B 974 " pdb=" CG MET B 974 " pdb=" SD MET B 974 " ideal model delta sigma weight residual 112.70 122.76 -10.06 3.00e+00 1.11e-01 1.13e+01 ... (remaining 14791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 5958 17.63 - 35.27: 472 35.27 - 52.90: 105 52.90 - 70.53: 36 70.53 - 88.17: 11 Dihedral angle restraints: 6582 sinusoidal: 2683 harmonic: 3899 Sorted by residual: dihedral pdb=" CA ASN A 228 " pdb=" C ASN A 228 " pdb=" N PRO A 229 " pdb=" CA PRO A 229 " ideal model delta harmonic sigma weight residual 180.00 157.51 22.49 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA ARG A 288 " pdb=" C ARG A 288 " pdb=" N GLY A 289 " pdb=" CA GLY A 289 " ideal model delta harmonic sigma weight residual 180.00 157.53 22.47 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA LEU A1038 " pdb=" C LEU A1038 " pdb=" N CYS A1039 " pdb=" CA CYS A1039 " ideal model delta harmonic sigma weight residual 180.00 157.77 22.23 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 6579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1100 0.036 - 0.073: 372 0.073 - 0.109: 127 0.109 - 0.145: 31 0.145 - 0.182: 4 Chirality restraints: 1634 Sorted by residual: chirality pdb=" CA PHE B1259 " pdb=" N PHE B1259 " pdb=" C PHE B1259 " pdb=" CB PHE B1259 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.24e-01 chirality pdb=" CA THR A 525 " pdb=" N THR A 525 " pdb=" C THR A 525 " pdb=" CB THR A 525 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.68e-01 chirality pdb=" CB ILE B1011 " pdb=" CA ILE B1011 " pdb=" CG1 ILE B1011 " pdb=" CG2 ILE B1011 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.67e-01 ... (remaining 1631 not shown) Planarity restraints: 1938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 60 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.10e+00 pdb=" C ASN C 60 " -0.035 2.00e-02 2.50e+03 pdb=" O ASN C 60 " 0.013 2.00e-02 2.50e+03 pdb=" N ILE C 61 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B1259 " 0.033 5.00e-02 4.00e+02 5.03e-02 4.05e+00 pdb=" N PRO B1260 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B1260 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B1260 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 297 " -0.029 5.00e-02 4.00e+02 4.41e-02 3.10e+00 pdb=" N PRO A 298 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 298 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 298 " -0.024 5.00e-02 4.00e+02 ... (remaining 1935 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 5775 3.01 - 3.48: 10865 3.48 - 3.96: 17119 3.96 - 4.43: 20088 4.43 - 4.90: 31873 Nonbonded interactions: 85720 Sorted by model distance: nonbonded pdb=" OD1 ASP A1042 " pdb=" O GLU A1046 " model vdw 2.538 3.040 nonbonded pdb=" O ASN C 60 " pdb=" OD1 ASN C 60 " model vdw 2.557 3.040 nonbonded pdb=" N ASP A1042 " pdb=" OD1 ASP A1042 " model vdw 2.557 3.120 nonbonded pdb=" O ALA A 478 " pdb=" OE1 GLU A 482 " model vdw 2.579 3.040 nonbonded pdb=" O GLU B1102 " pdb=" CA MET B1103 " model vdw 2.606 2.776 ... (remaining 85715 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 7.960 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: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.840 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 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 : 0.003 0.048 10912 Z= 0.137 Angle : 0.657 10.490 14796 Z= 0.345 Chirality : 0.042 0.182 1634 Planarity : 0.005 0.058 1938 Dihedral : 14.475 88.165 4066 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.51 % Allowed : 9.61 % Favored : 89.88 % 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 are not related in a simple way. whole: 0.55 (0.23), residues: 1339 helix: 0.79 (0.23), residues: 527 sheet: 0.49 (0.38), residues: 194 loop : 0.08 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1137 TYR 0.013 0.001 TYR A 948 PHE 0.021 0.002 PHE B1259 TRP 0.025 0.002 TRP B1136 HIS 0.012 0.001 HIS B1130 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (10912) covalent geometry : angle 0.65701 / 0.34 (14796) hydrogen bonds : bond 0.14956 / 9.98 ( 498) hydrogen bonds : angle 6.45040 / 4.59 ( 1374) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.4969 (OUTLIER) cc_final: 0.3341 (tpp) REVERT: A 505 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7187 (ppp) REVERT: A 585 ASP cc_start: 0.8581 (t70) cc_final: 0.8335 (t0) REVERT: A 844 MET cc_start: 0.5472 (ptp) cc_final: 0.4898 (ttm) REVERT: A 963 LEU cc_start: 0.8718 (mm) cc_final: 0.8323 (tp) REVERT: A 996 MET cc_start: 0.8274 (tpt) cc_final: 0.8014 (mmm) REVERT: B 971 GLU cc_start: 0.6656 (tp30) cc_final: 0.6405 (tp30) REVERT: C 64 GLU cc_start: 0.8754 (mp0) cc_final: 0.8411 (mp0) outliers start: 6 outliers final: 3 residues processed: 68 average time/residue: 0.0987 time to fit residues: 9.9800 Evaluate side-chains 67 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 1015 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 720 ASN A 916 HIS B1101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4853 r_free = 0.4853 target = 0.191596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.115751 restraints weight = 22624.431| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 4.64 r_work: 0.3518 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 10912 Z= 0.323 Angle : 0.681 8.796 14796 Z= 0.350 Chirality : 0.045 0.176 1634 Planarity : 0.005 0.060 1938 Dihedral : 5.794 58.688 1474 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.63 % Allowed : 9.69 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.23), residues: 1339 helix: 0.84 (0.23), residues: 540 sheet: 0.16 (0.36), residues: 206 loop : -0.05 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1137 TYR 0.018 0.002 TYR A 590 PHE 0.022 0.002 PHE A 564 TRP 0.017 0.001 TRP B1136 HIS 0.007 0.002 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00757 / 0.32 (10912) covalent geometry : angle 0.68144 / 0.35 (14796) hydrogen bonds : bond 0.04967 / 3.31 ( 498) hydrogen bonds : angle 5.25019 / 3.70 ( 1374) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.5061 (OUTLIER) cc_final: 0.3469 (tpp) REVERT: A 254 GLN cc_start: 0.6564 (OUTLIER) cc_final: 0.6089 (pt0) REVERT: A 844 MET cc_start: 0.5577 (ptp) cc_final: 0.4995 (ttm) REVERT: A 996 MET cc_start: 0.8479 (tpt) cc_final: 0.7585 (mmm) REVERT: B 1261 LEU cc_start: 0.5172 (OUTLIER) cc_final: 0.4835 (tt) REVERT: C 51 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7528 (pp20) REVERT: C 64 GLU cc_start: 0.8857 (mp0) cc_final: 0.8351 (mp0) outliers start: 19 outliers final: 13 residues processed: 76 average time/residue: 0.0900 time to fit residues: 10.4257 Evaluate side-chains 76 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 254 GLN Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1015 MET Chi-restraints excluded: chain A residue 1016 THR Chi-restraints excluded: chain A residue 1040 CYS Chi-restraints excluded: chain B residue 1261 LEU Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 66 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: [15, 132, 36, 58, 90, 85, 51, 123, 29, 127, 64] chunk 15 optimal weight: 0.7980 chunk 132 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 58 optimal weight: 9.9990 chunk 90 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 123 optimal weight: 7.9990 chunk 29 optimal weight: 0.3980 chunk 127 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1024 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4898 r_free = 0.4898 target = 0.195557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.129894 restraints weight = 22609.962| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 5.80 r_work: 0.3551 rms_B_bonded: 5.54 restraints_weight: 2.0000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10912 Z= 0.114 Angle : 0.540 8.146 14796 Z= 0.274 Chirality : 0.040 0.163 1634 Planarity : 0.004 0.051 1938 Dihedral : 5.425 58.770 1474 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.72 % Allowed : 10.21 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.23), residues: 1339 helix: 1.00 (0.23), residues: 544 sheet: 0.34 (0.37), residues: 205 loop : 0.01 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1137 TYR 0.008 0.001 TYR A 910 PHE 0.014 0.001 PHE B1259 TRP 0.015 0.001 TRP B1136 HIS 0.005 0.001 HIS B1130 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (10912) covalent geometry : angle 0.53961 / 0.27 (14796) hydrogen bonds : bond 0.03937 / 2.63 ( 498) hydrogen bonds : angle 4.82328 / 3.41 ( 1374) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.4680 (ppp) cc_final: 0.3080 (tpp) REVERT: A 505 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7180 (ppp) REVERT: A 844 MET cc_start: 0.5729 (ptp) cc_final: 0.5150 (ttm) REVERT: A 996 MET cc_start: 0.8292 (tpt) cc_final: 0.7547 (mmm) REVERT: B 1261 LEU cc_start: 0.5381 (OUTLIER) cc_final: 0.5055 (tt) REVERT: C 51 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7372 (pp20) REVERT: C 64 GLU cc_start: 0.8919 (mp0) cc_final: 0.8442 (mp0) outliers start: 20 outliers final: 10 residues processed: 78 average time/residue: 0.1044 time to fit residues: 11.9259 Evaluate side-chains 74 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 1015 MET Chi-restraints excluded: chain A residue 1016 THR Chi-restraints excluded: chain B residue 1261 LEU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 52 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: [129, 127, 84, 48, 5, 12, 57, 119, 99, 102, 29] chunk 129 optimal weight: 1.9990 chunk 127 optimal weight: 0.0570 chunk 84 optimal weight: 0.1980 chunk 48 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 119 optimal weight: 0.0770 chunk 99 optimal weight: 0.9980 chunk 102 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1024 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4908 r_free = 0.4908 target = 0.196624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.131025 restraints weight = 22748.999| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 5.80 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10912 Z= 0.102 Angle : 0.520 8.351 14796 Z= 0.262 Chirality : 0.040 0.151 1634 Planarity : 0.004 0.051 1938 Dihedral : 5.098 57.472 1471 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.54 % Allowed : 11.15 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.23), residues: 1339 helix: 1.21 (0.23), residues: 545 sheet: 0.51 (0.38), residues: 196 loop : 0.03 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1025 TYR 0.007 0.001 TYR B1002 PHE 0.013 0.001 PHE B1259 TRP 0.014 0.001 TRP B1136 HIS 0.004 0.001 HIS B1130 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (10912) covalent geometry : angle 0.51981 / 0.26 (14796) hydrogen bonds : bond 0.03611 / 2.42 ( 498) hydrogen bonds : angle 4.57853 / 3.24 ( 1374) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.4887 (ppp) cc_final: 0.3259 (tpp) REVERT: A 482 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7429 (mp0) REVERT: A 505 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.6641 (ppp) REVERT: A 844 MET cc_start: 0.5297 (ptp) cc_final: 0.4765 (ttm) REVERT: A 996 MET cc_start: 0.8286 (tpt) cc_final: 0.7599 (mmm) REVERT: B 971 GLU cc_start: 0.6206 (tp30) cc_final: 0.5800 (tp30) REVERT: B 1261 LEU cc_start: 0.2460 (OUTLIER) cc_final: 0.2112 (tt) REVERT: C 51 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6659 (pp20) outliers start: 18 outliers final: 9 residues processed: 79 average time/residue: 0.0826 time to fit residues: 10.0187 Evaluate side-chains 70 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain A residue 1016 THR Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain B residue 1261 LEU Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 52 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: [40, 50, 2, 94, 100, 77, 45, 118, 31, 21, 48] chunk 40 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 118 optimal weight: 20.0000 chunk 31 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 GLN A 254 GLN ** B1024 GLN ** 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 = 0.4888 r_free = 0.4888 target = 0.195228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.124229 restraints weight = 22423.673| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 5.84 r_work: 0.3547 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10912 Z= 0.185 Angle : 0.559 10.009 14796 Z= 0.280 Chirality : 0.041 0.150 1634 Planarity : 0.004 0.056 1938 Dihedral : 4.990 59.471 1468 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.80 % Allowed : 11.84 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.23), residues: 1339 helix: 1.27 (0.23), residues: 543 sheet: 0.20 (0.38), residues: 208 loop : -0.09 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1025 TYR 0.010 0.001 TYR A 471 PHE 0.015 0.001 PHE A 564 TRP 0.013 0.001 TRP B1136 HIS 0.005 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (10912) covalent geometry : angle 0.55885 / 0.28 (14796) hydrogen bonds : bond 0.03733 / 2.49 ( 498) hydrogen bonds : angle 4.57241 / 3.24 ( 1374) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.4847 (OUTLIER) cc_final: 0.3298 (tpp) REVERT: A 505 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7117 (ppp) REVERT: A 844 MET cc_start: 0.5704 (ptp) cc_final: 0.5155 (ttm) REVERT: A 996 MET cc_start: 0.8340 (tpt) cc_final: 0.7615 (mmm) REVERT: B 971 GLU cc_start: 0.6399 (tp30) cc_final: 0.5996 (tp30) REVERT: B 1261 LEU cc_start: 0.3894 (OUTLIER) cc_final: 0.3443 (tt) REVERT: C 51 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7370 (pp20) outliers start: 21 outliers final: 12 residues processed: 76 average time/residue: 0.0856 time to fit residues: 10.0314 Evaluate side-chains 74 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain A residue 1016 THR Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain B residue 1261 LEU Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 52 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: [67, 2, 91, 95, 24, 9, 97, 25, 18, 7, 31] chunk 67 optimal weight: 50.0000 chunk 2 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 24 optimal weight: 0.0370 chunk 9 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 25 optimal weight: 0.2980 chunk 18 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.0664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 GLN A 282 ASN ** B1024 GLN ** 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 = 0.4897 r_free = 0.4897 target = 0.195892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.126874 restraints weight = 22576.903| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 5.73 r_work: 0.3549 rms_B_bonded: 5.41 restraints_weight: 2.0000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10912 Z= 0.140 Angle : 0.540 10.160 14796 Z= 0.270 Chirality : 0.040 0.153 1634 Planarity : 0.004 0.056 1938 Dihedral : 4.917 59.304 1468 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.89 % Allowed : 12.26 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.24), residues: 1339 helix: 1.37 (0.23), residues: 543 sheet: 0.26 (0.38), residues: 208 loop : -0.08 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1025 TYR 0.008 0.001 TYR A 471 PHE 0.012 0.001 PHE B1259 TRP 0.011 0.001 TRP B1136 HIS 0.004 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (10912) covalent geometry : angle 0.54021 / 0.27 (14796) hydrogen bonds : bond 0.03530 / 2.36 ( 498) hydrogen bonds : angle 4.46593 / 3.17 ( 1374) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.4967 (OUTLIER) cc_final: 0.3322 (tpp) REVERT: A 282 ASN cc_start: 0.9277 (t160) cc_final: 0.8995 (p0) REVERT: A 482 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.7813 (mp0) REVERT: A 505 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7111 (ppp) REVERT: A 844 MET cc_start: 0.5725 (ptp) cc_final: 0.5222 (ttm) REVERT: A 996 MET cc_start: 0.8261 (tpt) cc_final: 0.7606 (mmm) REVERT: B 1261 LEU cc_start: 0.5309 (OUTLIER) cc_final: 0.4932 (tt) REVERT: C 51 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7361 (pp20) outliers start: 22 outliers final: 13 residues processed: 77 average time/residue: 0.0861 time to fit residues: 10.0678 Evaluate side-chains 76 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain A residue 1016 THR Chi-restraints excluded: chain B residue 1015 VAL Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain B residue 1261 LEU Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 52 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: [45, 65, 67, 78, 27, 42, 63, 129, 40, 105, 131] chunk 45 optimal weight: 0.6980 chunk 65 optimal weight: 10.0000 chunk 67 optimal weight: 20.0000 chunk 78 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 63 optimal weight: 30.0000 chunk 129 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 105 optimal weight: 0.0570 chunk 131 optimal weight: 0.5980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1024 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.196886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.132342 restraints weight = 22445.023| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 5.87 r_work: 0.3586 rms_B_bonded: 5.47 restraints_weight: 2.0000 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10912 Z= 0.102 Angle : 0.520 10.478 14796 Z= 0.259 Chirality : 0.040 0.152 1634 Planarity : 0.004 0.054 1938 Dihedral : 4.810 59.899 1468 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.89 % Allowed : 12.35 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.24), residues: 1339 helix: 1.50 (0.23), residues: 544 sheet: 0.37 (0.38), residues: 208 loop : -0.03 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1025 TYR 0.008 0.001 TYR B1100 PHE 0.013 0.001 PHE B1259 TRP 0.010 0.001 TRP B1136 HIS 0.002 0.000 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (10912) covalent geometry : angle 0.52040 / 0.26 (14796) hydrogen bonds : bond 0.03304 / 2.21 ( 498) hydrogen bonds : angle 4.32584 / 3.08 ( 1374) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.4935 (ppp) cc_final: 0.3302 (tpp) REVERT: A 282 ASN cc_start: 0.9318 (t0) cc_final: 0.8974 (p0) REVERT: A 393 ASP cc_start: 0.8631 (OUTLIER) cc_final: 0.7904 (p0) REVERT: A 482 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.7807 (mp0) REVERT: A 505 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7031 (ppp) REVERT: A 523 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7501 (t0) REVERT: A 844 MET cc_start: 0.5778 (ptp) cc_final: 0.5286 (ttm) REVERT: A 996 MET cc_start: 0.8273 (tpt) cc_final: 0.7655 (mmm) REVERT: B 1261 LEU cc_start: 0.5586 (OUTLIER) cc_final: 0.5221 (tt) REVERT: C 51 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7264 (pp20) outliers start: 22 outliers final: 13 residues processed: 77 average time/residue: 0.0829 time to fit residues: 9.8145 Evaluate side-chains 78 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain A residue 1016 THR Chi-restraints excluded: chain B residue 1015 VAL Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain B residue 1261 LEU Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 52 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: [37, 81, 8, 110, 59, 30, 100, 87, 14, 61, 28] chunk 37 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 8 optimal weight: 0.0020 chunk 110 optimal weight: 30.0000 chunk 59 optimal weight: 20.0000 chunk 30 optimal weight: 0.0470 chunk 100 optimal weight: 20.0000 chunk 87 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.9490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 ASN B1024 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4880 r_free = 0.4880 target = 0.194892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.125379 restraints weight = 22277.416| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 5.04 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10912 Z= 0.133 Angle : 0.532 10.705 14796 Z= 0.263 Chirality : 0.040 0.148 1634 Planarity : 0.004 0.055 1938 Dihedral : 4.812 59.274 1468 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.89 % Allowed : 12.61 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.24), residues: 1339 helix: 1.53 (0.23), residues: 544 sheet: 0.38 (0.38), residues: 208 loop : -0.05 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1025 TYR 0.008 0.001 TYR A 471 PHE 0.012 0.001 PHE B1259 TRP 0.009 0.001 TRP B1136 HIS 0.004 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (10912) covalent geometry : angle 0.53249 / 0.26 (14796) hydrogen bonds : bond 0.03354 / 2.24 ( 498) hydrogen bonds : angle 4.32355 / 3.08 ( 1374) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.4971 (OUTLIER) cc_final: 0.3407 (tpp) REVERT: A 282 ASN cc_start: 0.9136 (t0) cc_final: 0.8846 (p0) REVERT: A 393 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.7763 (p0) REVERT: A 482 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7424 (mp0) REVERT: A 505 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.6714 (ppp) REVERT: A 523 ASP cc_start: 0.7803 (OUTLIER) cc_final: 0.7442 (t0) REVERT: A 844 MET cc_start: 0.5647 (ptp) cc_final: 0.5120 (ttm) REVERT: A 996 MET cc_start: 0.8522 (tpt) cc_final: 0.7901 (mmm) REVERT: B 1261 LEU cc_start: 0.3222 (OUTLIER) cc_final: 0.2733 (tt) REVERT: C 51 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6818 (pp20) outliers start: 22 outliers final: 13 residues processed: 76 average time/residue: 0.0782 time to fit residues: 9.4246 Evaluate side-chains 78 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain A residue 1016 THR Chi-restraints excluded: chain B residue 1015 VAL Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain B residue 1261 LEU Chi-restraints excluded: chain C residue 51 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: [33, 30, 18, 10, 86, 76, 108, 39, 46, 59, 94] chunk 33 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 10 optimal weight: 0.3980 chunk 86 optimal weight: 2.9990 chunk 76 optimal weight: 40.0000 chunk 108 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 59 optimal weight: 20.0000 chunk 94 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.195530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.131693 restraints weight = 22252.798| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 5.47 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10912 Z= 0.114 Angle : 0.534 11.217 14796 Z= 0.263 Chirality : 0.040 0.192 1634 Planarity : 0.004 0.054 1938 Dihedral : 4.768 59.037 1468 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.89 % Allowed : 13.12 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.24), residues: 1339 helix: 1.59 (0.23), residues: 544 sheet: 0.41 (0.38), residues: 208 loop : -0.03 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1025 TYR 0.010 0.001 TYR B1100 PHE 0.012 0.001 PHE B1259 TRP 0.009 0.001 TRP B1136 HIS 0.003 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (10912) covalent geometry : angle 0.53374 / 0.26 (14796) hydrogen bonds : bond 0.03257 / 2.19 ( 498) hydrogen bonds : angle 4.27138 / 3.04 ( 1374) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.5135 (OUTLIER) cc_final: 0.3587 (tpp) REVERT: A 282 ASN cc_start: 0.8979 (t0) cc_final: 0.8763 (p0) REVERT: A 393 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.7814 (p0) REVERT: A 482 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7397 (mp0) REVERT: A 505 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.6612 (ppp) REVERT: A 523 ASP cc_start: 0.7681 (OUTLIER) cc_final: 0.7475 (t0) REVERT: A 844 MET cc_start: 0.5461 (ptp) cc_final: 0.4928 (ttm) REVERT: B 1261 LEU cc_start: 0.2383 (OUTLIER) cc_final: 0.1930 (tt) REVERT: B 1285 MET cc_start: -0.1688 (tpt) cc_final: -0.2263 (ptp) REVERT: C 51 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6708 (pp20) outliers start: 22 outliers final: 14 residues processed: 79 average time/residue: 0.0838 time to fit residues: 10.2672 Evaluate side-chains 81 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1016 THR Chi-restraints excluded: chain B residue 1015 VAL Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain B residue 1261 LEU Chi-restraints excluded: chain C residue 51 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: [27, 132, 94, 58, 113, 99, 82, 62, 116, 130, 24] chunk 27 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 113 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 82 optimal weight: 20.0000 chunk 62 optimal weight: 3.9990 chunk 116 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 2 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.190708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.120582 restraints weight = 22133.343| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 5.46 r_work: 0.3480 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 10912 Z= 0.262 Angle : 0.626 13.860 14796 Z= 0.311 Chirality : 0.043 0.179 1634 Planarity : 0.004 0.057 1938 Dihedral : 5.048 55.150 1468 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.80 % Allowed : 13.12 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.24), residues: 1339 helix: 1.43 (0.23), residues: 543 sheet: 0.03 (0.37), residues: 211 loop : -0.13 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1025 TYR 0.014 0.001 TYR A 117 PHE 0.020 0.002 PHE A 564 TRP 0.008 0.001 TRP B1136 HIS 0.007 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00619 / 0.26 (10912) covalent geometry : angle 0.62622 / 0.31 (14796) hydrogen bonds : bond 0.03840 / 2.57 ( 498) hydrogen bonds : angle 4.51372 / 3.21 ( 1374) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 59 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.5235 (OUTLIER) cc_final: 0.3721 (tpp) REVERT: A 482 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8003 (mp0) REVERT: A 844 MET cc_start: 0.5987 (ptp) cc_final: 0.5401 (ttm) REVERT: A 996 MET cc_start: 0.8351 (tpt) cc_final: 0.7340 (tpt) REVERT: B 1261 LEU cc_start: 0.4864 (OUTLIER) cc_final: 0.4380 (tt) REVERT: B 1285 MET cc_start: -0.0666 (tpt) cc_final: -0.1251 (ptp) REVERT: C 51 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7478 (pp20) outliers start: 21 outliers final: 15 residues processed: 76 average time/residue: 0.0807 time to fit residues: 9.7550 Evaluate side-chains 77 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain A residue 1016 THR Chi-restraints excluded: chain B residue 1015 VAL Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain B residue 1261 LEU Chi-restraints excluded: chain C residue 51 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: [41, 92, 29, 11, 74, 59, 58, 82, 21, 52, 101] chunk 41 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 82 optimal weight: 20.0000 chunk 21 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4875 r_free = 0.4875 target = 0.194238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.129923 restraints weight = 22338.981| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 5.66 r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10912 Z= 0.124 Angle : 0.558 13.841 14796 Z= 0.274 Chirality : 0.040 0.184 1634 Planarity : 0.004 0.054 1938 Dihedral : 4.879 56.612 1468 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.72 % Allowed : 13.29 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.24), residues: 1339 helix: 1.52 (0.23), residues: 545 sheet: 0.25 (0.37), residues: 208 loop : -0.07 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1025 TYR 0.007 0.001 TYR B1100 PHE 0.012 0.001 PHE B1259 TRP 0.007 0.001 TRP B1136 HIS 0.002 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (10912) covalent geometry : angle 0.55794 / 0.27 (14796) hydrogen bonds : bond 0.03358 / 2.25 ( 498) hydrogen bonds : angle 4.34909 / 3.09 ( 1374) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2932.38 seconds wall clock time: 50 minutes 52.07 seconds (3052.07 seconds total)