Starting phenix.real_space_refine on Sat Sep 12 07:27:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6mcb_9066/09_2026/6mcb_9066.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mcb_9066/09_2026/6mcb_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6mcb_9066/09_2026/6mcb_9066.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6mcb_9066/09_2026/6mcb_9066.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6mcb_9066/09_2026/6mcb_9066.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mcb_9066/09_2026/6mcb_9066.map" model { file = "/net/cci-nas-00/data/ceres_data/6mcb_9066/09_2026/6mcb_9066.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mcb_9066/09_2026/6mcb_9066.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: {'RNAv2': 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: 3.00, per 1000 atoms: 0.21 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: 0.90 Conformation dependent library (CDL) restraints added in 519.9 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: 1.76 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: 2.78 Time building geometry restraints manager: 1.27 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: 19638 2.81 - 5.62: 706 5.62 - 8.43: 77 8.43 - 11.23: 16 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=" C3' A B 86 " pdb=" O3' A B 86 " pdb=" P A B 87 " ideal model delta sigma weight residual 119.70 126.47 -6.77 1.20e+00 6.94e-01 3.18e+01 angle pdb=" C3' A B 60 " pdb=" O3' A B 60 " pdb=" P G B 61 " ideal model delta sigma weight residual 119.70 125.89 -6.19 1.20e+00 6.94e-01 2.66e+01 angle pdb=" C3' C B 35 " pdb=" O3' C B 35 " pdb=" P U B 36 " ideal model delta sigma weight residual 119.70 125.72 -6.02 1.20e+00 6.94e-01 2.52e+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 ... (remaining 20437 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 8280 35.45 - 70.89: 312 70.89 - 106.34: 22 106.34 - 141.79: 2 141.79 - 177.24: 2 Dihedral angle restraints: 8618 sinusoidal: 4238 harmonic: 4380 Sorted by residual: dihedral pdb=" C4' A B 47 " pdb=" C3' A B 47 " pdb=" C2' A B 47 " pdb=" C1' A B 47 " ideal model delta sinusoidal sigma weight residual 36.35 -41.78 78.13 1 3.10e+00 1.04e-01 7.93e+02 dihedral pdb=" C4' G B 11 " pdb=" C3' G B 11 " pdb=" C2' G B 11 " pdb=" C1' G B 11 " ideal model delta sinusoidal sigma weight residual 36.34 -37.12 73.47 1 3.10e+00 1.04e-01 7.15e+02 dihedral pdb=" C4' C B 73 " pdb=" C3' C B 73 " pdb=" C2' C B 73 " pdb=" C1' C B 73 " ideal model delta sinusoidal sigma weight residual 36.35 -37.02 73.37 1 3.10e+00 1.04e-01 7.13e+02 ... (remaining 8615 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1950 0.087 - 0.175: 296 0.175 - 0.262: 122 0.262 - 0.349: 37 0.349 - 0.437: 2 Chirality restraints: 2407 Sorted by residual: chirality pdb=" P A B 48 " pdb=" OP1 A B 48 " pdb=" OP2 A B 48 " pdb=" O5' A B 48 " both_signs ideal model delta sigma weight residual True 2.17 -2.61 -0.44 2.00e-01 2.50e+01 4.77e+00 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 -2.50 -2.11 -0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" C2' G B 11 " pdb=" C3' G B 11 " pdb=" O2' G B 11 " pdb=" C1' G B 11 " both_signs ideal model delta sigma weight residual False -2.79 -2.44 -0.35 2.00e-01 2.50e+01 2.99e+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: 2.770 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.660 Find NCS groups from input model: 0.050 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 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= 0.440 Angle : 1.213 14.042 20442 Z= 0.613 Chirality : 0.084 0.437 2407 Planarity : 0.007 0.072 2197 Dihedral : 16.392 177.237 5784 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/Z covalent geometry : bond 0.00992 / 0.44 (14692) covalent geometry : angle 1.21309 / 0.61 (20442) hydrogen bonds : bond 0.16238 / 8.60 ( 542) hydrogen bonds : angle 7.54196 / 3.10 ( 1518) Misc. bond : bond 0.04511 / 2.26 ( 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 : 0.469 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: 0.1255 time to fit residues: 41.0445 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 : 0.384 ------------------------------------------------------------------------------- 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: 4.9990 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... A 77 ASN ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 ASN A 240 ASN 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.169979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.132150 restraints weight = 22029.808| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 2.31 r_work: 0.3794 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14693 Z= 0.174 Angle : 0.979 20.858 20442 Z= 0.431 Chirality : 0.074 0.951 2407 Planarity : 0.005 0.054 2197 Dihedral : 16.628 177.142 3012 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.12 % Favored : 94.74 % Rotamer: Outliers : 2.77 % Allowed : 10.26 % Favored : 86.97 % 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: -3.11 (0.19), residues: 1483 helix: -1.72 (0.17), residues: 682 sheet: -2.09 (0.42), residues: 128 loop : -2.35 (0.21), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 340 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/Z covalent geometry : bond 0.00375 / 0.17 (14692) covalent geometry : angle 0.97947 / 0.43 (20442) hydrogen bonds : bond 0.04820 / 2.48 ( 542) hydrogen bonds : angle 5.20938 / 2.16 ( 1518) Misc. bond : bond 0.00216 / 0.11 ( 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 222 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 188 time to evaluate : 0.418 Fit side-chains REVERT: A 74 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7204 (mpt90) REVERT: A 97 PHE cc_start: 0.8563 (t80) cc_final: 0.8292 (t80) REVERT: A 110 ASP cc_start: 0.8294 (m-30) cc_final: 0.8085 (m-30) REVERT: A 152 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.7214 (ptt90) REVERT: A 241 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8032 (mt) REVERT: A 370 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.8018 (pt0) REVERT: A 534 MET cc_start: 0.5646 (ptt) cc_final: 0.4947 (mmt) REVERT: A 551 LEU cc_start: 0.8087 (tp) cc_final: 0.7835 (tt) REVERT: A 631 MET cc_start: 0.8019 (mmm) cc_final: 0.7522 (mmt) REVERT: A 634 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7956 (tm-30) REVERT: A 825 ASP cc_start: 0.7600 (m-30) cc_final: 0.6112 (p0) REVERT: A 933 GLN cc_start: 0.8744 (tm-30) cc_final: 0.8330 (tm-30) REVERT: A 1089 MET cc_start: 0.8446 (mmm) cc_final: 0.7757 (mmm) REVERT: A 1179 ILE cc_start: 0.8796 (pt) cc_final: 0.7818 (pt) REVERT: A 1211 LYS cc_start: 0.8750 (mttt) cc_final: 0.8512 (mtmm) REVERT: A 1281 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8712 (mm) REVERT: C 20 MET cc_start: 0.8089 (pp-130) cc_final: 0.7476 (ppp) REVERT: C 106 GLU cc_start: 0.8260 (tt0) cc_final: 0.7901 (tt0) outliers start: 34 outliers final: 13 residues processed: 210 average time/residue: 0.1128 time to fit residues: 35.4089 Evaluate side-chains 163 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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: 0.0010 chunk 7 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 94 optimal weight: 30.0000 chunk 11 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 149 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 HIS A 235 ASN A 971 GLN C 114 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.171348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.132554 restraints weight = 22217.834| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.42 r_work: 0.3754 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14693 Z= 0.152 Angle : 0.843 14.171 20442 Z= 0.374 Chirality : 0.062 0.496 2407 Planarity : 0.004 0.045 2197 Dihedral : 16.314 169.969 3012 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.12 % Favored : 94.74 % Rotamer: Outliers : 3.83 % Allowed : 12.05 % Favored : 84.12 % 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: -2.42 (0.20), residues: 1483 helix: -0.98 (0.18), residues: 698 sheet: -1.85 (0.43), residues: 138 loop : -2.18 (0.22), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 629 TYR 0.022 0.002 TYR C 10 PHE 0.029 0.001 PHE C 31 TRP 0.020 0.002 TRP A 476 HIS 0.011 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (14692) covalent geometry : angle 0.84290 / 0.37 (20442) hydrogen bonds : bond 0.04029 / 2.08 ( 542) hydrogen bonds : angle 4.76981 / 1.98 ( 1518) Misc. bond : bond 0.00154 / 0.08 ( 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 220 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 173 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8086 (mp0) cc_final: 0.7631 (pt0) REVERT: A 74 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7260 (mtt90) REVERT: A 97 PHE cc_start: 0.8540 (t80) cc_final: 0.8219 (t80) REVERT: A 152 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.7179 (ptt90) REVERT: A 215 ARG cc_start: 0.6458 (tpt170) cc_final: 0.5820 (mmm-85) REVERT: A 370 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8042 (pt0) REVERT: A 551 LEU cc_start: 0.8118 (tp) cc_final: 0.7897 (tt) REVERT: A 586 ARG cc_start: 0.6803 (ptm160) cc_final: 0.6505 (ptm-80) REVERT: A 631 MET cc_start: 0.7951 (mmm) cc_final: 0.7524 (mmt) REVERT: A 634 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7888 (tm-30) REVERT: A 645 ASP cc_start: 0.8229 (t0) cc_final: 0.7721 (m-30) REVERT: A 738 LEU cc_start: 0.8722 (tp) cc_final: 0.8476 (tt) REVERT: A 825 ASP cc_start: 0.7785 (m-30) cc_final: 0.6585 (p0) REVERT: A 933 GLN cc_start: 0.8831 (tm-30) cc_final: 0.8532 (tm-30) REVERT: A 1089 MET cc_start: 0.8480 (mmm) cc_final: 0.7866 (mmm) REVERT: A 1106 SER cc_start: 0.8908 (p) cc_final: 0.8675 (m) REVERT: A 1211 LYS cc_start: 0.8710 (mttt) cc_final: 0.8476 (mtmm) REVERT: C 12 GLU cc_start: 0.8883 (pm20) cc_final: 0.8483 (pm20) REVERT: C 90 ASN cc_start: 0.9042 (OUTLIER) cc_final: 0.8581 (p0) REVERT: C 122 LEU cc_start: 0.6369 (OUTLIER) cc_final: 0.6151 (pp) outliers start: 47 outliers final: 21 residues processed: 204 average time/residue: 0.1028 time to fit residues: 32.2167 Evaluate side-chains 166 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 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 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 696 LEU 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 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 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: 5.9990 chunk 75 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 3 optimal weight: 10.0000 chunk 151 optimal weight: 0.5980 chunk 133 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 235 ASN A 698 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.170596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.130628 restraints weight = 22353.714| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.46 r_work: 0.3721 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14693 Z= 0.160 Angle : 0.820 10.002 20442 Z= 0.365 Chirality : 0.060 0.527 2407 Planarity : 0.004 0.044 2197 Dihedral : 16.072 171.771 3010 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.33 % Favored : 94.61 % Rotamer: Outliers : 3.42 % Allowed : 13.27 % Favored : 83.31 % 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: -2.00 (0.21), residues: 1483 helix: -0.57 (0.19), residues: 699 sheet: -1.38 (0.46), residues: 126 loop : -2.11 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1212 TYR 0.025 0.002 TYR A1356 PHE 0.024 0.002 PHE C 31 TRP 0.017 0.001 TRP A 476 HIS 0.009 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (14692) covalent geometry : angle 0.81951 / 0.37 (20442) hydrogen bonds : bond 0.03851 / 1.98 ( 542) hydrogen bonds : angle 4.55656 / 1.88 ( 1518) Misc. bond : bond 0.00155 / 0.08 ( 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 196 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 154 time to evaluate : 0.339 Fit side-chains REVERT: A 74 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.7292 (mpt90) REVERT: A 97 PHE cc_start: 0.8554 (t80) cc_final: 0.8175 (t80) REVERT: A 110 ASP cc_start: 0.8389 (m-30) cc_final: 0.8175 (m-30) REVERT: A 152 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.7158 (ptt90) REVERT: A 215 ARG cc_start: 0.6593 (tpt170) cc_final: 0.5873 (mmm-85) REVERT: A 586 ARG cc_start: 0.6905 (ptm160) cc_final: 0.6656 (ptm-80) REVERT: A 645 ASP cc_start: 0.8099 (t0) cc_final: 0.7578 (m-30) REVERT: A 738 LEU cc_start: 0.8717 (tp) cc_final: 0.8450 (tt) REVERT: A 825 ASP cc_start: 0.7795 (m-30) cc_final: 0.6580 (p0) REVERT: A 933 GLN cc_start: 0.8875 (tm-30) cc_final: 0.8597 (tm-30) REVERT: A 1089 MET cc_start: 0.8515 (mmm) cc_final: 0.7895 (mmm) REVERT: C 115 GLU cc_start: 0.8577 (pm20) cc_final: 0.8371 (pm20) outliers start: 42 outliers final: 22 residues processed: 184 average time/residue: 0.1017 time to fit residues: 28.9501 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 : 0.364 ------------------------------------------------------------------------------- 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 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 423 LEU Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 868 ASP 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 69 TYR Chi-restraints excluded: chain C residue 79 THR 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: 0.9980 chunk 93 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 87 optimal weight: 20.0000 chunk 100 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 235 ASN A 971 GLN A1241 HIS C 47 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.165731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.125927 restraints weight = 22302.852| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.40 r_work: 0.3635 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 14693 Z= 0.241 Angle : 0.877 11.671 20442 Z= 0.395 Chirality : 0.063 0.588 2407 Planarity : 0.004 0.047 2197 Dihedral : 16.073 171.910 3010 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.34 % Favored : 93.59 % Rotamer: Outliers : 4.56 % Allowed : 13.36 % Favored : 82.08 % 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: -1.92 (0.21), residues: 1483 helix: -0.48 (0.19), residues: 693 sheet: -1.23 (0.46), residues: 126 loop : -2.13 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 467 TYR 0.021 0.002 TYR A1356 PHE 0.018 0.002 PHE C 31 TRP 0.009 0.002 TRP A 476 HIS 0.009 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.24 (14692) covalent geometry : angle 0.87731 / 0.40 (20442) hydrogen bonds : bond 0.04183 / 2.16 ( 542) hydrogen bonds : angle 4.70295 / 1.93 ( 1518) Misc. bond : bond 0.00158 / 0.08 ( 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 193 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 137 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: A 74 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7258 (mpt90) REVERT: A 110 ASP cc_start: 0.8354 (m-30) cc_final: 0.8126 (m-30) REVERT: A 152 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7281 (ptt90) REVERT: A 215 ARG cc_start: 0.6641 (tpt170) cc_final: 0.6105 (mtp180) REVERT: A 281 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.7503 (mp-120) REVERT: A 334 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8066 (tt) REVERT: A 465 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.6763 (ttt) REVERT: A 645 ASP cc_start: 0.8155 (t0) cc_final: 0.7640 (m-30) REVERT: A 738 LEU cc_start: 0.8756 (tp) cc_final: 0.8497 (tt) REVERT: A 825 ASP cc_start: 0.7720 (m-30) cc_final: 0.6426 (p0) REVERT: A 933 GLN cc_start: 0.8917 (tm-30) cc_final: 0.8537 (tm-30) REVERT: A 973 TYR cc_start: 0.8985 (m-80) cc_final: 0.8421 (m-80) REVERT: C 117 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8566 (mp) outliers start: 56 outliers final: 31 residues processed: 172 average time/residue: 0.1130 time to fit residues: 29.6084 Evaluate side-chains 168 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 131 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 226 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 281 GLN Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 353 ASP 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 466 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 1049 GLU 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 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 89 ILE Chi-restraints excluded: chain C residue 117 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 40 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 125 optimal weight: 0.5980 chunk 111 optimal weight: 0.0070 chunk 43 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 112 optimal weight: 0.5980 chunk 105 optimal weight: 7.9990 chunk 141 optimal weight: 0.8980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 235 ASN A 971 GLN C 95 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 = 0.4373 r_free = 0.4373 target = 0.173656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.133913 restraints weight = 22259.498| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 2.45 r_work: 0.3758 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14693 Z= 0.128 Angle : 0.782 9.902 20442 Z= 0.347 Chirality : 0.057 0.463 2407 Planarity : 0.004 0.043 2197 Dihedral : 15.947 170.324 3010 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.38 % Favored : 95.55 % Rotamer: Outliers : 2.52 % Allowed : 15.72 % Favored : 81.76 % 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: -1.52 (0.21), residues: 1483 helix: -0.06 (0.19), residues: 698 sheet: -1.13 (0.48), residues: 121 loop : -2.02 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1212 TYR 0.027 0.001 TYR C 50 PHE 0.017 0.001 PHE C 31 TRP 0.009 0.001 TRP A 476 HIS 0.008 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (14692) covalent geometry : angle 0.78245 / 0.35 (20442) hydrogen bonds : bond 0.03559 / 1.85 ( 542) hydrogen bonds : angle 4.48278 / 1.85 ( 1518) Misc. bond : bond 0.00150 / 0.08 ( 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 194 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8048 (mp0) cc_final: 0.7665 (pt0) REVERT: A 97 PHE cc_start: 0.8625 (t80) cc_final: 0.8162 (t80) REVERT: A 215 ARG cc_start: 0.6569 (tpt170) cc_final: 0.5997 (mtp180) REVERT: A 277 ASN cc_start: 0.7505 (p0) cc_final: 0.7281 (p0) REVERT: A 281 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.7662 (mp-120) REVERT: A 465 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.6544 (ttt) REVERT: A 645 ASP cc_start: 0.7795 (t0) cc_final: 0.7386 (m-30) REVERT: A 677 LYS cc_start: 0.6418 (OUTLIER) cc_final: 0.5932 (mtpp) REVERT: A 825 ASP cc_start: 0.7749 (m-30) cc_final: 0.6413 (p0) REVERT: A 933 GLN cc_start: 0.8845 (tm-30) cc_final: 0.8574 (tm-30) REVERT: A 971 GLN cc_start: 0.7053 (mt0) cc_final: 0.6407 (mp10) REVERT: A 973 TYR cc_start: 0.8895 (m-80) cc_final: 0.8272 (m-80) REVERT: A 1189 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7570 (tm-30) REVERT: C 12 GLU cc_start: 0.8912 (pm20) cc_final: 0.8226 (pm20) REVERT: C 109 MET cc_start: 0.8486 (tpp) cc_final: 0.7841 (mmt) outliers start: 31 outliers final: 16 residues processed: 181 average time/residue: 0.1030 time to fit residues: 28.8529 Evaluate side-chains 158 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 281 GLN Chi-restraints excluded: chain A residue 353 ASP 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 432 PHE Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 677 LYS Chi-restraints excluded: chain A residue 1049 GLU Chi-restraints excluded: chain A residue 1142 SER 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 69 TYR 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: 0.9980 chunk 5 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 152 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 GLN A 235 ASN A 612 ASN A 650 GLN C 113 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.170171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.129970 restraints weight = 22152.878| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.44 r_work: 0.3719 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14693 Z= 0.163 Angle : 0.806 9.831 20442 Z= 0.358 Chirality : 0.058 0.501 2407 Planarity : 0.004 0.043 2197 Dihedral : 15.893 168.868 3010 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.92 % Favored : 95.01 % Rotamer: Outliers : 3.26 % Allowed : 15.96 % Favored : 80.78 % 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: -1.39 (0.21), residues: 1483 helix: 0.03 (0.20), residues: 695 sheet: -1.16 (0.50), residues: 104 loop : -1.90 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 424 TYR 0.022 0.001 TYR C 50 PHE 0.026 0.002 PHE C 17 TRP 0.005 0.001 TRP A 476 HIS 0.008 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (14692) covalent geometry : angle 0.80578 / 0.36 (20442) hydrogen bonds : bond 0.03678 / 1.90 ( 542) hydrogen bonds : angle 4.48247 / 1.84 ( 1518) Misc. bond : bond 0.00146 / 0.07 ( 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 184 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 144 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 ARG cc_start: 0.6661 (tpt170) cc_final: 0.6053 (mtp180) REVERT: A 261 ASP cc_start: 0.7919 (t70) cc_final: 0.7153 (m-30) REVERT: A 277 ASN cc_start: 0.7575 (p0) cc_final: 0.7199 (p0) REVERT: A 281 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.7435 (mp-120) REVERT: A 465 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.6727 (ttt) REVERT: A 645 ASP cc_start: 0.7746 (t0) cc_final: 0.7312 (m-30) REVERT: A 677 LYS cc_start: 0.6517 (mtpt) cc_final: 0.5916 (mtpp) REVERT: A 933 GLN cc_start: 0.8848 (tm-30) cc_final: 0.8580 (tm-30) REVERT: A 973 TYR cc_start: 0.8943 (m-80) cc_final: 0.8381 (m-80) REVERT: A 1189 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7539 (tm-30) REVERT: C 9 LYS cc_start: 0.8242 (mtmt) cc_final: 0.8012 (mtmt) REVERT: C 12 GLU cc_start: 0.8924 (pm20) cc_final: 0.8432 (pm20) REVERT: C 109 MET cc_start: 0.8496 (tpp) cc_final: 0.7858 (mmt) REVERT: C 115 GLU cc_start: 0.8701 (pm20) cc_final: 0.8408 (pm20) outliers start: 40 outliers final: 22 residues processed: 168 average time/residue: 0.0936 time to fit residues: 24.7869 Evaluate side-chains 159 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 281 GLN Chi-restraints excluded: chain A residue 353 ASP 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 432 PHE 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 1049 GLU 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 1331 ILE Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 39 SER 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 34 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 123 optimal weight: 0.4980 chunk 51 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 98 optimal weight: 8.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 GLN A 235 ASN A 698 HIS C 113 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.172745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.133074 restraints weight = 22012.033| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.43 r_work: 0.3736 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14693 Z= 0.135 Angle : 0.795 15.023 20442 Z= 0.350 Chirality : 0.057 0.486 2407 Planarity : 0.004 0.042 2197 Dihedral : 15.832 167.020 3008 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.59 % Favored : 95.35 % Rotamer: Outliers : 2.93 % Allowed : 16.21 % Favored : 80.86 % 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: -1.26 (0.21), residues: 1483 helix: 0.13 (0.20), residues: 693 sheet: -1.00 (0.50), residues: 103 loop : -1.83 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 424 TYR 0.027 0.001 TYR A 988 PHE 0.021 0.001 PHE C 17 TRP 0.007 0.001 TRP A 476 HIS 0.008 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (14692) covalent geometry : angle 0.79478 / 0.35 (20442) hydrogen bonds : bond 0.03595 / 1.87 ( 542) hydrogen bonds : angle 4.43536 / 1.82 ( 1518) Misc. bond : bond 0.00143 / 0.07 ( 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 185 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 ARG cc_start: 0.6598 (tpt170) cc_final: 0.5998 (mtp180) REVERT: A 261 ASP cc_start: 0.7873 (t70) cc_final: 0.7143 (m-30) REVERT: A 277 ASN cc_start: 0.7551 (p0) cc_final: 0.7298 (p0) REVERT: A 281 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.7562 (mp-120) REVERT: A 645 ASP cc_start: 0.7675 (t0) cc_final: 0.7223 (m-30) REVERT: A 677 LYS cc_start: 0.6383 (mtpt) cc_final: 0.5860 (mtpp) REVERT: A 933 GLN cc_start: 0.8843 (tm-30) cc_final: 0.8580 (tm-30) REVERT: A 973 TYR cc_start: 0.8904 (m-80) cc_final: 0.8315 (m-80) REVERT: A 1189 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7547 (tm-30) REVERT: C 9 LYS cc_start: 0.8238 (mtmt) cc_final: 0.7991 (mtmt) REVERT: C 12 GLU cc_start: 0.8909 (pm20) cc_final: 0.8474 (pm20) REVERT: C 109 MET cc_start: 0.8425 (tpp) cc_final: 0.7833 (mmt) outliers start: 36 outliers final: 21 residues processed: 172 average time/residue: 0.1041 time to fit residues: 28.0316 Evaluate side-chains 158 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 281 GLN Chi-restraints excluded: chain A residue 353 ASP 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 583 VAL Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 1049 GLU Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1142 SER 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 69 TYR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 36 optimal weight: 6.9990 chunk 61 optimal weight: 0.0980 chunk 22 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 75 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 153 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 137 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 235 ASN A 420 HIS A 698 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.174376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.133995 restraints weight = 22255.731| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.50 r_work: 0.3749 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14693 Z= 0.131 Angle : 0.787 12.656 20442 Z= 0.347 Chirality : 0.056 0.488 2407 Planarity : 0.003 0.042 2197 Dihedral : 15.718 164.172 3008 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.72 % Favored : 95.21 % Rotamer: Outliers : 2.36 % Allowed : 17.10 % Favored : 80.54 % 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: -1.12 (0.22), residues: 1483 helix: 0.21 (0.20), residues: 695 sheet: -0.81 (0.52), residues: 97 loop : -1.74 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1212 TYR 0.022 0.001 TYR A 988 PHE 0.024 0.001 PHE A 97 TRP 0.008 0.001 TRP A 476 HIS 0.007 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (14692) covalent geometry : angle 0.78684 / 0.35 (20442) hydrogen bonds : bond 0.03508 / 1.82 ( 542) hydrogen bonds : angle 4.36765 / 1.79 ( 1518) Misc. bond : bond 0.00136 / 0.07 ( 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 174 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8045 (mp0) cc_final: 0.7739 (pt0) REVERT: A 215 ARG cc_start: 0.6619 (tpt170) cc_final: 0.5969 (mtp180) REVERT: A 261 ASP cc_start: 0.7873 (t70) cc_final: 0.7253 (m-30) REVERT: A 645 ASP cc_start: 0.7498 (t0) cc_final: 0.6808 (m-30) REVERT: A 677 LYS cc_start: 0.6457 (mtpt) cc_final: 0.5951 (mtpp) REVERT: A 933 GLN cc_start: 0.8843 (tm-30) cc_final: 0.8583 (tm-30) REVERT: A 973 TYR cc_start: 0.8863 (m-80) cc_final: 0.8256 (m-80) REVERT: A 1043 MET cc_start: 0.7760 (mmm) cc_final: 0.7553 (mmm) REVERT: A 1189 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7567 (tm-30) REVERT: C 9 LYS cc_start: 0.8187 (mtmt) cc_final: 0.7934 (mtmt) REVERT: C 12 GLU cc_start: 0.8877 (pm20) cc_final: 0.8408 (pm20) REVERT: C 109 MET cc_start: 0.8393 (tpp) cc_final: 0.7822 (mmt) outliers start: 29 outliers final: 22 residues processed: 167 average time/residue: 0.1052 time to fit residues: 27.5167 Evaluate side-chains 155 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 353 ASP 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 583 VAL Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 1049 GLU 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 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 91 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 101 optimal weight: 8.9990 chunk 106 optimal weight: 0.0030 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 113 optimal weight: 20.0000 chunk 126 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 39 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 overall best weight: 1.0592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 235 ASN A 341 GLN A 698 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.172957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.133377 restraints weight = 22066.727| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.43 r_work: 0.3761 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14693 Z= 0.146 Angle : 0.799 13.764 20442 Z= 0.352 Chirality : 0.057 0.501 2407 Planarity : 0.004 0.043 2197 Dihedral : 15.682 162.650 3008 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.59 % Favored : 95.35 % Rotamer: Outliers : 2.12 % Allowed : 17.92 % 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: -1.09 (0.22), residues: 1483 helix: 0.19 (0.20), residues: 696 sheet: -0.56 (0.53), residues: 97 loop : -1.71 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1212 TYR 0.028 0.001 TYR A 988 PHE 0.019 0.001 PHE C 17 TRP 0.006 0.001 TRP A 476 HIS 0.007 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (14692) covalent geometry : angle 0.79877 / 0.35 (20442) hydrogen bonds : bond 0.03574 / 1.86 ( 542) hydrogen bonds : angle 4.38555 / 1.80 ( 1518) Misc. bond : bond 0.00132 / 0.07 ( 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 165 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8049 (mp0) cc_final: 0.7728 (pt0) REVERT: A 215 ARG cc_start: 0.6620 (tpt170) cc_final: 0.5932 (mtp180) REVERT: A 261 ASP cc_start: 0.7908 (t70) cc_final: 0.7382 (m-30) REVERT: A 645 ASP cc_start: 0.7384 (t0) cc_final: 0.6728 (m-30) REVERT: A 734 LYS cc_start: 0.8086 (mttt) cc_final: 0.7853 (mttp) REVERT: A 933 GLN cc_start: 0.8846 (tm-30) cc_final: 0.8599 (tm-30) REVERT: A 964 SER cc_start: 0.8764 (t) cc_final: 0.8341 (p) REVERT: A 973 TYR cc_start: 0.8878 (m-80) cc_final: 0.8253 (m-80) REVERT: A 1043 MET cc_start: 0.7752 (mmm) cc_final: 0.7519 (mmm) REVERT: A 1189 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7542 (tm-30) REVERT: C 9 LYS cc_start: 0.8170 (mtmt) cc_final: 0.7921 (mtmt) REVERT: C 12 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8477 (pm20) REVERT: C 109 MET cc_start: 0.8363 (tpp) cc_final: 0.7837 (mmt) REVERT: C 115 GLU cc_start: 0.8700 (pm20) cc_final: 0.8442 (pm20) outliers start: 26 outliers final: 23 residues processed: 155 average time/residue: 0.1066 time to fit residues: 25.7327 Evaluate side-chains 158 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 353 ASP 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 396 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 845 SER Chi-restraints excluded: chain A residue 1049 GLU 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 1331 ILE Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 12 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 91 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 128 optimal weight: 0.0000 chunk 127 optimal weight: 0.8980 chunk 23 optimal weight: 0.0980 chunk 124 optimal weight: 0.8980 chunk 143 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 144 optimal weight: 0.2980 chunk 20 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 235 ASN A 698 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.176542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.137441 restraints weight = 22160.457| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 2.44 r_work: 0.3783 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 14693 Z= 0.122 Angle : 0.779 13.527 20442 Z= 0.342 Chirality : 0.056 0.516 2407 Planarity : 0.003 0.041 2197 Dihedral : 15.622 163.383 3008 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.65 % Favored : 95.28 % Rotamer: Outliers : 2.12 % Allowed : 18.00 % Favored : 79.89 % 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: -0.87 (0.22), residues: 1483 helix: 0.43 (0.20), residues: 680 sheet: -0.98 (0.51), residues: 107 loop : -1.52 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1212 TYR 0.026 0.001 TYR A 988 PHE 0.020 0.001 PHE A1045 TRP 0.008 0.001 TRP A 476 HIS 0.007 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (14692) covalent geometry : angle 0.77901 / 0.34 (20442) hydrogen bonds : bond 0.03462 / 1.79 ( 542) hydrogen bonds : angle 4.32670 / 1.78 ( 1518) Misc. bond : bond 0.00128 / 0.06 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3029.52 seconds wall clock time: 52 minutes 51.25 seconds (3171.25 seconds total)