Starting phenix.real_space_refine on Fri Jun 13 00:43:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mcb_9066/06_2025/6mcb_9066.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mcb_9066/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6mcb_9066/06_2025/6mcb_9066.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mcb_9066/06_2025/6mcb_9066.map" model { file = "/net/cci-nas-00/data/ceres_data/6mcb_9066/06_2025/6mcb_9066.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mcb_9066/06_2025/6mcb_9066.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.049 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 7, 'TYR:plan': 2, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 19, 'ARG:plan': 9} 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: {'GLU:plan': 6, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 33 Time building chain proxies: 8.57, per 1000 atoms: 0.60 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: 3.81 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 6.15 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: 7.37 Time building geometry restraints manager: 4.51 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: 2.080 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: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 40.970 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.060 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.015 0.003 TRP A1074 HIS 0.023 0.003 HIS A 328 PHE 0.040 0.004 PHE A1008 TYR 0.040 0.003 TYR A 450 ARG 0.022 0.002 ARG A 100 Details of bonding type rmsd hydrogen bonds : bond 0.16238 ( 542) hydrogen bonds : angle 7.54196 ( 1518) covalent geometry : bond 0.00985 (14692) covalent geometry : angle 1.14342 (20442) 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 : 1.931 Fit side-chains 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 913 LYS cc_start: 0.7377 (mttp) cc_final: 0.7132 (mttt) 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: 0.8742 (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: 0.4338 time to fit residues: 145.6887 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 : 2.228 ------------------------------------------------------------------------------- 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 134 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 64 optimal weight: 0.0050 chunk 124 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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 899 ASN A 971 GLN C 7 GLN ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.171238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.133587 restraints weight = 22048.523| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.30 r_work: 0.3773 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14693 Z= 0.134 Angle : 0.657 11.142 20442 Z= 0.341 Chirality : 0.042 0.314 2407 Planarity : 0.005 0.050 2197 Dihedral : 19.929 175.997 3372 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.86 % Favored : 95.01 % Rotamer: Outliers : 2.69 % Allowed : 10.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.19), residues: 1483 helix: -1.64 (0.17), residues: 684 sheet: -2.06 (0.42), residues: 128 loop : -2.31 (0.21), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 476 HIS 0.008 0.001 HIS A 328 PHE 0.029 0.001 PHE C 31 TYR 0.027 0.001 TYR C 50 ARG 0.007 0.001 ARG A 976 Details of bonding type rmsd hydrogen bonds : bond 0.04366 ( 542) hydrogen bonds : angle 5.11222 ( 1518) covalent geometry : bond 0.00281 (14692) covalent geometry : angle 0.65740 (20442) Misc. bond : bond 0.00189 ( 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 231 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 198 time to evaluate : 1.551 Fit side-chains revert: symmetry clash REVERT: A 74 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7235 (mpt90) REVERT: A 97 PHE cc_start: 0.8478 (t80) cc_final: 0.8156 (t80) REVERT: A 152 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.7163 (ptt90) REVERT: A 215 ARG cc_start: 0.6486 (tpt90) cc_final: 0.5996 (mtp180) REVERT: A 237 LEU cc_start: 0.7864 (tp) cc_final: 0.7490 (tp) REVERT: A 370 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7950 (pt0) REVERT: A 534 MET cc_start: 0.5610 (ptt) cc_final: 0.4906 (mmt) REVERT: A 551 LEU cc_start: 0.8042 (tp) cc_final: 0.7794 (tt) REVERT: A 631 MET cc_start: 0.7976 (mmm) cc_final: 0.7508 (mmt) REVERT: A 634 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7900 (tm-30) REVERT: A 645 ASP cc_start: 0.8229 (t0) cc_final: 0.7991 (m-30) REVERT: A 825 ASP cc_start: 0.7663 (m-30) cc_final: 0.6292 (p0) REVERT: A 879 MET cc_start: 0.4751 (mmt) cc_final: 0.4168 (mmt) REVERT: A 933 GLN cc_start: 0.8762 (tm-30) cc_final: 0.8377 (tm-30) REVERT: A 1089 MET cc_start: 0.8480 (mmm) cc_final: 0.7848 (mmm) REVERT: A 1179 ILE cc_start: 0.8799 (pt) cc_final: 0.7863 (pt) REVERT: A 1211 LYS cc_start: 0.8773 (mttt) cc_final: 0.8571 (mtmm) REVERT: A 1357 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7315 (mt-10) REVERT: C 20 MET cc_start: 0.8075 (pp-130) cc_final: 0.7435 (ppp) REVERT: C 106 GLU cc_start: 0.8235 (tt0) cc_final: 0.7776 (tt0) outliers start: 33 outliers final: 12 residues processed: 220 average time/residue: 0.3060 time to fit residues: 100.6244 Evaluate side-chains 165 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 1.430 ------------------------------------------------------------------------------- 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 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 1143 VAL Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 28 THR 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 71 optimal weight: 0.0020 chunk 122 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 157 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.2980 chunk 153 optimal weight: 2.9990 chunk 112 optimal weight: 0.0070 chunk 59 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 overall best weight: 0.8408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 HIS A 758 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 = 0.4348 r_free = 0.4348 target = 0.170785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.131539 restraints weight = 22152.181| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.41 r_work: 0.3746 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2489 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= 0.129 Angle : 0.624 10.220 20442 Z= 0.318 Chirality : 0.041 0.265 2407 Planarity : 0.004 0.045 2197 Dihedral : 19.636 176.356 3370 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.72 % Favored : 95.14 % Rotamer: Outliers : 3.42 % Allowed : 12.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.20), residues: 1483 helix: -0.86 (0.19), residues: 692 sheet: -1.82 (0.43), residues: 138 loop : -2.11 (0.22), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 476 HIS 0.004 0.001 HIS A 420 PHE 0.027 0.001 PHE C 31 TYR 0.022 0.001 TYR C 10 ARG 0.005 0.001 ARG A1212 Details of bonding type rmsd hydrogen bonds : bond 0.04070 ( 542) hydrogen bonds : angle 4.70399 ( 1518) covalent geometry : bond 0.00280 (14692) covalent geometry : angle 0.62376 (20442) Misc. bond : bond 0.00144 ( 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 214 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 172 time to evaluate : 1.700 Fit side-chains REVERT: A 74 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7219 (mtt90) REVERT: A 97 PHE cc_start: 0.8487 (t80) cc_final: 0.8149 (t80) REVERT: A 152 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.7107 (ptt90) REVERT: A 645 ASP cc_start: 0.8197 (t0) cc_final: 0.7686 (m-30) REVERT: A 933 GLN cc_start: 0.8828 (tm-30) cc_final: 0.8550 (tm-30) REVERT: A 1089 MET cc_start: 0.8528 (mmm) cc_final: 0.7950 (mmm) REVERT: A 1106 SER cc_start: 0.8922 (p) cc_final: 0.8690 (m) REVERT: A 1357 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7338 (mt-10) REVERT: C 12 GLU cc_start: 0.8894 (pm20) cc_final: 0.8435 (pm20) REVERT: C 20 MET cc_start: 0.7914 (pp-130) cc_final: 0.7252 (ppp) REVERT: C 90 ASN cc_start: 0.9028 (OUTLIER) cc_final: 0.8579 (p0) REVERT: C 109 MET cc_start: 0.8394 (tpp) cc_final: 0.7839 (mmt) REVERT: C 122 LEU cc_start: 0.6250 (OUTLIER) cc_final: 0.6044 (pp) outliers start: 42 outliers final: 22 residues processed: 200 average time/residue: 0.2619 time to fit residues: 81.1288 Evaluate side-chains 169 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 1.580 ------------------------------------------------------------------------------- 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 266 LEU Chi-restraints excluded: chain A residue 284 ASP 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 583 VAL 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 1299 ASP 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 90 ASN Chi-restraints excluded: chain C residue 118 LEU 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 87 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 156 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 152 optimal weight: 4.9990 chunk 116 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 64 optimal weight: 0.0970 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 899 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.170817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.131870 restraints weight = 22025.938| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 2.40 r_work: 0.3736 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2837 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= 0.132 Angle : 0.604 10.078 20442 Z= 0.308 Chirality : 0.041 0.224 2407 Planarity : 0.004 0.042 2197 Dihedral : 19.466 176.782 3368 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.92 % Favored : 94.94 % Rotamer: Outliers : 3.34 % Allowed : 13.03 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.21), residues: 1483 helix: -0.48 (0.19), residues: 698 sheet: -1.77 (0.43), residues: 137 loop : -2.00 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 476 HIS 0.004 0.001 HIS A 116 PHE 0.022 0.001 PHE C 31 TYR 0.023 0.001 TYR C 10 ARG 0.004 0.001 ARG A 976 Details of bonding type rmsd hydrogen bonds : bond 0.03817 ( 542) hydrogen bonds : angle 4.50184 ( 1518) covalent geometry : bond 0.00290 (14692) covalent geometry : angle 0.60391 (20442) Misc. bond : bond 0.00155 ( 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 197 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 156 time to evaluate : 1.735 Fit side-chains REVERT: A 74 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7222 (mpt90) REVERT: A 97 PHE cc_start: 0.8470 (t80) cc_final: 0.8031 (t80) REVERT: A 152 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.7102 (ptt90) REVERT: A 215 ARG cc_start: 0.5850 (tpt170) cc_final: 0.5156 (mmm-85) REVERT: A 370 GLU cc_start: 0.8305 (tm-30) cc_final: 0.8071 (tt0) REVERT: A 645 ASP cc_start: 0.8067 (t0) cc_final: 0.7562 (m-30) REVERT: A 933 GLN cc_start: 0.8821 (tm-30) cc_final: 0.8561 (tm-30) REVERT: A 1089 MET cc_start: 0.8547 (mmm) cc_final: 0.8141 (mmm) REVERT: A 1357 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7325 (mt-10) REVERT: C 12 GLU cc_start: 0.8857 (pm20) cc_final: 0.8643 (pm20) outliers start: 41 outliers final: 21 residues processed: 186 average time/residue: 0.3082 time to fit residues: 88.1123 Evaluate side-chains 163 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR 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 266 LEU 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 1049 GLU 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 118 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 11 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 152 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 42 optimal weight: 0.0970 chunk 119 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 ASN A 698 HIS A1241 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.167949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.128769 restraints weight = 22004.639| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.38 r_work: 0.3700 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14693 Z= 0.170 Angle : 0.633 9.554 20442 Z= 0.322 Chirality : 0.042 0.225 2407 Planarity : 0.004 0.043 2197 Dihedral : 19.386 177.333 3368 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.66 % Favored : 94.27 % Rotamer: Outliers : 3.42 % Allowed : 15.15 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.21), residues: 1483 helix: -0.32 (0.19), residues: 699 sheet: -1.43 (0.46), residues: 110 loop : -2.05 (0.22), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 476 HIS 0.003 0.001 HIS A 328 PHE 0.033 0.002 PHE A1008 TYR 0.025 0.002 TYR A1356 ARG 0.004 0.001 ARG A 467 Details of bonding type rmsd hydrogen bonds : bond 0.04013 ( 542) hydrogen bonds : angle 4.49741 ( 1518) covalent geometry : bond 0.00383 (14692) covalent geometry : angle 0.63290 (20442) 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 180 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 138 time to evaluate : 1.384 Fit side-chains REVERT: A 74 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7225 (mpt90) REVERT: A 152 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.7168 (ptt90) REVERT: A 215 ARG cc_start: 0.6266 (tpt170) cc_final: 0.5399 (mmm-85) REVERT: A 370 GLU cc_start: 0.8392 (tm-30) cc_final: 0.8138 (tt0) REVERT: A 645 ASP cc_start: 0.8064 (t0) cc_final: 0.7549 (m-30) REVERT: A 933 GLN cc_start: 0.8870 (tm-30) cc_final: 0.8617 (tm-30) REVERT: A 1089 MET cc_start: 0.8528 (mmm) cc_final: 0.8324 (mmm) REVERT: C 9 LYS cc_start: 0.8214 (mtmt) cc_final: 0.7833 (mtmt) REVERT: C 109 MET cc_start: 0.8443 (tpp) cc_final: 0.7906 (mmt) outliers start: 42 outliers final: 27 residues processed: 167 average time/residue: 0.2572 time to fit residues: 65.6233 Evaluate side-chains 162 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 284 ASP 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 583 VAL Chi-restraints excluded: chain A residue 845 SER 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 1299 ASP 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 89 ILE Chi-restraints excluded: chain C residue 118 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 125 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 73 optimal weight: 0.4980 chunk 70 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 30 optimal weight: 0.3980 chunk 75 optimal weight: 2.9990 chunk 90 optimal weight: 20.0000 chunk 62 optimal weight: 1.9990 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 235 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.171547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.132693 restraints weight = 22103.828| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.40 r_work: 0.3744 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 14693 Z= 0.119 Angle : 0.603 9.868 20442 Z= 0.303 Chirality : 0.040 0.257 2407 Planarity : 0.003 0.041 2197 Dihedral : 19.327 177.723 3368 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.72 % Favored : 95.21 % Rotamer: Outliers : 3.01 % Allowed : 15.31 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.21), residues: 1483 helix: -0.04 (0.20), residues: 699 sheet: -1.09 (0.46), residues: 128 loop : -1.98 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 476 HIS 0.002 0.001 HIS A 420 PHE 0.028 0.001 PHE A1008 TYR 0.022 0.001 TYR A1356 ARG 0.002 0.000 ARG A1212 Details of bonding type rmsd hydrogen bonds : bond 0.03655 ( 542) hydrogen bonds : angle 4.37162 ( 1518) covalent geometry : bond 0.00267 (14692) covalent geometry : angle 0.60257 (20442) Misc. bond : bond 0.00165 ( 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 195 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 1.561 Fit side-chains REVERT: A 215 ARG cc_start: 0.6296 (tpt170) cc_final: 0.5445 (mmm-85) REVERT: A 281 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.7640 (mp-120) REVERT: A 370 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7957 (tt0) REVERT: A 465 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.6607 (ttt) REVERT: A 645 ASP cc_start: 0.7898 (t0) cc_final: 0.7424 (m-30) REVERT: A 933 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8606 (tm-30) REVERT: C 109 MET cc_start: 0.8430 (tpp) cc_final: 0.7898 (mmt) REVERT: C 115 GLU cc_start: 0.8662 (pm20) cc_final: 0.8435 (pm20) outliers start: 37 outliers final: 22 residues processed: 184 average time/residue: 0.2471 time to fit residues: 70.0213 Evaluate side-chains 157 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 1.407 ------------------------------------------------------------------------------- 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 266 LEU Chi-restraints excluded: chain A residue 281 GLN 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 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 1015 VAL Chi-restraints excluded: chain A residue 1049 GLU Chi-restraints excluded: chain A residue 1106 SER 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 69 TYR Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 85 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 11 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 157 optimal weight: 0.6980 chunk 111 optimal weight: 0.7980 chunk 120 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 4 optimal weight: 20.0000 chunk 20 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 19 optimal weight: 0.3980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 235 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.172193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.133660 restraints weight = 22130.405| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 2.38 r_work: 0.3746 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 14693 Z= 0.119 Angle : 0.606 11.972 20442 Z= 0.302 Chirality : 0.041 0.294 2407 Planarity : 0.003 0.041 2197 Dihedral : 19.279 177.849 3368 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.59 % Favored : 95.35 % Rotamer: Outliers : 3.26 % Allowed : 16.12 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.21), residues: 1483 helix: 0.17 (0.20), residues: 695 sheet: -1.00 (0.46), residues: 121 loop : -1.88 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 476 HIS 0.003 0.001 HIS A 116 PHE 0.052 0.002 PHE A1008 TYR 0.023 0.001 TYR A1356 ARG 0.005 0.000 ARG A 424 Details of bonding type rmsd hydrogen bonds : bond 0.03560 ( 542) hydrogen bonds : angle 4.32537 ( 1518) covalent geometry : bond 0.00267 (14692) covalent geometry : angle 0.60576 (20442) 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 181 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 1.655 Fit side-chains REVERT: A 215 ARG cc_start: 0.6297 (tpt170) cc_final: 0.5389 (mmm-85) REVERT: A 281 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.7609 (mp-120) REVERT: A 370 GLU cc_start: 0.8271 (tm-30) cc_final: 0.8031 (tt0) REVERT: A 465 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.6544 (ttt) REVERT: A 645 ASP cc_start: 0.7694 (t0) cc_final: 0.7271 (m-30) REVERT: A 933 GLN cc_start: 0.8817 (tm-30) cc_final: 0.8595 (tm-30) REVERT: C 12 GLU cc_start: 0.8869 (pm20) cc_final: 0.8198 (pm20) REVERT: C 109 MET cc_start: 0.8425 (tpp) cc_final: 0.7917 (mmt) outliers start: 40 outliers final: 21 residues processed: 168 average time/residue: 0.3306 time to fit residues: 86.7182 Evaluate side-chains 160 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 281 GLN 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 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 1049 GLU 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 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 75 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 135 optimal weight: 9.9990 chunk 23 optimal weight: 0.0970 chunk 92 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 149 optimal weight: 0.3980 chunk 3 optimal weight: 10.0000 chunk 42 optimal weight: 0.0570 chunk 155 optimal weight: 0.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 ASN ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 612 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.172037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.133277 restraints weight = 21966.989| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.38 r_work: 0.3758 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14693 Z= 0.127 Angle : 0.619 12.115 20442 Z= 0.309 Chirality : 0.041 0.256 2407 Planarity : 0.003 0.041 2197 Dihedral : 19.267 177.807 3366 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.65 % Favored : 95.28 % Rotamer: Outliers : 2.93 % Allowed : 16.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.21), residues: 1483 helix: 0.21 (0.20), residues: 694 sheet: -1.01 (0.45), residues: 121 loop : -1.83 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 476 HIS 0.003 0.001 HIS A 116 PHE 0.057 0.002 PHE A1008 TYR 0.023 0.001 TYR A1356 ARG 0.008 0.000 ARG A 629 Details of bonding type rmsd hydrogen bonds : bond 0.03543 ( 542) hydrogen bonds : angle 4.34289 ( 1518) covalent geometry : bond 0.00288 (14692) covalent geometry : angle 0.61943 (20442) Misc. bond : bond 0.00164 ( 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 173 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 1.239 Fit side-chains REVERT: A 215 ARG cc_start: 0.6350 (tpt170) cc_final: 0.5445 (mmm-85) REVERT: A 281 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.7575 (mp-120) REVERT: A 370 GLU cc_start: 0.8322 (tm-30) cc_final: 0.8031 (tt0) REVERT: A 465 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.6633 (ttt) REVERT: A 645 ASP cc_start: 0.7611 (t0) cc_final: 0.7019 (m-30) REVERT: A 698 HIS cc_start: 0.7981 (OUTLIER) cc_final: 0.7248 (m90) REVERT: A 933 GLN cc_start: 0.8816 (tm-30) cc_final: 0.8603 (tm-30) REVERT: A 973 TYR cc_start: 0.8890 (m-80) cc_final: 0.8417 (m-80) REVERT: C 12 GLU cc_start: 0.8855 (pm20) cc_final: 0.8269 (pm20) REVERT: C 109 MET cc_start: 0.8385 (tpp) cc_final: 0.7902 (mmt) outliers start: 36 outliers final: 25 residues processed: 158 average time/residue: 0.3297 time to fit residues: 82.7132 Evaluate side-chains 156 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 2.137 ------------------------------------------------------------------------------- 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 281 GLN 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 432 PHE 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 822 MET Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 1015 VAL 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 1302 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 89 ILE 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 49 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 45 optimal weight: 0.2980 chunk 23 optimal weight: 0.0030 chunk 87 optimal weight: 0.0770 chunk 60 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 overall best weight: 0.3748 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 ASN A 342 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 = 0.4398 r_free = 0.4398 target = 0.175537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.137028 restraints weight = 21948.830| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 2.40 r_work: 0.3802 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 14693 Z= 0.109 Angle : 0.601 11.582 20442 Z= 0.301 Chirality : 0.040 0.241 2407 Planarity : 0.003 0.040 2197 Dihedral : 19.216 178.002 3366 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.52 % Favored : 95.41 % Rotamer: Outliers : 2.28 % Allowed : 17.10 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.22), residues: 1483 helix: 0.32 (0.20), residues: 694 sheet: -0.87 (0.47), residues: 103 loop : -1.69 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1074 HIS 0.004 0.000 HIS A 116 PHE 0.052 0.001 PHE A1008 TYR 0.021 0.001 TYR A1356 ARG 0.004 0.000 ARG A 424 Details of bonding type rmsd hydrogen bonds : bond 0.03458 ( 542) hydrogen bonds : angle 4.31053 ( 1518) covalent geometry : bond 0.00241 (14692) covalent geometry : angle 0.60109 (20442) 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 175 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 1.707 Fit side-chains REVERT: A 215 ARG cc_start: 0.6292 (tpt170) cc_final: 0.5386 (mmm-85) REVERT: A 370 GLU cc_start: 0.8278 (tm-30) cc_final: 0.8000 (tt0) REVERT: A 465 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.6553 (ttt) REVERT: A 645 ASP cc_start: 0.7430 (t0) cc_final: 0.6851 (m-30) REVERT: A 698 HIS cc_start: 0.7989 (OUTLIER) cc_final: 0.7099 (m170) REVERT: A 964 SER cc_start: 0.8715 (t) cc_final: 0.8331 (p) REVERT: A 973 TYR cc_start: 0.8842 (m-80) cc_final: 0.8315 (m-80) REVERT: C 12 GLU cc_start: 0.8802 (pm20) cc_final: 0.8377 (pm20) REVERT: C 109 MET cc_start: 0.8322 (tpp) cc_final: 0.7925 (mmt) REVERT: C 115 GLU cc_start: 0.8709 (pm20) cc_final: 0.8312 (pm20) outliers start: 28 outliers final: 21 residues processed: 164 average time/residue: 0.2733 time to fit residues: 71.7790 Evaluate side-chains 155 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 1.850 ------------------------------------------------------------------------------- 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 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 698 HIS Chi-restraints excluded: chain A residue 921 LEU 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 1302 ILE 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 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 5 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 50 optimal weight: 0.0050 chunk 89 optimal weight: 7.9990 chunk 106 optimal weight: 0.7980 chunk 32 optimal weight: 0.0970 chunk 84 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 235 ASN A 255 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.175605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.136780 restraints weight = 22005.601| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 2.44 r_work: 0.3799 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 14693 Z= 0.109 Angle : 0.602 11.773 20442 Z= 0.298 Chirality : 0.040 0.236 2407 Planarity : 0.003 0.040 2197 Dihedral : 19.171 177.929 3366 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.52 % Favored : 95.41 % Rotamer: Outliers : 2.04 % Allowed : 17.51 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.22), residues: 1483 helix: 0.43 (0.20), residues: 695 sheet: -0.91 (0.48), residues: 109 loop : -1.60 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 476 HIS 0.003 0.001 HIS A 116 PHE 0.048 0.001 PHE A1008 TYR 0.030 0.001 TYR C 50 ARG 0.003 0.000 ARG A 424 Details of bonding type rmsd hydrogen bonds : bond 0.03379 ( 542) hydrogen bonds : angle 4.21235 ( 1518) covalent geometry : bond 0.00242 (14692) covalent geometry : angle 0.60201 (20442) Misc. bond : bond 0.00160 ( 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 167 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 1.597 Fit side-chains REVERT: A 215 ARG cc_start: 0.6310 (tpt170) cc_final: 0.5374 (mmm-85) REVERT: A 370 GLU cc_start: 0.8306 (tm-30) cc_final: 0.8011 (tt0) REVERT: A 450 TYR cc_start: 0.8046 (m-80) cc_final: 0.7688 (m-80) REVERT: A 465 MET cc_start: 0.7746 (OUTLIER) cc_final: 0.6582 (tpt) REVERT: A 645 ASP cc_start: 0.7283 (t0) cc_final: 0.6667 (m-30) REVERT: A 964 SER cc_start: 0.8701 (t) cc_final: 0.8316 (p) REVERT: A 973 TYR cc_start: 0.8820 (m-80) cc_final: 0.8256 (m-80) REVERT: C 12 GLU cc_start: 0.8787 (pm20) cc_final: 0.8434 (pm20) REVERT: C 109 MET cc_start: 0.8353 (tpp) cc_final: 0.7947 (mmt) REVERT: C 115 GLU cc_start: 0.8588 (pm20) cc_final: 0.8320 (pm20) outliers start: 25 outliers final: 20 residues processed: 155 average time/residue: 0.2681 time to fit residues: 67.0307 Evaluate side-chains 156 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR 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 465 MET Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 957 THR 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 1146 VAL Chi-restraints excluded: chain A residue 1228 LEU 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 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.2973 > 50: distance: 4 - 26: 31.462 distance: 12 - 34: 35.931 distance: 16 - 43: 32.194 distance: 20 - 26: 30.120 distance: 21 - 51: 35.131 distance: 26 - 27: 57.338 distance: 27 - 28: 49.327 distance: 27 - 30: 46.473 distance: 28 - 29: 38.871 distance: 28 - 34: 38.771 distance: 30 - 31: 44.357 distance: 31 - 32: 16.512 distance: 34 - 35: 56.527 distance: 35 - 36: 41.025 distance: 35 - 38: 68.340 distance: 36 - 37: 38.802 distance: 36 - 43: 40.273 distance: 38 - 39: 34.888 distance: 39 - 40: 34.734 distance: 40 - 41: 43.530 distance: 40 - 42: 55.186 distance: 43 - 44: 60.135 distance: 44 - 45: 62.126 distance: 44 - 47: 17.295 distance: 45 - 46: 39.578 distance: 45 - 51: 39.416 distance: 48 - 50: 40.129 distance: 51 - 52: 57.325 distance: 52 - 53: 40.055 distance: 52 - 55: 56.865 distance: 53 - 58: 13.329 distance: 55 - 56: 56.181 distance: 55 - 57: 57.918 distance: 58 - 59: 4.837 distance: 59 - 60: 52.790 distance: 59 - 62: 23.884 distance: 60 - 61: 41.517 distance: 60 - 63: 29.550 distance: 63 - 64: 36.316 distance: 64 - 65: 3.638 distance: 64 - 67: 57.398 distance: 65 - 66: 40.435 distance: 65 - 70: 38.689 distance: 67 - 68: 43.674 distance: 67 - 69: 39.303 distance: 71 - 72: 57.560 distance: 71 - 74: 38.502 distance: 72 - 79: 17.518 distance: 74 - 75: 56.111 distance: 75 - 76: 56.292 distance: 76 - 77: 67.430 distance: 79 - 80: 22.803 distance: 79 - 133: 26.422 distance: 80 - 81: 50.409 distance: 80 - 83: 56.859 distance: 81 - 82: 65.076 distance: 81 - 91: 27.478 distance: 83 - 84: 43.370 distance: 84 - 85: 47.935 distance: 84 - 86: 57.534 distance: 85 - 87: 26.710 distance: 86 - 88: 40.165 distance: 87 - 89: 27.259 distance: 88 - 89: 53.758 distance: 89 - 90: 11.994 distance: 91 - 92: 31.115 distance: 91 - 183: 29.697 distance: 92 - 93: 47.135 distance: 92 - 95: 14.138 distance: 93 - 94: 37.201 distance: 93 - 98: 57.630 distance: 95 - 96: 41.323 distance: 98 - 99: 55.564 distance: 99 - 100: 62.725 distance: 99 - 102: 56.701 distance: 100 - 101: 42.911 distance: 100 - 105: 28.217 distance: 102 - 104: 49.353