Starting phenix.real_space_refine on Tue Nov 18 13:38:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mcb_9066/11_2025/6mcb_9066.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mcb_9066/11_2025/6mcb_9066.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6mcb_9066/11_2025/6mcb_9066.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mcb_9066/11_2025/6mcb_9066.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6mcb_9066/11_2025/6mcb_9066.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mcb_9066/11_2025/6mcb_9066.map" } resolution = 3.4 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= 0.049 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 118 5.49 5 S 28 5.16 5 C 8544 2.51 5 N 2459 2.21 5 O 3038 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14187 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 2494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 2494 Unusual residues: {'GTP': 1} Classifications: {'RNA': 115, 'undetermined': 1} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 7, 'rna3p_pur': 56, 'rna3p_pyr': 41} Link IDs: {'rna2p': 18, 'rna3p': 96, None: 1} Not linked: pdbres="GTP B 1 " pdbres=" G B 2 " Chain: "A" Number of atoms: 10747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1364, 10747 Classifications: {'peptide': 1364} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PTRANS': 35, 'TRANS': 1328} Unresolved non-hydrogen bonds: 407 Unresolved non-hydrogen angles: 464 Unresolved non-hydrogen dihedrals: 360 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 19, 'ARG:plan': 9, 'PHE:plan': 2, 'GLN:plan1': 7, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 193 Chain: "C" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 1, 'TRANS': 121} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 6} Unresolved non-hydrogen planarities: 33 Time building chain proxies: 3.66, per 1000 atoms: 0.26 Number of scatterers: 14187 At special positions: 0 Unit cell: (136.12, 117.86, 110.39, 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 28 16.00 P 118 15.00 O 3038 8.00 N 2459 7.00 C 8544 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.45 Conformation dependent library (CDL) restraints added in 495.0 milliseconds 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2834 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 11 sheets defined 48.0% alpha, 7.2% beta 28 base pairs and 66 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 5.435A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 121 through 132 removed outlier: 3.861A pdb=" N GLU A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 126 " --> pdb=" O ILE A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 144 removed outlier: 3.910A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP A 144 " --> pdb=" O LYS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 removed outlier: 3.567A pdb=" N PHE A 164 " --> pdb=" O HIS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 196 Processing helix chain 'A' and resid 207 through 213 Processing helix chain 'A' and resid 217 through 229 removed outlier: 3.934A pdb=" N LEU A 225 " --> pdb=" O ARG A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 247 Processing helix chain 'A' and resid 270 through 283 removed outlier: 3.559A pdb=" N ASP A 274 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLN A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 306 Processing helix chain 'A' and resid 317 through 343 Processing helix chain 'A' and resid 347 through 352 Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 368 through 377 removed outlier: 3.690A pdb=" N PHE A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 382 Processing helix chain 'A' and resid 390 through 395 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.875A pdb=" N ASN A 407 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 410 " --> pdb=" O ASN A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 410' Processing helix chain 'A' and resid 411 through 426 removed outlier: 4.189A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.644A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN A 436 " --> pdb=" O PHE A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 445 Processing helix chain 'A' and resid 475 through 479 removed outlier: 3.940A pdb=" N PHE A 478 " --> pdb=" O PRO A 475 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU A 479 " --> pdb=" O TRP A 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 475 through 479' Processing helix chain 'A' and resid 483 through 496 Processing helix chain 'A' and resid 512 through 525 Processing helix chain 'A' and resid 541 through 552 Processing helix chain 'A' and resid 560 through 568 Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 603 through 608 removed outlier: 3.736A pdb=" N LEU A 607 " --> pdb=" O ASP A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 628 through 634 Processing helix chain 'A' and resid 637 through 642 removed outlier: 4.206A pdb=" N HIS A 641 " --> pdb=" O THR A 638 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 642 " --> pdb=" O TYR A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 652 Processing helix chain 'A' and resid 663 through 668 Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 698 Processing helix chain 'A' and resid 703 through 713 removed outlier: 3.554A pdb=" N ALA A 711 " --> pdb=" O ASP A 707 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL A 713 " --> pdb=" O GLN A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 726 removed outlier: 3.506A pdb=" N HIS A 723 " --> pdb=" O SER A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 751 Processing helix chain 'A' and resid 769 through 773 removed outlier: 3.656A pdb=" N GLY A 773 " --> pdb=" O THR A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 792 Processing helix chain 'A' and resid 808 through 817 removed outlier: 3.578A pdb=" N TYR A 812 " --> pdb=" O ASN A 808 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN A 817 " --> pdb=" O LEU A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 879 removed outlier: 3.582A pdb=" N LYS A 878 " --> pdb=" O GLU A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 888 removed outlier: 3.728A pdb=" N ARG A 884 " --> pdb=" O LYS A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 901 Processing helix chain 'A' and resid 909 through 922 removed outlier: 4.300A pdb=" N GLN A 920 " --> pdb=" O PHE A 916 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 922 " --> pdb=" O LYS A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 940 removed outlier: 4.055A pdb=" N LYS A 929 " --> pdb=" O ARG A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 970 removed outlier: 4.473A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 1001 Processing helix chain 'A' and resid 1004 through 1009 removed outlier: 3.757A pdb=" N PHE A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1047 removed outlier: 4.409A pdb=" N PHE A1045 " --> pdb=" O ILE A1042 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE A1046 " --> pdb=" O MET A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1087 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 removed outlier: 3.911A pdb=" N ASN A1177 " --> pdb=" O SER A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1186 removed outlier: 3.532A pdb=" N GLY A1186 " --> pdb=" O LEU A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1241 Processing helix chain 'A' and resid 1248 through 1262 removed outlier: 3.515A pdb=" N HIS A1262 " --> pdb=" O PHE A1258 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1278 removed outlier: 4.258A pdb=" N ASP A1267 " --> pdb=" O LYS A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1313 Processing helix chain 'A' and resid 1314 through 1316 No H-bonds generated for 'chain 'A' and resid 1314 through 1316' Processing helix chain 'C' and resid 5 through 19 removed outlier: 3.540A pdb=" N ALA C 11 " --> pdb=" O GLN C 7 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASN C 19 " --> pdb=" O HIS C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 38 removed outlier: 3.642A pdb=" N LEU C 36 " --> pdb=" O ALA C 32 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS C 37 " --> pdb=" O LYS C 33 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP C 38 " --> pdb=" O GLU C 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 32 through 38' Processing helix chain 'C' and resid 104 through 114 removed outlier: 4.045A pdb=" N GLU C 108 " --> pdb=" O THR C 104 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N MET C 109 " --> pdb=" O ASP C 105 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY C 112 " --> pdb=" O GLU C 108 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957 removed outlier: 6.079A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 33 removed outlier: 3.760A pdb=" N LYS A 45 " --> pdb=" O LYS A 30 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36 removed outlier: 6.568A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 539 removed outlier: 3.503A pdb=" N ALA A 538 " --> pdb=" O TYR A 529 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU A 579 " --> pdb=" O VAL A 530 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 838 through 840 Processing sheet with id=AA6, first strand: chain 'A' and resid 1063 through 1065 removed outlier: 3.777A pdb=" N TRP A1074 " --> pdb=" O GLU A1064 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1106 through 1111 removed outlier: 3.991A pdb=" N ASP A1135 " --> pdb=" O LYS A1107 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N SER A1109 " --> pdb=" O GLY A1133 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLY A1133 " --> pdb=" O SER A1109 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1139 through 1141 removed outlier: 7.303A pdb=" N ILE A1166 " --> pdb=" O ALA A1140 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1145 through 1151 Processing sheet with id=AB1, first strand: chain 'A' and resid 1324 through 1325 removed outlier: 3.876A pdb=" N PHE A1324 " --> pdb=" O ILE A1331 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE A1331 " --> pdb=" O PHE A1324 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 72 through 80 removed outlier: 4.789A pdb=" N LEU C 74 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLU C 93 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP C 76 " --> pdb=" O ILE C 91 " (cutoff:3.500A) 474 hydrogen bonds defined for protein. 1386 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 68 hydrogen bonds 132 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 66 stacking parallelities Total time for adding SS restraints: 2.89 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2207 1.31 - 1.44: 4470 1.44 - 1.56: 7731 1.56 - 1.69: 232 1.69 - 1.82: 52 Bond restraints: 14692 Sorted by residual: bond pdb=" C6 GTP B 1 " pdb=" O6 GTP B 1 " ideal model delta sigma weight residual 1.230 1.387 -0.157 2.00e-02 2.50e+03 6.17e+01 bond pdb=" C2 GTP B 1 " pdb=" N2 GTP B 1 " ideal model delta sigma weight residual 1.330 1.422 -0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" CB ARG A 139 " pdb=" CG ARG A 139 " ideal model delta sigma weight residual 1.520 1.420 0.100 3.00e-02 1.11e+03 1.11e+01 bond pdb=" C5 GTP B 1 " pdb=" C6 GTP B 1 " ideal model delta sigma weight residual 1.390 1.457 -0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C LYS A 377 " pdb=" N PRO A 378 " ideal model delta sigma weight residual 1.335 1.378 -0.042 1.30e-02 5.92e+03 1.06e+01 ... (remaining 14687 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 19804 2.81 - 5.62: 547 5.62 - 8.43: 71 8.43 - 11.23: 15 11.23 - 14.04: 5 Bond angle restraints: 20442 Sorted by residual: angle pdb=" C PRO C 29 " pdb=" N ASP C 30 " pdb=" CA ASP C 30 " ideal model delta sigma weight residual 121.54 134.10 -12.56 1.91e+00 2.74e-01 4.32e+01 angle pdb=" N TYR A1326 " pdb=" CA TYR A1326 " pdb=" C TYR A1326 " ideal model delta sigma weight residual 110.52 103.33 7.19 1.48e+00 4.57e-01 2.36e+01 angle pdb=" CB ARG A 139 " pdb=" CG ARG A 139 " pdb=" CD ARG A 139 " ideal model delta sigma weight residual 111.30 100.31 10.99 2.30e+00 1.89e-01 2.28e+01 angle pdb=" C ASP C 30 " pdb=" N PHE C 31 " pdb=" CA PHE C 31 " ideal model delta sigma weight residual 121.54 130.43 -8.89 1.91e+00 2.74e-01 2.17e+01 angle pdb=" O3' A B 86 " pdb=" C3' A B 86 " pdb=" C2' A B 86 " ideal model delta sigma weight residual 113.70 120.45 -6.75 1.50e+00 4.44e-01 2.02e+01 ... (remaining 20437 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 8587 35.45 - 70.89: 343 70.89 - 106.34: 42 106.34 - 141.79: 2 141.79 - 177.24: 4 Dihedral angle restraints: 8978 sinusoidal: 4598 harmonic: 4380 Sorted by residual: dihedral pdb=" CA ASP C 30 " pdb=" C ASP C 30 " pdb=" N PHE C 31 " pdb=" CA PHE C 31 " ideal model delta harmonic sigma weight residual 180.00 128.96 51.04 0 5.00e+00 4.00e-02 1.04e+02 dihedral pdb=" CA THR C 28 " pdb=" C THR C 28 " pdb=" N PRO C 29 " pdb=" CA PRO C 29 " ideal model delta harmonic sigma weight residual 180.00 132.07 47.93 0 5.00e+00 4.00e-02 9.19e+01 dihedral pdb=" O4' C B 88 " pdb=" C1' C B 88 " pdb=" N1 C B 88 " pdb=" C2 C B 88 " ideal model delta sinusoidal sigma weight residual 200.00 42.87 157.13 1 1.50e+01 4.44e-03 8.20e+01 ... (remaining 8975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1943 0.074 - 0.149: 405 0.149 - 0.223: 48 0.223 - 0.297: 8 0.297 - 0.372: 3 Chirality restraints: 2407 Sorted by residual: chirality pdb=" C3' C B 35 " pdb=" C4' C B 35 " pdb=" O3' C B 35 " pdb=" C2' C B 35 " both_signs ideal model delta sigma weight residual False -2.48 -2.11 -0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" C1' A B 45 " pdb=" O4' A B 45 " pdb=" C2' A B 45 " pdb=" N9 A B 45 " both_signs ideal model delta sigma weight residual False 2.46 2.11 0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" CB ILE A 956 " pdb=" CA ILE A 956 " pdb=" CG1 ILE A 956 " pdb=" CG2 ILE A 956 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 2404 not shown) Planarity restraints: 2197 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U B 39 " -0.044 2.00e-02 2.50e+03 2.55e-02 1.46e+01 pdb=" N1 U B 39 " 0.047 2.00e-02 2.50e+03 pdb=" C2 U B 39 " -0.018 2.00e-02 2.50e+03 pdb=" O2 U B 39 " 0.010 2.00e-02 2.50e+03 pdb=" N3 U B 39 " 0.022 2.00e-02 2.50e+03 pdb=" C4 U B 39 " -0.020 2.00e-02 2.50e+03 pdb=" O4 U B 39 " -0.011 2.00e-02 2.50e+03 pdb=" C5 U B 39 " -0.004 2.00e-02 2.50e+03 pdb=" C6 U B 39 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 45 " 0.040 2.00e-02 2.50e+03 1.88e-02 9.68e+00 pdb=" N9 A B 45 " -0.045 2.00e-02 2.50e+03 pdb=" C8 A B 45 " -0.004 2.00e-02 2.50e+03 pdb=" N7 A B 45 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A B 45 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A B 45 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A B 45 " 0.009 2.00e-02 2.50e+03 pdb=" N1 A B 45 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A B 45 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A B 45 " -0.006 2.00e-02 2.50e+03 pdb=" C4 A B 45 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 82 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.17e+00 pdb=" C VAL C 82 " -0.052 2.00e-02 2.50e+03 pdb=" O VAL C 82 " 0.020 2.00e-02 2.50e+03 pdb=" N ASN C 83 " 0.018 2.00e-02 2.50e+03 ... (remaining 2194 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3421 2.78 - 3.31: 12768 3.31 - 3.84: 25303 3.84 - 4.37: 29067 4.37 - 4.90: 46306 Nonbonded interactions: 116865 Sorted by model distance: nonbonded pdb=" OH TYR A 373 " pdb=" O LEU A 398 " model vdw 2.253 3.040 nonbonded pdb=" OG1 THR A 404 " pdb=" OD1 ASP A 406 " model vdw 2.265 3.040 nonbonded pdb=" OG1 THR A 560 " pdb=" O ASP A 585 " model vdw 2.274 3.040 nonbonded pdb=" OG1 THR A 525 " pdb=" O ARG A 691 " model vdw 2.289 3.040 nonbonded pdb=" O ILE A 305 " pdb=" OG SER A 320 " model vdw 2.290 3.040 ... (remaining 116860 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: 2.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 16.340 Find NCS groups from input model: 0.060 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 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 : 0.010 0.157 14693 Z= 0.443 Angle : 1.143 14.042 20442 Z= 0.608 Chirality : 0.061 0.372 2407 Planarity : 0.007 0.072 2197 Dihedral : 17.613 177.237 6144 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.22 % Favored : 92.65 % Rotamer: Outliers : 0.65 % Allowed : 6.27 % Favored : 93.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.35 % 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: -4.48 (0.16), residues: 1483 helix: -3.17 (0.13), residues: 665 sheet: -2.38 (0.42), residues: 125 loop : -2.79 (0.19), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.002 ARG A 100 TYR 0.040 0.003 TYR A 450 PHE 0.040 0.004 PHE A1008 TRP 0.015 0.003 TRP A1074 HIS 0.023 0.003 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00985 (14692) covalent geometry : angle 1.14342 (20442) hydrogen bonds : bond 0.16238 ( 542) hydrogen bonds : angle 7.54196 ( 1518) Misc. bond : bond 0.04511 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 223 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.5279 (ptt) cc_final: 0.4965 (mmt) REVERT: A 551 LEU cc_start: 0.7891 (tp) cc_final: 0.7616 (tt) REVERT: A 825 ASP cc_start: 0.7591 (m-30) cc_final: 0.6068 (p0) REVERT: A 933 GLN cc_start: 0.8930 (tm-30) cc_final: 0.8512 (tm-30) REVERT: A 1257 LEU cc_start: 0.8947 (tm) cc_final: 0.8743 (tm) REVERT: A 1357 GLU cc_start: 0.7346 (mt-10) cc_final: 0.7075 (mt-10) REVERT: C 110 LYS cc_start: 0.8645 (mttt) cc_final: 0.8429 (mtmm) outliers start: 8 outliers final: 3 residues processed: 226 average time/residue: 0.1274 time to fit residues: 40.8306 Evaluate side-chains 135 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 132 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 266 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 9.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 235 ASN A 240 ASN A 328 HIS A 369 GLN A 412 HIS A 504 ASN A 522 ASN A 723 HIS A 767 ASN A 803 ASN A 971 GLN C 7 GLN C 114 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.169237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.131071 restraints weight = 21943.855| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 2.30 r_work: 0.3776 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14693 Z= 0.147 Angle : 0.672 11.262 20442 Z= 0.348 Chirality : 0.042 0.314 2407 Planarity : 0.005 0.063 2197 Dihedral : 19.960 175.592 3372 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.06 % Favored : 94.81 % Rotamer: Outliers : 2.77 % Allowed : 10.18 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.07 % 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: -3.06 (0.19), residues: 1483 helix: -1.67 (0.17), residues: 682 sheet: -2.09 (0.42), residues: 128 loop : -2.33 (0.21), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 976 TYR 0.027 0.002 TYR C 50 PHE 0.027 0.002 PHE C 31 TRP 0.004 0.001 TRP A 476 HIS 0.009 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00320 (14692) covalent geometry : angle 0.67199 (20442) hydrogen bonds : bond 0.04463 ( 542) hydrogen bonds : angle 5.13326 ( 1518) Misc. bond : bond 0.00179 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 192 time to evaluate : 0.502 Fit side-chains REVERT: A 74 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7210 (mpt90) REVERT: A 97 PHE cc_start: 0.8547 (t80) cc_final: 0.8267 (t80) REVERT: A 152 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.7264 (ptt90) REVERT: A 241 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8044 (mt) REVERT: A 370 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.8004 (pt0) REVERT: A 534 MET cc_start: 0.5619 (ptt) cc_final: 0.4923 (mmt) REVERT: A 551 LEU cc_start: 0.8086 (tp) cc_final: 0.7838 (tt) REVERT: A 631 MET cc_start: 0.7984 (mmm) cc_final: 0.7507 (mmt) REVERT: A 634 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7959 (tm-30) REVERT: A 645 ASP cc_start: 0.8224 (t0) cc_final: 0.7990 (m-30) REVERT: A 825 ASP cc_start: 0.7619 (m-30) cc_final: 0.6175 (p0) REVERT: A 933 GLN cc_start: 0.8731 (tm-30) cc_final: 0.8320 (tm-30) REVERT: A 1089 MET cc_start: 0.8491 (mmm) cc_final: 0.7844 (mmm) REVERT: A 1179 ILE cc_start: 0.8792 (pt) cc_final: 0.7816 (pt) REVERT: A 1211 LYS cc_start: 0.8773 (mttt) cc_final: 0.8562 (mtmm) REVERT: A 1281 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8705 (mm) REVERT: C 20 MET cc_start: 0.8090 (pp-130) cc_final: 0.7463 (ppp) REVERT: C 106 GLU cc_start: 0.8223 (tt0) cc_final: 0.7801 (tt0) outliers start: 34 outliers final: 13 residues processed: 213 average time/residue: 0.1147 time to fit residues: 36.0740 Evaluate side-chains 168 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 751 MET Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 1142 SER Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 79 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 112 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 24 optimal weight: 0.4980 chunk 94 optimal weight: 20.0000 chunk 11 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 149 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 23 optimal weight: 0.0270 overall best weight: 0.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 ASN A 971 GLN C 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.170122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.130973 restraints weight = 22114.906| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.46 r_work: 0.3722 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14693 Z= 0.131 Angle : 0.623 10.224 20442 Z= 0.319 Chirality : 0.041 0.265 2407 Planarity : 0.004 0.045 2197 Dihedral : 19.665 176.254 3372 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.92 % Favored : 94.94 % Rotamer: Outliers : 3.75 % Allowed : 12.21 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.20), residues: 1483 helix: -0.93 (0.18), residues: 692 sheet: -1.86 (0.42), residues: 138 loop : -2.12 (0.22), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1212 TYR 0.021 0.001 TYR C 10 PHE 0.029 0.001 PHE C 31 TRP 0.022 0.001 TRP A 476 HIS 0.004 0.001 HIS A1349 Details of bonding type rmsd covalent geometry : bond 0.00286 (14692) covalent geometry : angle 0.62251 (20442) hydrogen bonds : bond 0.04075 ( 542) hydrogen bonds : angle 4.71479 ( 1518) Misc. bond : bond 0.00145 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 178 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7254 (mpt90) REVERT: A 97 PHE cc_start: 0.8486 (t80) cc_final: 0.8163 (t80) REVERT: A 152 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.7130 (ptt90) REVERT: A 174 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7921 (mt) REVERT: A 215 ARG cc_start: 0.6352 (tpt90) cc_final: 0.5628 (mmm-85) REVERT: A 370 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8019 (pt0) REVERT: A 551 LEU cc_start: 0.8079 (tp) cc_final: 0.7863 (tt) REVERT: A 586 ARG cc_start: 0.6758 (ptm160) cc_final: 0.6470 (ptm-80) REVERT: A 645 ASP cc_start: 0.8226 (t0) cc_final: 0.7725 (m-30) REVERT: A 738 LEU cc_start: 0.8742 (tp) cc_final: 0.8500 (tt) REVERT: A 825 ASP cc_start: 0.7774 (m-30) cc_final: 0.6562 (p0) REVERT: A 933 GLN cc_start: 0.8868 (tm-30) cc_final: 0.8581 (tm-30) REVERT: A 1089 MET cc_start: 0.8488 (mmm) cc_final: 0.7928 (mmm) REVERT: A 1106 SER cc_start: 0.8909 (p) cc_final: 0.8680 (m) REVERT: A 1281 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8646 (mm) REVERT: C 12 GLU cc_start: 0.8880 (pm20) cc_final: 0.8492 (pm20) REVERT: C 90 ASN cc_start: 0.9037 (OUTLIER) cc_final: 0.8589 (p0) REVERT: C 109 MET cc_start: 0.8399 (tpp) cc_final: 0.7849 (mmt) REVERT: C 122 LEU cc_start: 0.6383 (OUTLIER) cc_final: 0.6167 (pp) outliers start: 46 outliers final: 19 residues processed: 212 average time/residue: 0.1079 time to fit residues: 34.9622 Evaluate side-chains 170 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1049 GLU Chi-restraints excluded: chain A residue 1142 SER Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1331 ILE Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 122 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 143 optimal weight: 0.1980 chunk 75 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 9.9990 chunk 151 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.170281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.131461 restraints weight = 22032.014| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 2.39 r_work: 0.3739 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14693 Z= 0.134 Angle : 0.610 9.748 20442 Z= 0.310 Chirality : 0.041 0.221 2407 Planarity : 0.004 0.043 2197 Dihedral : 19.501 176.619 3372 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.92 % Favored : 95.01 % Rotamer: Outliers : 3.66 % Allowed : 13.19 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.07 % 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: -1.95 (0.21), residues: 1483 helix: -0.53 (0.19), residues: 698 sheet: -1.50 (0.46), residues: 127 loop : -2.06 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 629 TYR 0.022 0.001 TYR C 77 PHE 0.024 0.001 PHE C 31 TRP 0.015 0.001 TRP A 476 HIS 0.003 0.001 HIS A 420 Details of bonding type rmsd covalent geometry : bond 0.00298 (14692) covalent geometry : angle 0.60965 (20442) hydrogen bonds : bond 0.03832 ( 542) hydrogen bonds : angle 4.50996 ( 1518) Misc. bond : bond 0.00157 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 162 time to evaluate : 0.461 Fit side-chains REVERT: A 74 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7234 (mpt90) REVERT: A 97 PHE cc_start: 0.8484 (t80) cc_final: 0.8033 (t80) REVERT: A 152 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.7080 (ptt90) REVERT: A 215 ARG cc_start: 0.6565 (tpt90) cc_final: 0.5735 (mtp180) REVERT: A 586 ARG cc_start: 0.6821 (ptm160) cc_final: 0.6586 (ptm-80) REVERT: A 645 ASP cc_start: 0.8026 (t0) cc_final: 0.7529 (m-30) REVERT: A 738 LEU cc_start: 0.8689 (tp) cc_final: 0.8436 (tt) REVERT: A 933 GLN cc_start: 0.8864 (tm-30) cc_final: 0.8595 (tm-30) REVERT: A 1089 MET cc_start: 0.8561 (mmm) cc_final: 0.8169 (mmm) REVERT: A 1281 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8601 (mm) REVERT: C 115 GLU cc_start: 0.8567 (pm20) cc_final: 0.8359 (pm20) outliers start: 45 outliers final: 23 residues processed: 191 average time/residue: 0.1071 time to fit residues: 31.4517 Evaluate side-chains 163 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1142 SER Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1331 ILE Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 118 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 4.9990 chunk 93 optimal weight: 20.0000 chunk 76 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 87 optimal weight: 20.0000 chunk 100 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 22 optimal weight: 0.0970 chunk 33 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 HIS A 235 ASN A 650 GLN A 698 HIS A1241 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.171996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.133108 restraints weight = 22078.407| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.40 r_work: 0.3750 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14693 Z= 0.117 Angle : 0.594 9.453 20442 Z= 0.302 Chirality : 0.041 0.288 2407 Planarity : 0.004 0.041 2197 Dihedral : 19.374 178.206 3370 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.99 % Favored : 94.94 % Rotamer: Outliers : 3.34 % Allowed : 14.66 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.07 % 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: -1.63 (0.21), residues: 1483 helix: -0.20 (0.19), residues: 701 sheet: -1.25 (0.45), residues: 129 loop : -2.01 (0.22), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 629 TYR 0.024 0.001 TYR A1356 PHE 0.031 0.001 PHE A1008 TRP 0.010 0.001 TRP A 476 HIS 0.004 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00257 (14692) covalent geometry : angle 0.59418 (20442) hydrogen bonds : bond 0.03692 ( 542) hydrogen bonds : angle 4.43322 ( 1518) Misc. bond : bond 0.00161 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 147 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: A 152 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.7181 (ptt90) REVERT: A 215 ARG cc_start: 0.6503 (tpt90) cc_final: 0.5748 (mtp180) REVERT: A 338 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6389 (tp) REVERT: A 529 TYR cc_start: 0.5900 (p90) cc_final: 0.5625 (p90) REVERT: A 586 ARG cc_start: 0.6722 (ptm160) cc_final: 0.6491 (ptm-80) REVERT: A 645 ASP cc_start: 0.7941 (t0) cc_final: 0.7431 (m-30) REVERT: A 738 LEU cc_start: 0.8675 (tp) cc_final: 0.8474 (tt) REVERT: A 933 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8572 (tm-30) REVERT: C 109 MET cc_start: 0.8428 (tpp) cc_final: 0.7864 (mmt) outliers start: 41 outliers final: 23 residues processed: 175 average time/residue: 0.1117 time to fit residues: 29.5731 Evaluate side-chains 163 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1142 SER Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1331 ILE Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 89 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 40 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 125 optimal weight: 7.9990 chunk 111 optimal weight: 0.0050 chunk 43 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 112 optimal weight: 0.1980 chunk 105 optimal weight: 5.9990 chunk 141 optimal weight: 0.8980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 ASN C 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.173757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.134685 restraints weight = 22128.555| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 2.42 r_work: 0.3783 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 14693 Z= 0.112 Angle : 0.590 10.925 20442 Z= 0.296 Chirality : 0.040 0.277 2407 Planarity : 0.003 0.040 2197 Dihedral : 19.293 177.872 3370 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.38 % Favored : 95.55 % Rotamer: Outliers : 2.69 % Allowed : 16.37 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.07 % 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: -1.30 (0.21), residues: 1483 helix: 0.10 (0.20), residues: 701 sheet: -1.06 (0.47), residues: 122 loop : -1.89 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 780 TYR 0.022 0.001 TYR A1356 PHE 0.030 0.001 PHE A1008 TRP 0.009 0.001 TRP A 476 HIS 0.002 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00250 (14692) covalent geometry : angle 0.59034 (20442) hydrogen bonds : bond 0.03507 ( 542) hydrogen bonds : angle 4.35667 ( 1518) Misc. bond : bond 0.00161 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 151 time to evaluate : 0.511 Fit side-chains REVERT: A 215 ARG cc_start: 0.6435 (tpt90) cc_final: 0.5712 (mtp180) REVERT: A 465 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.6907 (ttt) REVERT: A 529 TYR cc_start: 0.6001 (p90) cc_final: 0.5712 (p90) REVERT: A 586 ARG cc_start: 0.6743 (ptm160) cc_final: 0.6512 (ptm-80) REVERT: A 645 ASP cc_start: 0.7591 (t0) cc_final: 0.7202 (m-30) REVERT: A 738 LEU cc_start: 0.8671 (tp) cc_final: 0.8454 (tt) REVERT: A 933 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8603 (tm-30) REVERT: A 964 SER cc_start: 0.8728 (t) cc_final: 0.8364 (p) REVERT: A 1089 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8309 (mtp) REVERT: A 1189 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7426 (tm-30) REVERT: C 20 MET cc_start: 0.8187 (ppp) cc_final: 0.7526 (ppp) REVERT: C 109 MET cc_start: 0.8411 (tpp) cc_final: 0.7830 (mmt) outliers start: 33 outliers final: 20 residues processed: 171 average time/residue: 0.1031 time to fit residues: 27.2517 Evaluate side-chains 160 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1088 SER Chi-restraints excluded: chain A residue 1089 MET Chi-restraints excluded: chain A residue 1142 SER Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1331 ILE Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 79 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 30 optimal weight: 0.2980 chunk 5 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 152 optimal weight: 7.9990 chunk 145 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 235 ASN C 113 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.168774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.129409 restraints weight = 22017.386| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.35 r_work: 0.3696 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 14693 Z= 0.175 Angle : 0.642 12.832 20442 Z= 0.323 Chirality : 0.043 0.262 2407 Planarity : 0.004 0.042 2197 Dihedral : 19.325 177.186 3368 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.92 % Favored : 95.01 % Rotamer: Outliers : 3.58 % Allowed : 15.23 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.07 % 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: -1.30 (0.21), residues: 1483 helix: 0.10 (0.20), residues: 689 sheet: -1.12 (0.48), residues: 106 loop : -1.82 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 467 TYR 0.024 0.002 TYR A1356 PHE 0.063 0.002 PHE A1008 TRP 0.008 0.001 TRP A1074 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00397 (14692) covalent geometry : angle 0.64200 (20442) hydrogen bonds : bond 0.03843 ( 542) hydrogen bonds : angle 4.41778 ( 1518) Misc. bond : bond 0.00164 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 142 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 465 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.7383 (ttt) REVERT: A 586 ARG cc_start: 0.6777 (ptm160) cc_final: 0.6571 (ptm-80) REVERT: A 645 ASP cc_start: 0.7668 (t0) cc_final: 0.7249 (m-30) REVERT: A 933 GLN cc_start: 0.8838 (tm-30) cc_final: 0.8599 (tm-30) REVERT: A 973 TYR cc_start: 0.8942 (m-80) cc_final: 0.8421 (m-80) REVERT: A 1189 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7431 (tm-30) REVERT: C 12 GLU cc_start: 0.8829 (pm20) cc_final: 0.8160 (pm20) REVERT: C 115 GLU cc_start: 0.8714 (pm20) cc_final: 0.8321 (pm20) outliers start: 44 outliers final: 28 residues processed: 166 average time/residue: 0.1055 time to fit residues: 27.0863 Evaluate side-chains 167 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1142 SER Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1302 ILE Chi-restraints excluded: chain A residue 1331 ILE Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 91 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 34 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 107 optimal weight: 0.5980 chunk 123 optimal weight: 0.4980 chunk 51 optimal weight: 0.3980 chunk 15 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 60 optimal weight: 0.0470 chunk 98 optimal weight: 20.0000 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 235 ASN A 420 HIS A 612 ASN C 113 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.174488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.135181 restraints weight = 21797.074| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 2.42 r_work: 0.3773 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 14693 Z= 0.110 Angle : 0.606 10.519 20442 Z= 0.300 Chirality : 0.040 0.258 2407 Planarity : 0.003 0.040 2197 Dihedral : 19.268 178.202 3368 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.59 % Favored : 95.35 % Rotamer: Outliers : 2.20 % Allowed : 16.78 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.07 % 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: -1.05 (0.22), residues: 1483 helix: 0.32 (0.20), residues: 692 sheet: -0.77 (0.47), residues: 115 loop : -1.77 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 215 TYR 0.023 0.001 TYR A1356 PHE 0.018 0.001 PHE A 97 TRP 0.009 0.001 TRP A 476 HIS 0.004 0.000 HIS A 116 Details of bonding type rmsd covalent geometry : bond 0.00244 (14692) covalent geometry : angle 0.60554 (20442) hydrogen bonds : bond 0.03474 ( 542) hydrogen bonds : angle 4.33887 ( 1518) Misc. bond : bond 0.00165 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.391 Fit side-chains REVERT: A 215 ARG cc_start: 0.6241 (tpt90) cc_final: 0.5565 (mtp180) REVERT: A 465 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.7335 (ttt) REVERT: A 586 ARG cc_start: 0.6784 (ptm160) cc_final: 0.6438 (ptm-80) REVERT: A 645 ASP cc_start: 0.7512 (t0) cc_final: 0.6889 (m-30) REVERT: A 738 LEU cc_start: 0.8652 (tp) cc_final: 0.8401 (tt) REVERT: A 933 GLN cc_start: 0.8805 (tm-30) cc_final: 0.8579 (tm-30) REVERT: A 973 TYR cc_start: 0.8873 (m-80) cc_final: 0.8349 (m-80) REVERT: A 1189 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7455 (tm-30) REVERT: C 12 GLU cc_start: 0.8783 (pm20) cc_final: 0.8134 (pm20) REVERT: C 109 MET cc_start: 0.8414 (tpp) cc_final: 0.7831 (mmt) REVERT: C 115 GLU cc_start: 0.8681 (pm20) cc_final: 0.8458 (pm20) outliers start: 27 outliers final: 19 residues processed: 170 average time/residue: 0.0946 time to fit residues: 25.4912 Evaluate side-chains 165 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1142 SER Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1331 ILE Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 91 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 36 optimal weight: 0.4980 chunk 61 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 chunk 122 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 153 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS A 698 HIS A 758 ASN C 114 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.172751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.133345 restraints weight = 22008.727| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 2.42 r_work: 0.3748 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14693 Z= 0.130 Angle : 0.609 10.591 20442 Z= 0.304 Chirality : 0.041 0.251 2407 Planarity : 0.003 0.041 2197 Dihedral : 19.243 177.850 3368 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.52 % Favored : 95.41 % Rotamer: Outliers : 2.52 % Allowed : 17.35 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.07 % 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: -1.05 (0.21), residues: 1483 helix: 0.27 (0.20), residues: 695 sheet: -0.69 (0.49), residues: 97 loop : -1.72 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 215 TYR 0.021 0.001 TYR A1356 PHE 0.017 0.001 PHE A 97 TRP 0.006 0.001 TRP A 476 HIS 0.004 0.001 HIS A 116 Details of bonding type rmsd covalent geometry : bond 0.00296 (14692) covalent geometry : angle 0.60900 (20442) hydrogen bonds : bond 0.03563 ( 542) hydrogen bonds : angle 4.33337 ( 1518) Misc. bond : bond 0.00162 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.510 Fit side-chains REVERT: A 215 ARG cc_start: 0.6371 (tpt90) cc_final: 0.5663 (mtp180) REVERT: A 341 GLN cc_start: 0.7426 (tm-30) cc_final: 0.7035 (pp30) REVERT: A 465 MET cc_start: 0.7725 (OUTLIER) cc_final: 0.7308 (ttt) REVERT: A 645 ASP cc_start: 0.7467 (t0) cc_final: 0.6780 (m-30) REVERT: A 698 HIS cc_start: 0.8010 (OUTLIER) cc_final: 0.7261 (m90) REVERT: A 933 GLN cc_start: 0.8805 (tm-30) cc_final: 0.8584 (tm-30) REVERT: A 964 SER cc_start: 0.8715 (t) cc_final: 0.8309 (p) REVERT: A 973 TYR cc_start: 0.8890 (m-80) cc_final: 0.8334 (m-80) REVERT: A 1189 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7533 (tm-30) REVERT: C 12 GLU cc_start: 0.8791 (pm20) cc_final: 0.8245 (pm20) REVERT: C 109 MET cc_start: 0.8433 (tpp) cc_final: 0.7825 (mmt) outliers start: 31 outliers final: 22 residues processed: 167 average time/residue: 0.0968 time to fit residues: 25.6034 Evaluate side-chains 161 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 698 HIS Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1142 SER Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1331 ILE Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 91 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 101 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 69 optimal weight: 10.0000 chunk 113 optimal weight: 20.0000 chunk 126 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 39 optimal weight: 0.2980 chunk 7 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 HIS A 698 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.170136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.131154 restraints weight = 22007.566| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.37 r_work: 0.3726 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14693 Z= 0.158 Angle : 0.639 10.836 20442 Z= 0.318 Chirality : 0.042 0.259 2407 Planarity : 0.004 0.042 2197 Dihedral : 19.263 177.112 3368 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.72 % Favored : 95.21 % Rotamer: Outliers : 2.36 % Allowed : 17.67 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.07 % 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: -1.01 (0.21), residues: 1483 helix: 0.31 (0.20), residues: 690 sheet: -0.79 (0.49), residues: 98 loop : -1.68 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 215 TYR 0.030 0.002 TYR C 50 PHE 0.017 0.002 PHE A 97 TRP 0.005 0.001 TRP A 476 HIS 0.006 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00362 (14692) covalent geometry : angle 0.63855 (20442) hydrogen bonds : bond 0.03691 ( 542) hydrogen bonds : angle 4.35416 ( 1518) Misc. bond : bond 0.00165 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 0.472 Fit side-chains REVERT: A 215 ARG cc_start: 0.6450 (tpt90) cc_final: 0.5724 (mtp180) REVERT: A 341 GLN cc_start: 0.7453 (tm-30) cc_final: 0.7054 (pp30) REVERT: A 465 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7420 (ttt) REVERT: A 482 VAL cc_start: 0.8209 (t) cc_final: 0.8003 (p) REVERT: A 523 GLU cc_start: 0.7859 (tt0) cc_final: 0.7436 (tt0) REVERT: A 645 ASP cc_start: 0.7500 (t0) cc_final: 0.6945 (m-30) REVERT: A 933 GLN cc_start: 0.8818 (tm-30) cc_final: 0.8603 (tm-30) REVERT: A 964 SER cc_start: 0.8750 (t) cc_final: 0.8354 (p) REVERT: A 973 TYR cc_start: 0.8881 (m-80) cc_final: 0.8321 (m-80) REVERT: A 1189 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7507 (tm-30) REVERT: C 12 GLU cc_start: 0.8795 (pm20) cc_final: 0.8295 (pm20) REVERT: C 109 MET cc_start: 0.8412 (tpp) cc_final: 0.7814 (mmt) outliers start: 29 outliers final: 26 residues processed: 158 average time/residue: 0.0995 time to fit residues: 24.7752 Evaluate side-chains 161 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1142 SER Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1331 ILE Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 91 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 128 optimal weight: 0.6980 chunk 127 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 93 optimal weight: 0.0770 chunk 142 optimal weight: 0.0070 chunk 41 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 63 optimal weight: 10.0000 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.175272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.136933 restraints weight = 22048.702| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 2.41 r_work: 0.3808 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 14693 Z= 0.111 Angle : 0.603 10.129 20442 Z= 0.298 Chirality : 0.040 0.234 2407 Planarity : 0.003 0.040 2197 Dihedral : 19.207 178.200 3368 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.32 % Favored : 95.62 % Rotamer: Outliers : 2.12 % Allowed : 18.08 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.07 % 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: -0.84 (0.22), residues: 1483 helix: 0.46 (0.20), residues: 692 sheet: -0.69 (0.46), residues: 111 loop : -1.61 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 215 TYR 0.024 0.001 TYR C 50 PHE 0.017 0.001 PHE A 97 TRP 0.011 0.001 TRP A1074 HIS 0.003 0.000 HIS A 116 Details of bonding type rmsd covalent geometry : bond 0.00248 (14692) covalent geometry : angle 0.60264 (20442) hydrogen bonds : bond 0.03440 ( 542) hydrogen bonds : angle 4.29163 ( 1518) Misc. bond : bond 0.00163 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3099.40 seconds wall clock time: 54 minutes 1.09 seconds (3241.09 seconds total)