Starting phenix.real_space_refine on Sun Mar 17 02:07:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4h_14497/03_2024/7z4h_14497.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4h_14497/03_2024/7z4h_14497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4h_14497/03_2024/7z4h_14497.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4h_14497/03_2024/7z4h_14497.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4h_14497/03_2024/7z4h_14497.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4h_14497/03_2024/7z4h_14497.pdb" } resolution = 3.49 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2494 atoms to isotropic. 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 139 5.49 5 S 23 5.16 5 C 8327 2.51 5 N 2435 2.21 5 O 2976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1008": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1336": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13900 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1970 Classifications: {'RNA': 92} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 49, 'rna3p_pyr': 31} Link IDs: {'rna2p': 12, 'rna3p': 79} Chain: "C" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 625 Classifications: {'DNA': 31} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 30} Chain: "D" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 389 Inner-chain residues flagged as termini: ['pdbres=" DA D -2 "'] Classifications: {'DNA': 19} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 18} Chain: "B" Number of atoms: 10916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 10916 Classifications: {'peptide': 1334} Link IDs: {'PTRANS': 35, 'TRANS': 1298} Chain breaks: 5 Time building chain proxies: 7.88, per 1000 atoms: 0.57 Number of scatterers: 13900 At special positions: 0 Unit cell: (98.8, 120.9, 122.2, 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 23 16.00 P 139 15.00 O 2976 8.00 N 2435 7.00 C 8327 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.30 Conformation dependent library (CDL) restraints added in 2.0 seconds 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2542 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 10 sheets defined 55.8% alpha, 8.4% beta 51 base pairs and 82 stacking pairs defined. Time for finding SS restraints: 5.44 Creating SS restraints... Processing helix chain 'B' and resid 22 through 26 removed outlier: 3.568A pdb=" N LYS B 26 " --> pdb=" O ASP B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 86 Processing helix chain 'B' and resid 86 through 94 Processing helix chain 'B' and resid 96 through 103 Processing helix chain 'B' and resid 121 through 132 Processing helix chain 'B' and resid 134 through 145 removed outlier: 3.593A pdb=" N LEU B 138 " --> pdb=" O THR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 164 Processing helix chain 'B' and resid 182 through 196 Processing helix chain 'B' and resid 207 through 213 Processing helix chain 'B' and resid 217 through 228 removed outlier: 3.519A pdb=" N GLN B 228 " --> pdb=" O ASN B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 247 Processing helix chain 'B' and resid 251 through 256 removed outlier: 4.457A pdb=" N ASN B 255 " --> pdb=" O ASN B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 279 Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 286 through 306 removed outlier: 3.963A pdb=" N ASP B 304 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 343 Processing helix chain 'B' and resid 343 through 353 removed outlier: 3.653A pdb=" N TYR B 347 " --> pdb=" O LEU B 343 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LYS B 348 " --> pdb=" O PRO B 344 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLU B 349 " --> pdb=" O GLU B 345 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP B 353 " --> pdb=" O GLU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 364 Processing helix chain 'B' and resid 368 through 383 Proline residue: B 378 - end of helix Processing helix chain 'B' and resid 387 through 395 Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.576A pdb=" N ASN B 407 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLY B 408 " --> pdb=" O PHE B 405 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER B 409 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 427 removed outlier: 4.095A pdb=" N HIS B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 436 removed outlier: 3.575A pdb=" N LYS B 434 " --> pdb=" O TYR B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 446 Processing helix chain 'B' and resid 477 through 482 Processing helix chain 'B' and resid 483 through 494 Processing helix chain 'B' and resid 512 through 526 removed outlier: 4.184A pdb=" N LYS B 526 " --> pdb=" O ASN B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 552 Processing helix chain 'B' and resid 560 through 568 removed outlier: 3.713A pdb=" N TYR B 568 " --> pdb=" O LEU B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 602 Processing helix chain 'B' and resid 603 through 609 Processing helix chain 'B' and resid 612 through 626 removed outlier: 3.894A pdb=" N PHE B 626 " --> pdb=" O THR B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 637 Processing helix chain 'B' and resid 638 through 640 No H-bonds generated for 'chain 'B' and resid 638 through 640' Processing helix chain 'B' and resid 644 through 654 Processing helix chain 'B' and resid 664 through 669 Processing helix chain 'B' and resid 678 through 685 Processing helix chain 'B' and resid 692 through 698 Processing helix chain 'B' and resid 702 through 713 removed outlier: 4.314A pdb=" N GLU B 706 " --> pdb=" O LEU B 702 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL B 713 " --> pdb=" O GLN B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 726 Processing helix chain 'B' and resid 730 through 751 Processing helix chain 'B' and resid 777 through 792 Processing helix chain 'B' and resid 794 through 799 Processing helix chain 'B' and resid 804 through 807 Processing helix chain 'B' and resid 808 through 817 Processing helix chain 'B' and resid 829 through 833 Processing helix chain 'B' and resid 851 through 855 Processing helix chain 'B' and resid 860 through 865 removed outlier: 3.603A pdb=" N GLY B 865 " --> pdb=" O LYS B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 889 removed outlier: 5.754A pdb=" N ASN B 881 " --> pdb=" O LYS B 877 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N TYR B 882 " --> pdb=" O LYS B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 901 Processing helix chain 'B' and resid 902 through 906 removed outlier: 3.511A pdb=" N GLY B 906 " --> pdb=" O ALA B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 922 Processing helix chain 'B' and resid 925 through 940 removed outlier: 3.870A pdb=" N LYS B 929 " --> pdb=" O ARG B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 970 removed outlier: 3.907A pdb=" N VAL B 963 " --> pdb=" O LYS B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 980 through 1001 removed outlier: 4.377A pdb=" N ALA B 984 " --> pdb=" O ASN B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1009 Processing helix chain 'B' and resid 1043 through 1047 removed outlier: 3.564A pdb=" N PHE B1046 " --> pdb=" O MET B1043 " (cutoff:3.500A) Processing helix chain 'B' and resid 1078 through 1088 Processing helix chain 'B' and resid 1127 through 1132 Processing helix chain 'B' and resid 1168 through 1177 removed outlier: 4.543A pdb=" N SER B1172 " --> pdb=" O ILE B1168 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N SER B1173 " --> pdb=" O MET B1169 " (cutoff:3.500A) Processing helix chain 'B' and resid 1177 through 1185 Processing helix chain 'B' and resid 1229 through 1240 Processing helix chain 'B' and resid 1249 through 1264 Processing helix chain 'B' and resid 1265 through 1281 removed outlier: 3.701A pdb=" N ILE B1269 " --> pdb=" O TYR B1265 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE B1270 " --> pdb=" O LEU B1266 " (cutoff:3.500A) Processing helix chain 'B' and resid 1283 through 1297 Processing helix chain 'B' and resid 1298 through 1300 No H-bonds generated for 'chain 'B' and resid 1298 through 1300' Processing helix chain 'B' and resid 1301 through 1313 Processing helix chain 'B' and resid 1314 through 1316 No H-bonds generated for 'chain 'B' and resid 1314 through 1316' Processing helix chain 'B' and resid 1340 through 1344 Processing helix chain 'B' and resid 1363 through 1365 No H-bonds generated for 'chain 'B' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'B' and resid 954 through 958 removed outlier: 4.292A pdb=" N MET B 763 " --> pdb=" O LEU B 958 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 46 removed outlier: 9.788A pdb=" N GLU B1357 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LYS B 33 " --> pdb=" O GLU B1357 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ARG B1359 " --> pdb=" O LYS B 33 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LEU B 35 " --> pdb=" O ARG B1359 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ASP B1361 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU B1203 " --> pdb=" O ILE B1348 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER B1202 " --> pdb=" O LEU B1214 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLU B1219 " --> pdb=" O ALA B1215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 507 through 509 removed outlier: 5.422A pdb=" N LEU B 508 " --> pdb=" O GLY B 660 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 538 through 539 removed outlier: 3.952A pdb=" N ALA B 538 " --> pdb=" O TYR B 529 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR B 529 " --> pdb=" O ALA B 538 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS B 528 " --> pdb=" O SER B 581 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 837 through 839 Processing sheet with id=AA6, first strand: chain 'B' and resid 1049 through 1051 Processing sheet with id=AA7, first strand: chain 'B' and resid 1063 through 1065 Processing sheet with id=AA8, first strand: chain 'B' and resid 1120 through 1121 Processing sheet with id=AA9, first strand: chain 'B' and resid 1156 through 1167 removed outlier: 3.558A pdb=" N GLU B1162 " --> pdb=" O VAL B1145 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B1145 " --> pdb=" O GLU B1162 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR B1141 " --> pdb=" O ILE B1166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1324 through 1326 515 hydrogen bonds defined for protein. 1473 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 126 hydrogen bonds 248 hydrogen bond angles 0 basepair planarities 51 basepair parallelities 82 stacking parallelities Total time for adding SS restraints: 7.30 Time building geometry restraints manager: 6.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2941 1.33 - 1.45: 3731 1.45 - 1.57: 7455 1.57 - 1.69: 277 1.69 - 1.81: 44 Bond restraints: 14448 Sorted by residual: bond pdb=" CA GLY B 8 " pdb=" C GLY B 8 " ideal model delta sigma weight residual 1.518 1.507 0.011 7.30e-03 1.88e+04 2.40e+00 bond pdb=" CB MET B 694 " pdb=" CG MET B 694 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.77e+00 bond pdb=" CA ILE B 473 " pdb=" CB ILE B 473 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.36e-02 5.41e+03 1.26e+00 bond pdb=" C GLU B1005 " pdb=" N SER B1006 " ideal model delta sigma weight residual 1.335 1.321 0.014 1.32e-02 5.74e+03 1.19e+00 bond pdb=" N SER B1006 " pdb=" CA SER B1006 " ideal model delta sigma weight residual 1.458 1.447 0.011 1.27e-02 6.20e+03 8.12e-01 ... (remaining 14443 not shown) Histogram of bond angle deviations from ideal: 96.60 - 104.08: 577 104.08 - 111.56: 7023 111.56 - 119.04: 5057 119.04 - 126.52: 6933 126.52 - 134.00: 516 Bond angle restraints: 20106 Sorted by residual: angle pdb=" CB MET B 694 " pdb=" CG MET B 694 " pdb=" SD MET B 694 " ideal model delta sigma weight residual 112.70 102.91 9.79 3.00e+00 1.11e-01 1.07e+01 angle pdb=" C ARG B 655 " pdb=" CA ARG B 655 " pdb=" CB ARG B 655 " ideal model delta sigma weight residual 111.43 107.79 3.64 1.24e+00 6.50e-01 8.64e+00 angle pdb=" C ASP B 585 " pdb=" CA ASP B 585 " pdb=" CB ASP B 585 " ideal model delta sigma weight residual 110.42 116.24 -5.82 1.99e+00 2.53e-01 8.56e+00 angle pdb=" N ARG B 655 " pdb=" CA ARG B 655 " pdb=" C ARG B 655 " ideal model delta sigma weight residual 107.20 111.87 -4.67 1.70e+00 3.46e-01 7.55e+00 angle pdb=" N SER B1006 " pdb=" CA SER B1006 " pdb=" CB SER B1006 " ideal model delta sigma weight residual 110.14 106.23 3.91 1.58e+00 4.01e-01 6.12e+00 ... (remaining 20101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 7882 17.94 - 35.88: 478 35.88 - 53.82: 230 53.82 - 71.76: 144 71.76 - 89.70: 21 Dihedral angle restraints: 8755 sinusoidal: 4831 harmonic: 3924 Sorted by residual: dihedral pdb=" CA PRO B 117 " pdb=" C PRO B 117 " pdb=" N ILE B 118 " pdb=" CA ILE B 118 " ideal model delta harmonic sigma weight residual 180.00 -163.51 -16.49 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA LYS B 878 " pdb=" C LYS B 878 " pdb=" N MET B 879 " pdb=" CA MET B 879 " ideal model delta harmonic sigma weight residual -180.00 -164.35 -15.65 0 5.00e+00 4.00e-02 9.79e+00 dihedral pdb=" CA GLU B1260 " pdb=" CB GLU B1260 " pdb=" CG GLU B1260 " pdb=" CD GLU B1260 " ideal model delta sinusoidal sigma weight residual 180.00 123.83 56.17 3 1.50e+01 4.44e-03 9.39e+00 ... (remaining 8752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1617 0.029 - 0.057: 475 0.057 - 0.086: 134 0.086 - 0.114: 63 0.114 - 0.143: 12 Chirality restraints: 2301 Sorted by residual: chirality pdb=" CA VAL B 308 " pdb=" N VAL B 308 " pdb=" C VAL B 308 " pdb=" CB VAL B 308 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" CA VAL B 870 " pdb=" N VAL B 870 " pdb=" C VAL B 870 " pdb=" CB VAL B 870 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA VAL B 842 " pdb=" N VAL B 842 " pdb=" C VAL B 842 " pdb=" CB VAL B 842 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.98e-01 ... (remaining 2298 not shown) Planarity restraints: 2055 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A A 42 " -0.026 2.00e-02 2.50e+03 1.17e-02 3.79e+00 pdb=" N9 A A 42 " 0.027 2.00e-02 2.50e+03 pdb=" C8 A A 42 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A A 42 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A A 42 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A A 42 " 0.001 2.00e-02 2.50e+03 pdb=" N6 A A 42 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A A 42 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A A 42 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A A 42 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A A 42 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 294 " -0.008 2.00e-02 2.50e+03 1.67e-02 2.80e+00 pdb=" C LYS B 294 " 0.029 2.00e-02 2.50e+03 pdb=" O LYS B 294 " -0.011 2.00e-02 2.50e+03 pdb=" N ASN B 295 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 295 " 0.007 2.00e-02 2.50e+03 1.48e-02 2.19e+00 pdb=" C ASN B 295 " -0.026 2.00e-02 2.50e+03 pdb=" O ASN B 295 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU B 296 " 0.009 2.00e-02 2.50e+03 ... (remaining 2052 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 182 2.61 - 3.19: 12046 3.19 - 3.76: 24087 3.76 - 4.33: 32186 4.33 - 4.90: 48769 Nonbonded interactions: 117270 Sorted by model distance: nonbonded pdb=" O2' U A 44 " pdb=" OE1 GLN B 402 " model vdw 2.043 2.440 nonbonded pdb=" ND2 ASN B 240 " pdb=" OD1 ASN B 255 " model vdw 2.193 2.520 nonbonded pdb=" OD1 ASP B 853 " pdb=" OG1 THR B 893 " model vdw 2.213 2.440 nonbonded pdb=" OE2 GLU B 762 " pdb=" OG SER B 960 " model vdw 2.222 2.440 nonbonded pdb=" O GLN B 817 " pdb=" OH TYR B 882 " model vdw 2.226 2.440 ... (remaining 117265 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 11.800 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 45.410 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14448 Z= 0.162 Angle : 0.452 9.791 20106 Z= 0.250 Chirality : 0.033 0.143 2301 Planarity : 0.003 0.031 2055 Dihedral : 16.008 89.704 6213 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.25 % Allowed : 4.92 % Favored : 93.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.67 (0.24), residues: 1322 helix: 2.32 (0.21), residues: 650 sheet: -0.32 (0.59), residues: 89 loop : -0.01 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 18 HIS 0.004 0.001 HIS B 328 PHE 0.010 0.001 PHE B1008 TYR 0.010 0.001 TYR B 347 ARG 0.003 0.000 ARG B 165 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 404 THR cc_start: 0.8602 (OUTLIER) cc_final: 0.8371 (p) REVERT: B 410 ILE cc_start: 0.9531 (mt) cc_final: 0.9313 (pt) REVERT: B 587 PHE cc_start: 0.8169 (m-80) cc_final: 0.7775 (m-10) REVERT: B 620 VAL cc_start: 0.9706 (t) cc_final: 0.9488 (p) REVERT: B 631 MET cc_start: 0.9098 (mmm) cc_final: 0.8818 (mmp) REVERT: B 654 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7743 (tpm170) REVERT: B 703 THR cc_start: 0.9328 (OUTLIER) cc_final: 0.8693 (t) REVERT: B 745 ASP cc_start: 0.8887 (t70) cc_final: 0.8360 (m-30) REVERT: B 933 GLN cc_start: 0.9348 (tm-30) cc_final: 0.9127 (tm-30) REVERT: B 1037 PHE cc_start: 0.6773 (OUTLIER) cc_final: 0.6467 (t80) REVERT: B 1272 GLN cc_start: 0.9513 (OUTLIER) cc_final: 0.9289 (mt0) outliers start: 15 outliers final: 3 residues processed: 139 average time/residue: 0.3352 time to fit residues: 65.0283 Evaluate side-chains 72 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 654 ARG Chi-restraints excluded: chain B residue 655 ARG Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1124 LYS Chi-restraints excluded: chain B residue 1263 LYS Chi-restraints excluded: chain B residue 1272 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 7.9990 chunk 110 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 85 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 HIS ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 754 HIS B 920 GLN B1241 HIS ** B1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14448 Z= 0.303 Angle : 0.559 10.974 20106 Z= 0.297 Chirality : 0.037 0.166 2301 Planarity : 0.004 0.048 2055 Dihedral : 19.019 84.720 3401 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.50 % Allowed : 8.68 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.67 (0.24), residues: 1322 helix: 2.31 (0.21), residues: 647 sheet: -0.52 (0.55), residues: 89 loop : 0.05 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 476 HIS 0.006 0.001 HIS B 595 PHE 0.014 0.002 PHE B1204 TYR 0.015 0.002 TYR B1242 ARG 0.006 0.001 ARG B 629 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 63 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 MET cc_start: 0.9410 (mmt) cc_final: 0.9208 (mmt) REVERT: B 383 MET cc_start: 0.8974 (mtt) cc_final: 0.8711 (tpp) REVERT: B 534 MET cc_start: 0.6945 (ppp) cc_final: 0.6699 (ppp) REVERT: B 587 PHE cc_start: 0.8484 (m-80) cc_final: 0.8088 (m-10) REVERT: B 688 PHE cc_start: 0.9430 (OUTLIER) cc_final: 0.9106 (t80) REVERT: B 933 GLN cc_start: 0.9382 (tm-30) cc_final: 0.9093 (tm-30) REVERT: B 1021 MET cc_start: 0.7745 (mmm) cc_final: 0.7472 (mpp) outliers start: 30 outliers final: 18 residues processed: 87 average time/residue: 0.3412 time to fit residues: 41.7269 Evaluate side-chains 69 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 50 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 688 PHE Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 818 ASN Chi-restraints excluded: chain B residue 943 TYR Chi-restraints excluded: chain B residue 964 SER Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain B residue 1043 MET Chi-restraints excluded: chain B residue 1124 LYS Chi-restraints excluded: chain B residue 1148 LYS Chi-restraints excluded: chain B residue 1263 LYS Chi-restraints excluded: chain B residue 1299 ASP Chi-restraints excluded: chain B residue 1316 THR Chi-restraints excluded: chain B residue 1328 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 110 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 36 optimal weight: 30.0000 chunk 132 optimal weight: 7.9990 chunk 143 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 HIS ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 698 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 14448 Z= 0.350 Angle : 0.588 11.527 20106 Z= 0.312 Chirality : 0.038 0.147 2301 Planarity : 0.004 0.048 2055 Dihedral : 19.036 83.677 3386 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.59 % Allowed : 9.77 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.36 (0.23), residues: 1322 helix: 1.97 (0.21), residues: 662 sheet: -0.69 (0.51), residues: 91 loop : -0.03 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 476 HIS 0.006 0.001 HIS B1262 PHE 0.015 0.002 PHE B1204 TYR 0.018 0.002 TYR B1356 ARG 0.008 0.001 ARG B 324 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 52 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 ILE cc_start: 0.9643 (OUTLIER) cc_final: 0.9303 (pt) REVERT: B 296 LEU cc_start: 0.9592 (OUTLIER) cc_final: 0.9265 (mm) REVERT: B 587 PHE cc_start: 0.8772 (m-80) cc_final: 0.8347 (m-80) REVERT: B 656 TYR cc_start: 0.8424 (OUTLIER) cc_final: 0.7221 (p90) REVERT: B 933 GLN cc_start: 0.9427 (tm-30) cc_final: 0.9123 (tm-30) REVERT: B 1021 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7683 (mpp) REVERT: B 1037 PHE cc_start: 0.6457 (t80) cc_final: 0.6105 (t80) outliers start: 31 outliers final: 19 residues processed: 76 average time/residue: 0.3195 time to fit residues: 35.5752 Evaluate side-chains 67 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 44 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 656 TYR Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 818 ASN Chi-restraints excluded: chain B residue 943 TYR Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain B residue 1043 MET Chi-restraints excluded: chain B residue 1124 LYS Chi-restraints excluded: chain B residue 1148 LYS Chi-restraints excluded: chain B residue 1263 LYS Chi-restraints excluded: chain B residue 1299 ASP Chi-restraints excluded: chain B residue 1328 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 0.9980 chunk 99 optimal weight: 40.0000 chunk 68 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 89 optimal weight: 30.0000 chunk 133 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 126 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14448 Z= 0.224 Angle : 0.485 9.453 20106 Z= 0.262 Chirality : 0.035 0.147 2301 Planarity : 0.003 0.043 2055 Dihedral : 18.858 80.743 3386 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.17 % Allowed : 11.10 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.57 (0.24), residues: 1322 helix: 2.16 (0.21), residues: 662 sheet: -0.71 (0.50), residues: 91 loop : 0.06 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 476 HIS 0.004 0.001 HIS B 328 PHE 0.011 0.001 PHE B 970 TYR 0.013 0.001 TYR B1001 ARG 0.003 0.000 ARG B 629 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 48 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 ILE cc_start: 0.9649 (OUTLIER) cc_final: 0.9283 (pt) REVERT: B 296 LEU cc_start: 0.9627 (OUTLIER) cc_final: 0.9345 (mm) REVERT: B 383 MET cc_start: 0.8975 (ttm) cc_final: 0.8663 (tpp) REVERT: B 534 MET cc_start: 0.7422 (ppp) cc_final: 0.7187 (ppp) REVERT: B 587 PHE cc_start: 0.8812 (m-80) cc_final: 0.8415 (m-80) REVERT: B 656 TYR cc_start: 0.8436 (OUTLIER) cc_final: 0.7170 (p90) REVERT: B 933 GLN cc_start: 0.9453 (tm-30) cc_final: 0.9156 (tm-30) REVERT: B 1008 PHE cc_start: 0.8751 (p90) cc_final: 0.8501 (p90) REVERT: B 1037 PHE cc_start: 0.6521 (t80) cc_final: 0.6295 (t80) REVERT: B 1213 MET cc_start: 0.7512 (mtt) cc_final: 0.7302 (mtt) outliers start: 26 outliers final: 16 residues processed: 71 average time/residue: 0.3074 time to fit residues: 32.4432 Evaluate side-chains 62 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 43 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 656 TYR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 943 TYR Chi-restraints excluded: chain B residue 978 ILE Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1043 MET Chi-restraints excluded: chain B residue 1124 LYS Chi-restraints excluded: chain B residue 1148 LYS Chi-restraints excluded: chain B residue 1299 ASP Chi-restraints excluded: chain B residue 1328 ASP Chi-restraints excluded: chain B residue 1352 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 chunk 97 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 35 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 ASN ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 899 ASN B 946 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 14448 Z= 0.396 Angle : 0.627 13.709 20106 Z= 0.330 Chirality : 0.039 0.158 2301 Planarity : 0.004 0.045 2055 Dihedral : 19.097 85.426 3382 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 19.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.67 % Allowed : 11.94 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.12 (0.23), residues: 1322 helix: 1.70 (0.21), residues: 657 sheet: -0.78 (0.50), residues: 89 loop : -0.03 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 476 HIS 0.005 0.001 HIS B1262 PHE 0.018 0.002 PHE B1204 TYR 0.028 0.002 TYR B 5 ARG 0.010 0.001 ARG B 780 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 43 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 ILE cc_start: 0.9693 (OUTLIER) cc_final: 0.9353 (pt) REVERT: B 296 LEU cc_start: 0.9613 (OUTLIER) cc_final: 0.9328 (mm) REVERT: B 587 PHE cc_start: 0.9033 (m-80) cc_final: 0.8682 (m-80) REVERT: B 631 MET cc_start: 0.9083 (mmp) cc_final: 0.8725 (mtp) REVERT: B 656 TYR cc_start: 0.8623 (OUTLIER) cc_final: 0.7369 (p90) REVERT: B 1036 TYR cc_start: 0.7654 (OUTLIER) cc_final: 0.7382 (m-10) REVERT: B 1037 PHE cc_start: 0.6676 (OUTLIER) cc_final: 0.6389 (t80) outliers start: 32 outliers final: 20 residues processed: 71 average time/residue: 0.3208 time to fit residues: 34.1071 Evaluate side-chains 65 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 40 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 656 TYR Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 943 TYR Chi-restraints excluded: chain B residue 978 ILE Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain B residue 1036 TYR Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1124 LYS Chi-restraints excluded: chain B residue 1148 LYS Chi-restraints excluded: chain B residue 1252 ASN Chi-restraints excluded: chain B residue 1299 ASP Chi-restraints excluded: chain B residue 1328 ASP Chi-restraints excluded: chain B residue 1352 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 6.9990 chunk 127 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 82 optimal weight: 0.4980 chunk 34 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 117 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 281 GLN ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14448 Z= 0.232 Angle : 0.510 10.451 20106 Z= 0.270 Chirality : 0.036 0.151 2301 Planarity : 0.003 0.044 2055 Dihedral : 18.891 80.716 3382 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.25 % Allowed : 12.69 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.38 (0.24), residues: 1322 helix: 1.96 (0.21), residues: 664 sheet: -0.67 (0.49), residues: 98 loop : 0.02 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 883 HIS 0.004 0.001 HIS B1262 PHE 0.012 0.001 PHE B 970 TYR 0.018 0.001 TYR B 5 ARG 0.007 0.000 ARG B 780 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 44 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 ILE cc_start: 0.9665 (OUTLIER) cc_final: 0.9280 (pt) REVERT: B 296 LEU cc_start: 0.9634 (OUTLIER) cc_final: 0.9361 (mm) REVERT: B 383 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8331 (tpt) REVERT: B 656 TYR cc_start: 0.8530 (OUTLIER) cc_final: 0.7240 (p90) REVERT: B 933 GLN cc_start: 0.9472 (tm-30) cc_final: 0.9182 (tm-30) REVERT: B 1037 PHE cc_start: 0.6579 (OUTLIER) cc_final: 0.6293 (t80) outliers start: 27 outliers final: 19 residues processed: 66 average time/residue: 0.2771 time to fit residues: 27.8705 Evaluate side-chains 66 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 42 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 656 TYR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 943 TYR Chi-restraints excluded: chain B residue 978 ILE Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1043 MET Chi-restraints excluded: chain B residue 1124 LYS Chi-restraints excluded: chain B residue 1148 LYS Chi-restraints excluded: chain B residue 1299 ASP Chi-restraints excluded: chain B residue 1328 ASP Chi-restraints excluded: chain B residue 1352 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 140 optimal weight: 0.1980 chunk 88 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 899 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14448 Z= 0.151 Angle : 0.449 7.464 20106 Z= 0.243 Chirality : 0.034 0.148 2301 Planarity : 0.003 0.040 2055 Dihedral : 18.637 84.888 3382 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.67 % Allowed : 13.11 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.58 (0.24), residues: 1322 helix: 2.14 (0.21), residues: 670 sheet: -0.55 (0.49), residues: 98 loop : 0.05 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 883 HIS 0.005 0.001 HIS B1264 PHE 0.009 0.001 PHE B 970 TYR 0.018 0.001 TYR B 812 ARG 0.005 0.000 ARG B 494 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 48 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 296 LEU cc_start: 0.9645 (OUTLIER) cc_final: 0.9377 (mm) REVERT: B 656 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.7112 (p90) REVERT: B 933 GLN cc_start: 0.9459 (tm-30) cc_final: 0.9126 (tm-30) REVERT: B 1037 PHE cc_start: 0.6579 (OUTLIER) cc_final: 0.6289 (t80) REVERT: B 1124 LYS cc_start: 0.9501 (OUTLIER) cc_final: 0.9160 (mmmm) REVERT: B 1213 MET cc_start: 0.7592 (mtt) cc_final: 0.7340 (mtt) outliers start: 20 outliers final: 11 residues processed: 65 average time/residue: 0.2719 time to fit residues: 27.0159 Evaluate side-chains 57 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 42 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 656 TYR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 943 TYR Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1043 MET Chi-restraints excluded: chain B residue 1124 LYS Chi-restraints excluded: chain B residue 1299 ASP Chi-restraints excluded: chain B residue 1328 ASP Chi-restraints excluded: chain B residue 1352 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 95 optimal weight: 30.0000 chunk 69 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 128 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 899 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 14448 Z= 0.296 Angle : 0.549 10.409 20106 Z= 0.289 Chirality : 0.037 0.160 2301 Planarity : 0.004 0.043 2055 Dihedral : 18.831 84.279 3382 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.09 % Allowed : 13.69 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.36 (0.24), residues: 1322 helix: 1.98 (0.21), residues: 664 sheet: -0.71 (0.51), residues: 89 loop : -0.05 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 883 HIS 0.005 0.001 HIS B1262 PHE 0.013 0.001 PHE B1204 TYR 0.019 0.001 TYR B 5 ARG 0.004 0.000 ARG B 494 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 45 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 296 LEU cc_start: 0.9636 (OUTLIER) cc_final: 0.9430 (mm) REVERT: B 383 MET cc_start: 0.8696 (tpt) cc_final: 0.8189 (tpt) REVERT: B 534 MET cc_start: 0.7466 (ppp) cc_final: 0.5649 (ppp) REVERT: B 656 TYR cc_start: 0.8542 (OUTLIER) cc_final: 0.7236 (p90) REVERT: B 933 GLN cc_start: 0.9470 (tm-30) cc_final: 0.9103 (tm-30) REVERT: B 1036 TYR cc_start: 0.7800 (OUTLIER) cc_final: 0.7530 (m-10) REVERT: B 1037 PHE cc_start: 0.6458 (OUTLIER) cc_final: 0.6184 (t80) REVERT: B 1213 MET cc_start: 0.7673 (mtt) cc_final: 0.7454 (mtt) REVERT: B 1284 ASP cc_start: 0.9132 (OUTLIER) cc_final: 0.8652 (p0) outliers start: 25 outliers final: 19 residues processed: 66 average time/residue: 0.3003 time to fit residues: 29.0644 Evaluate side-chains 67 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 43 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 656 TYR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 943 TYR Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain B residue 1036 TYR Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1043 MET Chi-restraints excluded: chain B residue 1124 LYS Chi-restraints excluded: chain B residue 1148 LYS Chi-restraints excluded: chain B residue 1284 ASP Chi-restraints excluded: chain B residue 1299 ASP Chi-restraints excluded: chain B residue 1328 ASP Chi-restraints excluded: chain B residue 1352 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 131 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 102 optimal weight: 8.9990 chunk 40 optimal weight: 0.7980 chunk 118 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 818 ASN B 899 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14448 Z= 0.136 Angle : 0.455 7.080 20106 Z= 0.244 Chirality : 0.035 0.197 2301 Planarity : 0.003 0.039 2055 Dihedral : 18.609 87.961 3382 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.59 % Allowed : 14.02 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.53 (0.24), residues: 1322 helix: 2.17 (0.21), residues: 663 sheet: -0.67 (0.50), residues: 98 loop : -0.01 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 883 HIS 0.004 0.001 HIS B 328 PHE 0.027 0.001 PHE B1008 TYR 0.015 0.001 TYR B1265 ARG 0.009 0.000 ARG B 535 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 44 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 296 LEU cc_start: 0.9646 (OUTLIER) cc_final: 0.9382 (mt) REVERT: B 383 MET cc_start: 0.8686 (tpt) cc_final: 0.8234 (tpt) REVERT: B 534 MET cc_start: 0.7036 (ppp) cc_final: 0.6637 (ppp) REVERT: B 564 LEU cc_start: 0.9774 (tp) cc_final: 0.9532 (pp) REVERT: B 656 TYR cc_start: 0.8360 (OUTLIER) cc_final: 0.7045 (p90) REVERT: B 933 GLN cc_start: 0.9466 (tm-30) cc_final: 0.9130 (tm-30) REVERT: B 1037 PHE cc_start: 0.6360 (OUTLIER) cc_final: 0.6122 (t80) REVERT: B 1124 LYS cc_start: 0.9507 (OUTLIER) cc_final: 0.9166 (mmmm) REVERT: B 1213 MET cc_start: 0.7649 (mtt) cc_final: 0.7433 (mtt) REVERT: B 1284 ASP cc_start: 0.9090 (OUTLIER) cc_final: 0.8613 (p0) outliers start: 19 outliers final: 14 residues processed: 61 average time/residue: 0.3124 time to fit residues: 28.4523 Evaluate side-chains 61 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 42 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 656 TYR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 818 ASN Chi-restraints excluded: chain B residue 943 TYR Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain B residue 1037 PHE Chi-restraints excluded: chain B residue 1043 MET Chi-restraints excluded: chain B residue 1124 LYS Chi-restraints excluded: chain B residue 1148 LYS Chi-restraints excluded: chain B residue 1284 ASP Chi-restraints excluded: chain B residue 1328 ASP Chi-restraints excluded: chain B residue 1352 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 5.9990 chunk 84 optimal weight: 0.0870 chunk 65 optimal weight: 5.9990 chunk 96 optimal weight: 30.0000 chunk 145 optimal weight: 10.0000 chunk 133 optimal weight: 0.0010 chunk 115 optimal weight: 8.9990 chunk 12 optimal weight: 20.0000 chunk 89 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 chunk 92 optimal weight: 7.9990 overall best weight: 2.6168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14448 Z= 0.187 Angle : 0.486 11.557 20106 Z= 0.257 Chirality : 0.035 0.189 2301 Planarity : 0.003 0.041 2055 Dihedral : 18.608 88.116 3382 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.84 % Allowed : 13.77 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.51 (0.24), residues: 1322 helix: 2.09 (0.21), residues: 669 sheet: -0.67 (0.51), residues: 98 loop : 0.03 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.107 0.004 TRP B 883 HIS 0.004 0.001 HIS B1264 PHE 0.033 0.001 PHE B1008 TYR 0.018 0.001 TYR B1265 ARG 0.004 0.000 ARG B 494 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 43 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 296 LEU cc_start: 0.9641 (OUTLIER) cc_final: 0.9386 (mt) REVERT: B 383 MET cc_start: 0.8728 (tpt) cc_final: 0.8262 (tpt) REVERT: B 534 MET cc_start: 0.7321 (ppp) cc_final: 0.6928 (ppp) REVERT: B 564 LEU cc_start: 0.9776 (tp) cc_final: 0.9541 (pp) REVERT: B 656 TYR cc_start: 0.8406 (OUTLIER) cc_final: 0.7089 (p90) REVERT: B 933 GLN cc_start: 0.9462 (tm-30) cc_final: 0.9159 (tm-30) REVERT: B 1124 LYS cc_start: 0.9516 (OUTLIER) cc_final: 0.9168 (mmmm) REVERT: B 1213 MET cc_start: 0.7672 (mtt) cc_final: 0.7453 (mtt) REVERT: B 1284 ASP cc_start: 0.9100 (OUTLIER) cc_final: 0.8623 (p0) outliers start: 22 outliers final: 16 residues processed: 62 average time/residue: 0.2957 time to fit residues: 26.9938 Evaluate side-chains 63 residues out of total 1198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 43 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 656 TYR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 943 TYR Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain B residue 1043 MET Chi-restraints excluded: chain B residue 1124 LYS Chi-restraints excluded: chain B residue 1148 LYS Chi-restraints excluded: chain B residue 1284 ASP Chi-restraints excluded: chain B residue 1328 ASP Chi-restraints excluded: chain B residue 1352 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 chunk 48 optimal weight: 0.0570 chunk 119 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 101 optimal weight: 8.9990 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.059203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.038061 restraints weight = 82506.880| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 5.94 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.4766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14448 Z= 0.121 Angle : 0.467 12.108 20106 Z= 0.249 Chirality : 0.035 0.167 2301 Planarity : 0.003 0.046 2055 Dihedral : 18.453 90.357 3382 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.42 % Allowed : 14.02 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.55 (0.24), residues: 1322 helix: 2.11 (0.21), residues: 669 sheet: -0.34 (0.56), residues: 85 loop : 0.01 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 883 HIS 0.004 0.001 HIS B 328 PHE 0.032 0.001 PHE B1008 TYR 0.016 0.001 TYR B1265 ARG 0.007 0.000 ARG B 780 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2553.39 seconds wall clock time: 47 minutes 31.33 seconds (2851.33 seconds total)