Starting phenix.real_space_refine on Tue Dec 31 01:56:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mcb_9066/12_2024/6mcb_9066.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mcb_9066/12_2024/6mcb_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_9066/12_2024/6mcb_9066.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mcb_9066/12_2024/6mcb_9066.map" model { file = "/net/cci-nas-00/data/ceres_data/6mcb_9066/12_2024/6mcb_9066.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mcb_9066/12_2024/6mcb_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-5532/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: 9.69, per 1000 atoms: 0.68 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: 3.92 Conformation dependent library (CDL) restraints added in 1.5 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: 5.48 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: 6.88 Time building geometry restraints manager: 4.52 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: 1.470 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: 0.630 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 41.750 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.070 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.157 14692 Z= 0.627 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 *********************** 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 : 1.461 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: 0.3065 time to fit residues: 97.8379 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 : 1.481 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 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 14692 Z= 0.180 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 *********************** 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 : 1.458 Fit side-chains revert: symmetry clash REVERT: A 74 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.6996 (mpt90) REVERT: A 97 PHE cc_start: 0.8289 (t80) cc_final: 0.8071 (t80) REVERT: A 152 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.7021 (ptt90) REVERT: A 215 ARG cc_start: 0.6342 (tpt90) cc_final: 0.6113 (mtp180) REVERT: A 237 LEU cc_start: 0.7734 (tp) cc_final: 0.7400 (tp) REVERT: A 370 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7460 (pt0) REVERT: A 534 MET cc_start: 0.5246 (ptt) cc_final: 0.4855 (mmt) REVERT: A 631 MET cc_start: 0.7647 (mmm) cc_final: 0.7196 (mmt) REVERT: A 634 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7676 (tm-30) REVERT: A 825 ASP cc_start: 0.7622 (m-30) cc_final: 0.6255 (p0) REVERT: A 879 MET cc_start: 0.4749 (mmt) cc_final: 0.4206 (mmt) REVERT: A 933 GLN cc_start: 0.8782 (tm-30) cc_final: 0.8393 (tm-30) REVERT: A 1089 MET cc_start: 0.8278 (mmm) cc_final: 0.7723 (mmm) REVERT: A 1179 ILE cc_start: 0.8641 (pt) cc_final: 0.7592 (pt) REVERT: A 1357 GLU cc_start: 0.7397 (mt-10) cc_final: 0.7192 (mt-10) REVERT: C 20 MET cc_start: 0.7945 (pp-130) cc_final: 0.7418 (ppp) REVERT: C 106 GLU cc_start: 0.8080 (tt0) cc_final: 0.7604 (tt0) outliers start: 33 outliers final: 12 residues processed: 220 average time/residue: 0.2798 time to fit residues: 91.2990 Evaluate side-chains 163 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 1.394 ------------------------------------------------------------------------------- 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 80 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 120 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 39 optimal weight: 0.6980 chunk 144 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 128 optimal weight: 0.0770 chunk 143 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 116 optimal weight: 9.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14692 Z= 0.165 Angle : 0.620 10.238 20442 Z= 0.315 Chirality : 0.040 0.267 2407 Planarity : 0.004 0.045 2197 Dihedral : 19.644 176.460 3370 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.59 % Favored : 95.28 % Rotamer: Outliers : 3.34 % Allowed : 12.62 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.20), residues: 1483 helix: -0.89 (0.19), residues: 698 sheet: -1.81 (0.43), residues: 138 loop : -2.11 (0.22), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 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 0.000 ARG A1212 *********************** 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: 41 poor density : 173 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.6924 (ptt90) REVERT: A 933 GLN cc_start: 0.8857 (tm-30) cc_final: 0.8593 (tm-30) REVERT: A 1106 SER cc_start: 0.8773 (p) cc_final: 0.8562 (m) REVERT: C 12 GLU cc_start: 0.8772 (pm20) cc_final: 0.8381 (pm20) REVERT: C 20 MET cc_start: 0.7799 (pp-130) cc_final: 0.7228 (ppp) REVERT: C 90 ASN cc_start: 0.8936 (OUTLIER) cc_final: 0.8504 (p0) REVERT: C 109 MET cc_start: 0.7956 (tpp) cc_final: 0.7742 (mmt) outliers start: 41 outliers final: 19 residues processed: 202 average time/residue: 0.2899 time to fit residues: 90.7380 Evaluate side-chains 163 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER 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 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 79 THR Chi-restraints excluded: chain C residue 90 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 3.9990 chunk 108 optimal weight: 0.0570 chunk 75 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 97 optimal weight: 7.9990 chunk 145 optimal weight: 7.9990 chunk 153 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 127 optimal weight: 0.4980 overall best weight: 2.5104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 ASN A 899 ASN A 971 GLN C 37 HIS C 47 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 14692 Z= 0.345 Angle : 0.698 10.033 20442 Z= 0.356 Chirality : 0.044 0.233 2407 Planarity : 0.004 0.048 2197 Dihedral : 19.547 175.368 3368 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.20 % Favored : 93.66 % Rotamer: Outliers : 3.99 % Allowed : 13.60 % Favored : 82.41 % 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: -2.22 (0.20), residues: 1483 helix: -0.74 (0.19), residues: 697 sheet: -2.10 (0.42), residues: 124 loop : -2.11 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 476 HIS 0.004 0.001 HIS A 99 PHE 0.023 0.002 PHE C 17 TYR 0.025 0.002 TYR C 10 ARG 0.006 0.001 ARG A 655 *********************** 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 188 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 139 time to evaluate : 1.625 Fit side-chains REVERT: A 152 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.7044 (ptt90) REVERT: A 215 ARG cc_start: 0.6212 (tpt170) cc_final: 0.5689 (mmm-85) REVERT: A 370 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7597 (tt0) REVERT: A 631 MET cc_start: 0.8043 (tpp) cc_final: 0.7833 (tpp) REVERT: A 645 ASP cc_start: 0.7293 (OUTLIER) cc_final: 0.7017 (m-30) REVERT: A 933 GLN cc_start: 0.8941 (tm-30) cc_final: 0.8573 (tm-30) REVERT: A 1274 SER cc_start: 0.8586 (m) cc_final: 0.8103 (p) REVERT: C 9 LYS cc_start: 0.8114 (mtmt) cc_final: 0.7879 (mtmt) outliers start: 49 outliers final: 30 residues processed: 176 average time/residue: 0.2658 time to fit residues: 72.6519 Evaluate side-chains 160 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 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 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 432 PHE 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 645 ASP Chi-restraints excluded: chain A residue 751 MET Chi-restraints excluded: chain A residue 845 SER 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 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 87 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 chunk 114 optimal weight: 20.0000 chunk 63 optimal weight: 0.9990 chunk 131 optimal weight: 0.5980 chunk 106 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 78 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 51 optimal weight: 0.2980 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 A 971 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14692 Z= 0.173 Angle : 0.611 9.696 20442 Z= 0.309 Chirality : 0.041 0.277 2407 Planarity : 0.004 0.043 2197 Dihedral : 19.463 178.042 3368 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.86 % Favored : 95.01 % Rotamer: Outliers : 2.61 % Allowed : 15.55 % Favored : 81.84 % 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: -1.77 (0.21), residues: 1483 helix: -0.34 (0.19), residues: 699 sheet: -1.35 (0.45), residues: 128 loop : -2.04 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 476 HIS 0.003 0.001 HIS A 420 PHE 0.030 0.001 PHE A1008 TYR 0.028 0.001 TYR C 77 ARG 0.003 0.000 ARG A 629 *********************** 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 185 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 1.524 Fit side-chains REVERT: A 152 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.7034 (ptt90) REVERT: A 215 ARG cc_start: 0.6199 (tpt170) cc_final: 0.5701 (mmm-85) REVERT: A 465 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.5883 (tpt) REVERT: A 933 GLN cc_start: 0.8890 (tm-30) cc_final: 0.8634 (tm-30) REVERT: C 109 MET cc_start: 0.8028 (tpp) cc_final: 0.7825 (mmt) outliers start: 32 outliers final: 19 residues processed: 175 average time/residue: 0.2526 time to fit residues: 67.3987 Evaluate side-chains 154 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 1089 MET Chi-restraints excluded: chain A residue 1142 SER Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 153 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 71 optimal weight: 0.0020 chunk 12 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 80 optimal weight: 0.4980 chunk 148 optimal weight: 0.9980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 ASN A 255 ASN A 650 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 14692 Z= 0.174 Angle : 0.604 11.400 20442 Z= 0.302 Chirality : 0.040 0.259 2407 Planarity : 0.003 0.041 2197 Dihedral : 19.337 177.530 3368 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.65 % Favored : 95.28 % Rotamer: Outliers : 2.69 % Allowed : 16.53 % 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 (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: -1.45 (0.21), residues: 1483 helix: 0.01 (0.20), residues: 693 sheet: -1.22 (0.46), residues: 127 loop : -1.95 (0.22), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 476 HIS 0.003 0.001 HIS A 160 PHE 0.024 0.001 PHE A1008 TYR 0.021 0.001 TYR C 10 ARG 0.003 0.000 ARG A 71 *********************** 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 174 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 141 time to evaluate : 1.515 Fit side-chains REVERT: A 215 ARG cc_start: 0.6187 (tpt170) cc_final: 0.5670 (mmm-85) REVERT: A 933 GLN cc_start: 0.8897 (tm-30) cc_final: 0.8659 (tm-30) outliers start: 33 outliers final: 22 residues processed: 164 average time/residue: 0.2443 time to fit residues: 61.9702 Evaluate side-chains 152 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 845 SER 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 1228 LEU 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 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 17 optimal weight: 0.6980 chunk 87 optimal weight: 0.4980 chunk 112 optimal weight: 0.0000 chunk 129 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 153 optimal weight: 8.9990 chunk 95 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 14692 Z= 0.166 Angle : 0.593 9.282 20442 Z= 0.297 Chirality : 0.040 0.241 2407 Planarity : 0.003 0.041 2197 Dihedral : 19.267 178.076 3366 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.79 % Favored : 95.14 % Rotamer: Outliers : 2.85 % Allowed : 16.78 % Favored : 80.37 % 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: -1.26 (0.21), residues: 1483 helix: 0.15 (0.20), residues: 695 sheet: -1.05 (0.46), residues: 122 loop : -1.85 (0.23), residues: 666 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 0.049 0.001 PHE A1008 TYR 0.022 0.001 TYR C 10 ARG 0.004 0.000 ARG A 152 *********************** 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: 35 poor density : 146 time to evaluate : 1.498 Fit side-chains REVERT: A 215 ARG cc_start: 0.6222 (tpt170) cc_final: 0.5572 (mmm-85) REVERT: A 465 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.6375 (ttt) REVERT: A 933 GLN cc_start: 0.8861 (tm-30) cc_final: 0.8637 (tm-30) REVERT: A 964 SER cc_start: 0.8725 (t) cc_final: 0.8316 (p) REVERT: C 12 GLU cc_start: 0.8654 (pm20) cc_final: 0.8192 (pm20) outliers start: 35 outliers final: 21 residues processed: 169 average time/residue: 0.2288 time to fit residues: 60.4190 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 : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 1089 MET Chi-restraints excluded: chain A residue 1142 SER Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 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 34 GLU Chi-restraints excluded: chain C residue 79 THR 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 91 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 30 optimal weight: 0.0570 chunk 29 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 120 optimal weight: 0.5980 chunk 139 optimal weight: 0.9990 chunk 146 optimal weight: 0.7980 overall best weight: 0.6698 ------------------------------------------------------------------------------- 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 342 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14692 Z= 0.165 Angle : 0.601 11.110 20442 Z= 0.299 Chirality : 0.041 0.326 2407 Planarity : 0.003 0.040 2197 Dihedral : 19.217 178.025 3366 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.65 % Favored : 95.28 % Rotamer: Outliers : 2.69 % Allowed : 17.18 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.07 % Rama-Z (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: -1.04 (0.22), residues: 1483 helix: 0.32 (0.20), residues: 695 sheet: -0.90 (0.44), residues: 130 loop : -1.75 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1074 HIS 0.004 0.001 HIS A 116 PHE 0.022 0.001 PHE A1008 TYR 0.018 0.001 TYR C 10 ARG 0.007 0.000 ARG A 424 *********************** 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 172 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 1.484 Fit side-chains REVERT: A 215 ARG cc_start: 0.6262 (tpt170) cc_final: 0.5604 (mmm-85) REVERT: A 465 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.6397 (ttt) REVERT: A 645 ASP cc_start: 0.6606 (OUTLIER) cc_final: 0.6215 (m-30) REVERT: A 698 HIS cc_start: 0.7736 (OUTLIER) cc_final: 0.6884 (m170) REVERT: A 964 SER cc_start: 0.8677 (t) cc_final: 0.8264 (p) REVERT: C 12 GLU cc_start: 0.8641 (pm20) cc_final: 0.8185 (pm20) REVERT: C 115 GLU cc_start: 0.8442 (pm20) cc_final: 0.8235 (pm20) outliers start: 33 outliers final: 20 residues processed: 162 average time/residue: 0.2443 time to fit residues: 61.5862 Evaluate side-chains 149 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 338 LEU 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 645 ASP Chi-restraints excluded: chain A residue 698 HIS Chi-restraints excluded: chain A residue 1089 MET 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 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 133 optimal weight: 0.0770 chunk 142 optimal weight: 0.4980 chunk 146 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 112 optimal weight: 0.2980 chunk 43 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 135 optimal weight: 0.0870 chunk 93 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 ASN C 114 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 14692 Z= 0.145 Angle : 0.583 12.039 20442 Z= 0.290 Chirality : 0.039 0.308 2407 Planarity : 0.003 0.040 2197 Dihedral : 19.148 178.830 3366 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.52 % Favored : 95.41 % Rotamer: Outliers : 1.95 % Allowed : 18.32 % Favored : 79.72 % 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: -0.85 (0.22), residues: 1483 helix: 0.46 (0.20), residues: 694 sheet: -0.75 (0.44), residues: 130 loop : -1.64 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1074 HIS 0.004 0.000 HIS A 116 PHE 0.032 0.001 PHE A 97 TYR 0.029 0.001 TYR C 50 ARG 0.003 0.000 ARG A1212 *********************** 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 181 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 1.547 Fit side-chains REVERT: A 215 ARG cc_start: 0.6172 (tpt170) cc_final: 0.5517 (mmm-85) REVERT: A 465 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.6696 (ttt) REVERT: A 645 ASP cc_start: 0.6265 (OUTLIER) cc_final: 0.5884 (m-30) REVERT: A 964 SER cc_start: 0.8680 (t) cc_final: 0.8270 (p) REVERT: A 1355 LEU cc_start: 0.8592 (mt) cc_final: 0.8388 (mt) REVERT: C 12 GLU cc_start: 0.8605 (pm20) cc_final: 0.8272 (pm20) outliers start: 24 outliers final: 18 residues processed: 172 average time/residue: 0.2374 time to fit residues: 63.9066 Evaluate side-chains 154 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 380 LEU 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 645 ASP Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 1089 MET 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 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 92 optimal weight: 7.9990 chunk 71 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 145 optimal weight: 0.3980 chunk 126 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 698 HIS ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14692 Z= 0.215 Angle : 0.616 12.431 20442 Z= 0.307 Chirality : 0.042 0.306 2407 Planarity : 0.003 0.042 2197 Dihedral : 19.163 177.995 3366 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.92 % Favored : 95.01 % Rotamer: Outliers : 1.95 % Allowed : 18.97 % Favored : 79.07 % 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: -0.88 (0.22), residues: 1483 helix: 0.41 (0.20), residues: 698 sheet: -0.68 (0.47), residues: 110 loop : -1.64 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 476 HIS 0.004 0.001 HIS A 420 PHE 0.024 0.002 PHE A 97 TYR 0.024 0.001 TYR C 50 ARG 0.004 0.000 ARG A 152 ********************** 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 156 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 1.505 Fit side-chains REVERT: A 215 ARG cc_start: 0.6294 (tpt170) cc_final: 0.5640 (mmm-85) REVERT: A 465 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.6460 (ttt) REVERT: A 645 ASP cc_start: 0.6473 (OUTLIER) cc_final: 0.6041 (m-30) REVERT: A 698 HIS cc_start: 0.7614 (OUTLIER) cc_final: 0.6890 (m90) REVERT: A 964 SER cc_start: 0.8733 (t) cc_final: 0.8311 (p) REVERT: A 973 TYR cc_start: 0.8641 (m-80) cc_final: 0.8151 (m-80) REVERT: C 12 GLU cc_start: 0.8635 (pm20) cc_final: 0.8315 (pm20) outliers start: 24 outliers final: 20 residues processed: 148 average time/residue: 0.2353 time to fit residues: 54.6867 Evaluate side-chains 151 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 380 LEU 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 645 ASP Chi-restraints excluded: chain A residue 698 HIS Chi-restraints excluded: chain A residue 1089 MET 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 59 THR 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 38 optimal weight: 1.9990 chunk 116 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 126 optimal weight: 0.0970 chunk 52 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 ASN A 342 GLN A 698 HIS ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.172500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.133321 restraints weight = 22113.397| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.42 r_work: 0.3745 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14692 Z= 0.195 Angle : 0.616 12.371 20442 Z= 0.306 Chirality : 0.041 0.306 2407 Planarity : 0.003 0.041 2197 Dihedral : 19.167 177.674 3366 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.59 % Favored : 95.35 % Rotamer: Outliers : 2.36 % Allowed : 18.81 % Favored : 78.83 % 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: -0.78 (0.22), residues: 1483 helix: 0.49 (0.20), residues: 692 sheet: -0.59 (0.47), residues: 110 loop : -1.57 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 476 HIS 0.008 0.001 HIS A 698 PHE 0.025 0.001 PHE A 97 TYR 0.025 0.001 TYR C 50 ARG 0.004 0.000 ARG A 152 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2920.10 seconds wall clock time: 54 minutes 10.67 seconds (3250.67 seconds total)