Starting phenix.real_space_refine on Sun Nov 17 01:30:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p1k_17352/11_2024/8p1k_17352.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p1k_17352/11_2024/8p1k_17352.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p1k_17352/11_2024/8p1k_17352.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p1k_17352/11_2024/8p1k_17352.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p1k_17352/11_2024/8p1k_17352.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p1k_17352/11_2024/8p1k_17352.cif" } resolution = 3.24 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= 0.038 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: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 7885 2.51 5 N 2062 2.21 5 O 2252 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 12261 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 12261 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1518, 12249 Classifications: {'peptide': 1518} Link IDs: {'PTRANS': 51, 'TRANS': 1466} Chain breaks: 5 Conformer: "B" Number of residues, atoms: 1518, 12249 Classifications: {'peptide': 1518} Link IDs: {'PTRANS': 51, 'TRANS': 1466} Chain breaks: 5 bond proxies already assigned to first conformer: 12507 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR A 662 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR A 662 " occ=0.50 Time building chain proxies: 12.46, per 1000 atoms: 1.02 Number of scatterers: 12261 At special positions: 0 Unit cell: (86.676, 125.82, 126.752, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 2252 8.00 N 2062 7.00 C 7885 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=0, symmetry=0 Time building additional restraints: 2.87 Conformation dependent library (CDL) restraints added in 3.2 seconds 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2900 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 12 sheets defined 61.2% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 1 through 13 removed outlier: 4.021A pdb=" N GLU A 13 " --> pdb=" O ASN A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 47 removed outlier: 3.863A pdb=" N VAL A 39 " --> pdb=" O ARG A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 65 Processing helix chain 'A' and resid 67 through 75 Processing helix chain 'A' and resid 87 through 94 removed outlier: 3.653A pdb=" N LYS A 93 " --> pdb=" O LYS A 89 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 145 removed outlier: 5.123A pdb=" N ALA A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N GLY A 131 " --> pdb=" O LYS A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 172 Processing helix chain 'A' and resid 176 through 198 removed outlier: 3.690A pdb=" N VAL A 180 " --> pdb=" O ARG A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 214 removed outlier: 4.359A pdb=" N ALA A 205 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ALA A 206 " --> pdb=" O GLU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 252 removed outlier: 3.797A pdb=" N LEU A 243 " --> pdb=" O ASN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 281 removed outlier: 3.561A pdb=" N GLN A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 323 removed outlier: 3.683A pdb=" N ILE A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 343 Processing helix chain 'A' and resid 345 through 354 removed outlier: 3.625A pdb=" N TYR A 353 " --> pdb=" O MET A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 391 Processing helix chain 'A' and resid 409 through 429 Processing helix chain 'A' and resid 449 through 463 removed outlier: 3.594A pdb=" N LYS A 453 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE A 454 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLN A 460 " --> pdb=" O GLN A 456 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LYS A 461 " --> pdb=" O ASN A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 470 through 490 removed outlier: 3.923A pdb=" N HIS A 474 " --> pdb=" O THR A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 572 Processing helix chain 'A' and resid 572 through 593 Processing helix chain 'A' and resid 597 through 614 Processing helix chain 'A' and resid 616 through 634 removed outlier: 3.975A pdb=" N TYR A 628 " --> pdb=" O ASP A 624 " (cutoff:3.500A) Proline residue: A 631 - end of helix Processing helix chain 'A' and resid 639 through 647 removed outlier: 3.614A pdb=" N LEU A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 674 removed outlier: 3.583A pdb=" N VAL A 658 " --> pdb=" O SER A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 726 removed outlier: 3.819A pdb=" N LEU A 716 " --> pdb=" O HIS A 712 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 720 " --> pdb=" O LEU A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 732 removed outlier: 6.300A pdb=" N GLY A 730 " --> pdb=" O PHE A 727 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU A 731 " --> pdb=" O GLU A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 760 removed outlier: 3.546A pdb=" N LYS A 740 " --> pdb=" O ASN A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 767 Processing helix chain 'A' and resid 769 through 777 Processing helix chain 'A' and resid 786 through 802 removed outlier: 3.893A pdb=" N VAL A 800 " --> pdb=" O GLU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 814 Processing helix chain 'A' and resid 820 through 824 removed outlier: 3.639A pdb=" N SER A 823 " --> pdb=" O PRO A 820 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN A 824 " --> pdb=" O TYR A 821 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 820 through 824' Processing helix chain 'A' and resid 848 through 859 removed outlier: 3.515A pdb=" N ASN A 858 " --> pdb=" O ARG A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 872 Processing helix chain 'A' and resid 883 through 887 removed outlier: 3.842A pdb=" N ARG A 887 " --> pdb=" O LYS A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 917 Processing helix chain 'A' and resid 918 through 920 No H-bonds generated for 'chain 'A' and resid 918 through 920' Processing helix chain 'A' and resid 927 through 931 removed outlier: 3.618A pdb=" N LYS A 930 " --> pdb=" O GLY A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 947 Processing helix chain 'A' and resid 983 through 992 removed outlier: 4.009A pdb=" N ARG A 987 " --> pdb=" O ALA A 983 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE A 988 " --> pdb=" O LYS A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1012 Processing helix chain 'A' and resid 1020 through 1030 removed outlier: 3.577A pdb=" N MET A1030 " --> pdb=" O TYR A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1044 removed outlier: 3.780A pdb=" N PHE A1044 " --> pdb=" O PHE A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1061 through 1084 Processing helix chain 'A' and resid 1114 through 1126 Processing helix chain 'A' and resid 1128 through 1133 removed outlier: 3.732A pdb=" N SER A1133 " --> pdb=" O HIS A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1153 removed outlier: 3.583A pdb=" N SER A1141 " --> pdb=" O GLU A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1175 removed outlier: 3.612A pdb=" N THR A1174 " --> pdb=" O GLU A1170 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE A1175 " --> pdb=" O PHE A1171 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1170 through 1175' Processing helix chain 'A' and resid 1184 through 1192 removed outlier: 4.133A pdb=" N ILE A1188 " --> pdb=" O PRO A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1218 Processing helix chain 'A' and resid 1221 through 1241 Processing helix chain 'A' and resid 1249 through 1253 Processing helix chain 'A' and resid 1257 through 1261 removed outlier: 3.688A pdb=" N THR A1261 " --> pdb=" O HIS A1258 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1266 Processing helix chain 'A' and resid 1272 through 1279 Processing helix chain 'A' and resid 1282 through 1300 removed outlier: 3.738A pdb=" N LYS A1286 " --> pdb=" O GLY A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1318 Processing helix chain 'A' and resid 1354 through 1365 Processing helix chain 'A' and resid 1366 through 1370 Processing helix chain 'A' and resid 1375 through 1388 Processing helix chain 'A' and resid 1389 through 1397 Processing helix chain 'A' and resid 1400 through 1409 Processing helix chain 'A' and resid 1410 through 1414 removed outlier: 4.198A pdb=" N HIS A1413 " --> pdb=" O ALA A1410 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET A1414 " --> pdb=" O LYS A1411 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1410 through 1414' Processing helix chain 'A' and resid 1425 through 1439 Processing helix chain 'A' and resid 1443 through 1454 Processing helix chain 'A' and resid 1502 through 1512 Processing helix chain 'A' and resid 1514 through 1525 Processing helix chain 'A' and resid 1531 through 1546 Processing helix chain 'A' and resid 1554 through 1568 Proline residue: A1561 - end of helix Processing helix chain 'A' and resid 1581 through 1592 Processing sheet with id=AA1, first strand: chain 'A' and resid 98 through 102 Processing sheet with id=AA2, first strand: chain 'A' and resid 260 through 261 Processing sheet with id=AA3, first strand: chain 'A' and resid 260 through 261 removed outlier: 7.692A pdb=" N LYS A 958 " --> pdb=" O LEU A 954 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 954 " --> pdb=" O LYS A 958 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 296 through 297 Processing sheet with id=AA5, first strand: chain 'A' and resid 499 through 503 Processing sheet with id=AA6, first strand: chain 'A' and resid 499 through 503 Processing sheet with id=AA7, first strand: chain 'A' and resid 701 through 702 Processing sheet with id=AA8, first strand: chain 'A' and resid 832 through 837 removed outlier: 5.626A pdb=" N SER A 844 " --> pdb=" O GLY A 835 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 895 through 897 removed outlier: 4.165A pdb=" N ALA A 877 " --> pdb=" O LYS A1014 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE A 881 " --> pdb=" O PHE A1018 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1417 through 1419 Processing sheet with id=AB2, first strand: chain 'A' and resid 1485 through 1486 Processing sheet with id=AB3, first strand: chain 'A' and resid 1489 through 1491 713 hydrogen bonds defined for protein. 2038 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.07 Time building geometry restraints manager: 3.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3903 1.34 - 1.46: 2364 1.46 - 1.58: 6162 1.58 - 1.70: 0 1.70 - 1.81: 106 Bond restraints: 12535 Sorted by residual: bond pdb=" C GLN A 223 " pdb=" N PRO A 224 " ideal model delta sigma weight residual 1.331 1.343 -0.012 7.90e-03 1.60e+04 2.17e+00 bond pdb=" CB GLN A 413 " pdb=" CG GLN A 413 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.26e+00 bond pdb=" CA THR A1454 " pdb=" CB THR A1454 " ideal model delta sigma weight residual 1.530 1.547 -0.017 1.50e-02 4.44e+03 1.26e+00 bond pdb=" CB MET A 735 " pdb=" CG MET A 735 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.18e+00 bond pdb=" CG GLN A 413 " pdb=" CD GLN A 413 " ideal model delta sigma weight residual 1.516 1.490 0.026 2.50e-02 1.60e+03 1.11e+00 ... (remaining 12530 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 16862 2.81 - 5.62: 67 5.62 - 8.43: 5 8.43 - 11.24: 3 11.24 - 14.06: 1 Bond angle restraints: 16938 Sorted by residual: angle pdb=" CB MET A 735 " pdb=" CG MET A 735 " pdb=" SD MET A 735 " ideal model delta sigma weight residual 112.70 126.76 -14.06 3.00e+00 1.11e-01 2.19e+01 angle pdb=" CB MET A 349 " pdb=" CG MET A 349 " pdb=" SD MET A 349 " ideal model delta sigma weight residual 112.70 122.38 -9.68 3.00e+00 1.11e-01 1.04e+01 angle pdb=" CB MET A1447 " pdb=" CG MET A1447 " pdb=" SD MET A1447 " ideal model delta sigma weight residual 112.70 121.75 -9.05 3.00e+00 1.11e-01 9.11e+00 angle pdb=" CA ARG A 30 " pdb=" CB ARG A 30 " pdb=" CG ARG A 30 " ideal model delta sigma weight residual 114.10 120.06 -5.96 2.00e+00 2.50e-01 8.89e+00 angle pdb=" CG1 ILE A1333 " pdb=" CB ILE A1333 " pdb=" CG2 ILE A1333 " ideal model delta sigma weight residual 110.70 102.01 8.69 3.00e+00 1.11e-01 8.38e+00 ... (remaining 16933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 6918 17.32 - 34.63: 528 34.63 - 51.95: 85 51.95 - 69.26: 10 69.26 - 86.58: 7 Dihedral angle restraints: 7548 sinusoidal: 3068 harmonic: 4480 Sorted by residual: dihedral pdb=" CA TYR A 128 " pdb=" C TYR A 128 " pdb=" N GLU A 129 " pdb=" CA GLU A 129 " ideal model delta harmonic sigma weight residual -180.00 -161.48 -18.52 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA MET A1246 " pdb=" C MET A1246 " pdb=" N VAL A1247 " pdb=" CA VAL A1247 " ideal model delta harmonic sigma weight residual -180.00 -163.48 -16.52 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA LYS A 10 " pdb=" C LYS A 10 " pdb=" N LEU A 11 " pdb=" CA LEU A 11 " ideal model delta harmonic sigma weight residual 180.00 163.90 16.10 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 7545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1479 0.045 - 0.090: 320 0.090 - 0.135: 78 0.135 - 0.180: 5 0.180 - 0.225: 1 Chirality restraints: 1883 Sorted by residual: chirality pdb=" CB ILE A1333 " pdb=" CA ILE A1333 " pdb=" CG1 ILE A1333 " pdb=" CG2 ILE A1333 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA GLN A 223 " pdb=" N GLN A 223 " pdb=" C GLN A 223 " pdb=" CB GLN A 223 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.89e-01 chirality pdb=" CB ILE A 482 " pdb=" CA ILE A 482 " pdb=" CG1 ILE A 482 " pdb=" CG2 ILE A 482 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.78e-01 ... (remaining 1880 not shown) Planarity restraints: 2138 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 662 " -0.016 2.00e-02 2.50e+03 1.67e-02 5.58e+00 pdb=" CG BTYR A 662 " 0.040 2.00e-02 2.50e+03 pdb=" CD1BTYR A 662 " -0.014 2.00e-02 2.50e+03 pdb=" CD2BTYR A 662 " -0.001 2.00e-02 2.50e+03 pdb=" CE1BTYR A 662 " 0.002 2.00e-02 2.50e+03 pdb=" CE2BTYR A 662 " -0.011 2.00e-02 2.50e+03 pdb=" CZ BTYR A 662 " -0.003 2.00e-02 2.50e+03 pdb=" OH BTYR A 662 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 513 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.71e+00 pdb=" N PRO A 514 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 514 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 514 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A1221 " -0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO A1222 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A1222 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A1222 " -0.020 5.00e-02 4.00e+02 ... (remaining 2135 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 225 2.70 - 3.25: 12165 3.25 - 3.80: 19870 3.80 - 4.35: 24923 4.35 - 4.90: 42709 Nonbonded interactions: 99892 Sorted by model distance: nonbonded pdb=" OH TYR A 855 " pdb=" OE1 GLU A 871 " model vdw 2.156 3.040 nonbonded pdb=" OG SER A 48 " pdb=" OD1 ASN A 50 " model vdw 2.181 3.040 nonbonded pdb=" OG SER A 515 " pdb=" O PHE A 524 " model vdw 2.206 3.040 nonbonded pdb=" OH TYR A 869 " pdb=" OD2 ASP A1007 " model vdw 2.217 3.040 nonbonded pdb=" OG1 THR A 459 " pdb=" OE1 GLN A1223 " model vdw 2.222 3.040 ... (remaining 99887 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=0.50 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: 0.010 Normalize map: mean=0, sd=1: 1.640 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 37.710 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.090 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 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 0.053 12535 Z= 0.152 Angle : 0.533 14.055 16938 Z= 0.284 Chirality : 0.039 0.225 1883 Planarity : 0.003 0.041 2138 Dihedral : 12.481 86.578 4648 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % 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: 1.65 (0.22), residues: 1509 helix: 1.89 (0.18), residues: 851 sheet: 1.29 (0.50), residues: 112 loop : -0.18 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1056 HIS 0.005 0.001 HIS A 489 PHE 0.010 0.001 PHE A1341 TYR 0.015 0.001 TYR A 713 ARG 0.008 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 1.365 Fit side-chains revert: symmetry clash REVERT: A 94 MET cc_start: 0.0844 (ptt) cc_final: 0.0090 (mpp) REVERT: A 239 ASN cc_start: 0.8289 (t0) cc_final: 0.7906 (t0) REVERT: A 245 ASP cc_start: 0.7464 (m-30) cc_final: 0.7142 (t0) REVERT: A 289 ARG cc_start: 0.7250 (mtp180) cc_final: 0.6900 (mmm-85) REVERT: A 325 ILE cc_start: 0.8706 (mt) cc_final: 0.8448 (tp) REVERT: A 359 PHE cc_start: 0.8154 (t80) cc_final: 0.7901 (t80) REVERT: A 363 GLN cc_start: 0.7505 (pm20) cc_final: 0.7152 (mt0) REVERT: A 457 ASN cc_start: 0.7565 (m-40) cc_final: 0.7307 (t0) REVERT: A 597 LEU cc_start: 0.8068 (mt) cc_final: 0.7808 (mt) REVERT: A 607 ASN cc_start: 0.7276 (m-40) cc_final: 0.6681 (m110) REVERT: A 628 TYR cc_start: 0.7857 (m-10) cc_final: 0.7629 (m-10) REVERT: A 728 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7467 (mm-30) REVERT: A 819 GLU cc_start: 0.7962 (pp20) cc_final: 0.7692 (pp20) REVERT: A 867 LYS cc_start: 0.7288 (tptm) cc_final: 0.6967 (tptt) REVERT: A 892 ARG cc_start: 0.6385 (tpt170) cc_final: 0.5897 (mtp85) REVERT: A 917 LYS cc_start: 0.7825 (ttpp) cc_final: 0.7599 (tttm) REVERT: A 963 LYS cc_start: 0.7112 (tttp) cc_final: 0.6835 (ttpt) REVERT: A 1147 GLU cc_start: 0.7483 (tt0) cc_final: 0.7238 (tt0) REVERT: A 1335 LYS cc_start: 0.7344 (ttpt) cc_final: 0.7132 (ttmm) REVERT: A 1366 VAL cc_start: 0.7750 (t) cc_final: 0.7533 (p) REVERT: A 1445 GLN cc_start: 0.8262 (mp10) cc_final: 0.7626 (mt0) REVERT: A 1483 ARG cc_start: 0.5344 (mmt180) cc_final: 0.4865 (tpp80) REVERT: A 1519 SER cc_start: 0.7060 (m) cc_final: 0.6846 (t) REVERT: A 1523 ASP cc_start: 0.7971 (m-30) cc_final: 0.7461 (m-30) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.2781 time to fit residues: 94.5907 Evaluate side-chains 150 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 ASN A 457 ASN A 489 HIS A1096 HIS A1298 HIS A1378 ASN ** A1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1575 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12535 Z= 0.200 Angle : 0.531 7.379 16938 Z= 0.273 Chirality : 0.041 0.165 1883 Planarity : 0.004 0.062 2138 Dihedral : 3.565 19.306 1650 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.96 % Allowed : 5.41 % Favored : 93.62 % 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: 1.62 (0.22), residues: 1509 helix: 1.83 (0.18), residues: 859 sheet: 1.25 (0.50), residues: 112 loop : -0.15 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1056 HIS 0.004 0.001 HIS A 278 PHE 0.027 0.001 PHE A1132 TYR 0.020 0.001 TYR A1026 ARG 0.005 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 1.382 Fit side-chains revert: symmetry clash REVERT: A 94 MET cc_start: 0.0667 (ptt) cc_final: -0.0013 (mpp) REVERT: A 239 ASN cc_start: 0.8308 (t0) cc_final: 0.7918 (t0) REVERT: A 245 ASP cc_start: 0.7456 (m-30) cc_final: 0.7142 (t0) REVERT: A 325 ILE cc_start: 0.8705 (mt) cc_final: 0.8364 (tp) REVERT: A 359 PHE cc_start: 0.8166 (t80) cc_final: 0.7964 (t80) REVERT: A 363 GLN cc_start: 0.7505 (pm20) cc_final: 0.7171 (mt0) REVERT: A 457 ASN cc_start: 0.7737 (m110) cc_final: 0.7253 (t0) REVERT: A 607 ASN cc_start: 0.7277 (m-40) cc_final: 0.6704 (m110) REVERT: A 728 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7400 (mm-30) REVERT: A 819 GLU cc_start: 0.8153 (pp20) cc_final: 0.7809 (pp20) REVERT: A 867 LYS cc_start: 0.7421 (tptm) cc_final: 0.6988 (tptt) REVERT: A 892 ARG cc_start: 0.6407 (tpt170) cc_final: 0.6044 (mtt-85) REVERT: A 963 LYS cc_start: 0.7173 (tttp) cc_final: 0.6792 (ttpt) REVERT: A 967 MET cc_start: 0.7736 (ttm) cc_final: 0.7290 (tpp) REVERT: A 1030 MET cc_start: 0.6988 (ptt) cc_final: 0.5239 (mmm) REVERT: A 1128 HIS cc_start: 0.6571 (m170) cc_final: 0.6308 (m170) REVERT: A 1335 LYS cc_start: 0.7207 (ttpt) cc_final: 0.6984 (ttmm) REVERT: A 1347 PHE cc_start: 0.7840 (m-80) cc_final: 0.7560 (m-80) REVERT: A 1445 GLN cc_start: 0.8174 (mp10) cc_final: 0.7544 (mt0) REVERT: A 1483 ARG cc_start: 0.5415 (mmt180) cc_final: 0.4880 (tpp80) REVERT: A 1575 GLN cc_start: 0.6852 (tt0) cc_final: 0.6233 (mt0) outliers start: 13 outliers final: 9 residues processed: 164 average time/residue: 0.2676 time to fit residues: 63.2081 Evaluate side-chains 148 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 139 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 1425 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 76 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 136 optimal weight: 0.0970 chunk 46 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1501 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12535 Z= 0.261 Angle : 0.536 14.020 16938 Z= 0.274 Chirality : 0.041 0.160 1883 Planarity : 0.004 0.050 2138 Dihedral : 3.648 19.461 1650 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.19 % Allowed : 6.60 % Favored : 92.22 % 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: 1.50 (0.21), residues: 1509 helix: 1.77 (0.17), residues: 853 sheet: 1.07 (0.49), residues: 112 loop : -0.20 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1056 HIS 0.005 0.001 HIS A1365 PHE 0.019 0.001 PHE A 585 TYR 0.016 0.001 TYR A1026 ARG 0.008 0.001 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.0485 (ptt) cc_final: -0.0186 (mpp) REVERT: A 239 ASN cc_start: 0.8334 (t0) cc_final: 0.7932 (t0) REVERT: A 245 ASP cc_start: 0.7594 (m-30) cc_final: 0.7317 (t0) REVERT: A 325 ILE cc_start: 0.8726 (mt) cc_final: 0.8363 (tp) REVERT: A 359 PHE cc_start: 0.8355 (t80) cc_final: 0.8085 (t80) REVERT: A 363 GLN cc_start: 0.7535 (pm20) cc_final: 0.7195 (mt0) REVERT: A 457 ASN cc_start: 0.7711 (m110) cc_final: 0.7301 (t0) REVERT: A 728 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7579 (mm-30) REVERT: A 819 GLU cc_start: 0.8179 (pp20) cc_final: 0.7792 (pp20) REVERT: A 867 LYS cc_start: 0.7408 (tptm) cc_final: 0.6960 (tptt) REVERT: A 892 ARG cc_start: 0.6529 (tpt170) cc_final: 0.6091 (mtt-85) REVERT: A 963 LYS cc_start: 0.7214 (tttp) cc_final: 0.6812 (ttpt) REVERT: A 1030 MET cc_start: 0.6972 (ptt) cc_final: 0.5324 (mmm) REVERT: A 1128 HIS cc_start: 0.6714 (m170) cc_final: 0.6425 (m170) REVERT: A 1172 LEU cc_start: 0.6443 (mm) cc_final: 0.6132 (mm) REVERT: A 1335 LYS cc_start: 0.7285 (ttpt) cc_final: 0.7030 (ttmm) REVERT: A 1445 GLN cc_start: 0.8153 (mp10) cc_final: 0.7541 (mt0) REVERT: A 1483 ARG cc_start: 0.5685 (mmt180) cc_final: 0.5046 (tpp80) outliers start: 16 outliers final: 12 residues processed: 155 average time/residue: 0.2668 time to fit residues: 60.3571 Evaluate side-chains 146 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 1321 THR Chi-restraints excluded: chain A residue 1351 ASP Chi-restraints excluded: chain A residue 1425 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 135 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 92 optimal weight: 0.0770 chunk 137 optimal weight: 4.9990 chunk 145 optimal weight: 8.9990 chunk 72 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 39 optimal weight: 9.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12535 Z= 0.198 Angle : 0.499 14.161 16938 Z= 0.255 Chirality : 0.040 0.166 1883 Planarity : 0.003 0.044 2138 Dihedral : 3.584 19.312 1650 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.92 % Favored : 97.01 % Rotamer: Outliers : 1.04 % Allowed : 7.93 % Favored : 91.03 % 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: 1.60 (0.22), residues: 1509 helix: 1.88 (0.18), residues: 854 sheet: 1.04 (0.49), residues: 112 loop : -0.20 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1131 HIS 0.003 0.001 HIS A 993 PHE 0.016 0.001 PHE A 585 TYR 0.014 0.001 TYR A1026 ARG 0.005 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.0485 (ptt) cc_final: -0.0263 (mpp) REVERT: A 239 ASN cc_start: 0.8305 (t0) cc_final: 0.7918 (t0) REVERT: A 245 ASP cc_start: 0.7582 (m-30) cc_final: 0.7306 (t0) REVERT: A 325 ILE cc_start: 0.8740 (mt) cc_final: 0.8449 (tp) REVERT: A 359 PHE cc_start: 0.8301 (t80) cc_final: 0.8015 (t80) REVERT: A 363 GLN cc_start: 0.7531 (pm20) cc_final: 0.7225 (mt0) REVERT: A 457 ASN cc_start: 0.7695 (m110) cc_final: 0.7285 (t0) REVERT: A 728 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7320 (mm-30) REVERT: A 819 GLU cc_start: 0.8175 (pp20) cc_final: 0.7767 (pp20) REVERT: A 867 LYS cc_start: 0.7354 (tptm) cc_final: 0.7092 (tptt) REVERT: A 892 ARG cc_start: 0.6499 (tpt170) cc_final: 0.6030 (mtt-85) REVERT: A 963 LYS cc_start: 0.7211 (tttp) cc_final: 0.6834 (ttpt) REVERT: A 1030 MET cc_start: 0.6970 (ptt) cc_final: 0.5520 (mmm) REVERT: A 1128 HIS cc_start: 0.6699 (m170) cc_final: 0.6452 (m170) REVERT: A 1172 LEU cc_start: 0.6433 (mm) cc_final: 0.6121 (mm) REVERT: A 1204 ASP cc_start: 0.6718 (m-30) cc_final: 0.6244 (m-30) REVERT: A 1335 LYS cc_start: 0.7258 (ttpt) cc_final: 0.6973 (mtmm) REVERT: A 1445 GLN cc_start: 0.8096 (mp10) cc_final: 0.7481 (mt0) REVERT: A 1483 ARG cc_start: 0.5676 (mmt180) cc_final: 0.5098 (tpp80) outliers start: 14 outliers final: 10 residues processed: 144 average time/residue: 0.2652 time to fit residues: 55.6839 Evaluate side-chains 142 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 834 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 121 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 74 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 HIS ** A1413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 12535 Z= 0.351 Angle : 0.567 14.953 16938 Z= 0.293 Chirality : 0.043 0.182 1883 Planarity : 0.004 0.043 2138 Dihedral : 3.801 21.156 1650 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.65 % Favored : 96.28 % Rotamer: Outliers : 1.11 % Allowed : 8.90 % Favored : 89.99 % 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: 1.32 (0.21), residues: 1509 helix: 1.63 (0.17), residues: 859 sheet: 1.11 (0.53), residues: 98 loop : -0.32 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1056 HIS 0.006 0.001 HIS A1365 PHE 0.022 0.002 PHE A 585 TYR 0.013 0.002 TYR A1382 ARG 0.006 0.001 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 1.286 Fit side-chains REVERT: A 94 MET cc_start: 0.1229 (ptt) cc_final: 0.0314 (mpp) REVERT: A 239 ASN cc_start: 0.8356 (t0) cc_final: 0.7976 (t0) REVERT: A 245 ASP cc_start: 0.7695 (m-30) cc_final: 0.7438 (t0) REVERT: A 325 ILE cc_start: 0.8773 (mt) cc_final: 0.8479 (tp) REVERT: A 359 PHE cc_start: 0.8268 (t80) cc_final: 0.7964 (t80) REVERT: A 363 GLN cc_start: 0.7610 (pm20) cc_final: 0.7347 (mt0) REVERT: A 728 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7439 (mm-30) REVERT: A 819 GLU cc_start: 0.8236 (pp20) cc_final: 0.7838 (pp20) REVERT: A 867 LYS cc_start: 0.7518 (tptm) cc_final: 0.7117 (tptt) REVERT: A 892 ARG cc_start: 0.6619 (tpt170) cc_final: 0.6076 (mtt-85) REVERT: A 963 LYS cc_start: 0.7210 (tttp) cc_final: 0.6808 (ttpt) REVERT: A 1030 MET cc_start: 0.6866 (ptt) cc_final: 0.5609 (mmm) REVERT: A 1128 HIS cc_start: 0.6802 (m170) cc_final: 0.6588 (m170) REVERT: A 1335 LYS cc_start: 0.7291 (ttpt) cc_final: 0.7045 (ttmm) REVERT: A 1445 GLN cc_start: 0.8125 (mp10) cc_final: 0.7521 (mt0) REVERT: A 1483 ARG cc_start: 0.5749 (mmt180) cc_final: 0.5002 (tpp80) REVERT: A 1575 GLN cc_start: 0.6902 (tt0) cc_final: 0.6368 (mt0) outliers start: 15 outliers final: 12 residues processed: 141 average time/residue: 0.2613 time to fit residues: 53.6348 Evaluate side-chains 137 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 1351 ASP Chi-restraints excluded: chain A residue 1352 MET Chi-restraints excluded: chain A residue 1425 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 49 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 36 optimal weight: 0.1980 chunk 146 optimal weight: 4.9990 chunk 121 optimal weight: 0.2980 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12535 Z= 0.176 Angle : 0.492 11.550 16938 Z= 0.256 Chirality : 0.040 0.188 1883 Planarity : 0.003 0.055 2138 Dihedral : 3.638 20.217 1650 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.66 % Favored : 97.28 % Rotamer: Outliers : 0.74 % Allowed : 9.56 % Favored : 89.70 % 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 (0.22), residues: 1509 helix: 1.85 (0.18), residues: 855 sheet: 0.89 (0.49), residues: 112 loop : -0.22 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1056 HIS 0.003 0.001 HIS A 608 PHE 0.016 0.001 PHE A 585 TYR 0.012 0.001 TYR A1382 ARG 0.014 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 1.594 Fit side-chains revert: symmetry clash REVERT: A 94 MET cc_start: 0.1217 (ptt) cc_final: 0.0338 (mpp) REVERT: A 239 ASN cc_start: 0.8309 (t0) cc_final: 0.7931 (t0) REVERT: A 245 ASP cc_start: 0.7589 (m-30) cc_final: 0.7280 (t0) REVERT: A 325 ILE cc_start: 0.8732 (mt) cc_final: 0.8433 (tp) REVERT: A 359 PHE cc_start: 0.8250 (t80) cc_final: 0.7948 (t80) REVERT: A 363 GLN cc_start: 0.7603 (pm20) cc_final: 0.7337 (mt0) REVERT: A 457 ASN cc_start: 0.7729 (m110) cc_final: 0.7303 (t0) REVERT: A 728 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7190 (mm-30) REVERT: A 819 GLU cc_start: 0.8209 (pp20) cc_final: 0.7799 (pp20) REVERT: A 867 LYS cc_start: 0.7513 (tptm) cc_final: 0.7082 (tptt) REVERT: A 892 ARG cc_start: 0.6608 (tpt170) cc_final: 0.6147 (mtt-85) REVERT: A 963 LYS cc_start: 0.7176 (tttp) cc_final: 0.6841 (ttpt) REVERT: A 1030 MET cc_start: 0.6975 (ptt) cc_final: 0.5731 (mmm) REVERT: A 1128 HIS cc_start: 0.6696 (m170) cc_final: 0.6461 (m170) REVERT: A 1445 GLN cc_start: 0.8150 (mp10) cc_final: 0.7531 (mt0) REVERT: A 1483 ARG cc_start: 0.5580 (mmt180) cc_final: 0.5008 (tpp80) REVERT: A 1575 GLN cc_start: 0.6959 (tt0) cc_final: 0.6399 (mt0) outliers start: 10 outliers final: 8 residues processed: 138 average time/residue: 0.2816 time to fit residues: 56.6775 Evaluate side-chains 138 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 1351 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 140 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 81 optimal weight: 0.0070 chunk 145 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12535 Z= 0.156 Angle : 0.476 10.148 16938 Z= 0.246 Chirality : 0.039 0.169 1883 Planarity : 0.003 0.036 2138 Dihedral : 3.505 18.939 1650 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.86 % Favored : 97.08 % Rotamer: Outliers : 0.74 % Allowed : 10.08 % Favored : 89.18 % 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 (0.22), residues: 1509 helix: 1.98 (0.18), residues: 855 sheet: 0.85 (0.49), residues: 112 loop : -0.20 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 473 HIS 0.003 0.001 HIS A1036 PHE 0.015 0.001 PHE A 585 TYR 0.012 0.001 TYR A 713 ARG 0.006 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 1.397 Fit side-chains revert: symmetry clash REVERT: A 94 MET cc_start: 0.0848 (ptt) cc_final: 0.0011 (mpp) REVERT: A 239 ASN cc_start: 0.8290 (t0) cc_final: 0.7912 (t0) REVERT: A 245 ASP cc_start: 0.7598 (m-30) cc_final: 0.7279 (t0) REVERT: A 325 ILE cc_start: 0.8728 (mt) cc_final: 0.8432 (tp) REVERT: A 359 PHE cc_start: 0.8245 (t80) cc_final: 0.7951 (t80) REVERT: A 363 GLN cc_start: 0.7605 (pm20) cc_final: 0.7314 (mt0) REVERT: A 457 ASN cc_start: 0.7703 (m110) cc_final: 0.7390 (t0) REVERT: A 728 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7133 (mm-30) REVERT: A 819 GLU cc_start: 0.8166 (pp20) cc_final: 0.7793 (pp20) REVERT: A 867 LYS cc_start: 0.7515 (tptm) cc_final: 0.7086 (tptt) REVERT: A 892 ARG cc_start: 0.6586 (tpt170) cc_final: 0.6117 (mtt-85) REVERT: A 963 LYS cc_start: 0.7264 (tttp) cc_final: 0.6946 (ttpt) REVERT: A 1030 MET cc_start: 0.6965 (ptt) cc_final: 0.5659 (mmm) REVERT: A 1128 HIS cc_start: 0.6769 (m170) cc_final: 0.6555 (m170) REVERT: A 1445 GLN cc_start: 0.8144 (mp10) cc_final: 0.7532 (mt0) REVERT: A 1483 ARG cc_start: 0.5762 (mmt180) cc_final: 0.5134 (tpp80) REVERT: A 1575 GLN cc_start: 0.6922 (tt0) cc_final: 0.6438 (mt0) outliers start: 10 outliers final: 10 residues processed: 141 average time/residue: 0.2603 time to fit residues: 53.8962 Evaluate side-chains 141 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 1271 MET Chi-restraints excluded: chain A residue 1351 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 90 optimal weight: 10.0000 chunk 58 optimal weight: 0.1980 chunk 86 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 99 optimal weight: 0.0670 chunk 71 optimal weight: 0.0970 chunk 13 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 12535 Z= 0.129 Angle : 0.459 9.085 16938 Z= 0.237 Chirality : 0.038 0.163 1883 Planarity : 0.003 0.038 2138 Dihedral : 3.386 18.760 1650 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.46 % Favored : 97.48 % Rotamer: Outliers : 0.52 % Allowed : 10.45 % Favored : 89.03 % 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: 1.79 (0.22), residues: 1509 helix: 2.09 (0.18), residues: 856 sheet: 0.91 (0.50), residues: 112 loop : -0.18 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 473 HIS 0.003 0.001 HIS A1036 PHE 0.013 0.001 PHE A 585 TYR 0.014 0.001 TYR A 911 ARG 0.006 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 142 time to evaluate : 1.391 Fit side-chains revert: symmetry clash REVERT: A 94 MET cc_start: 0.0388 (ptt) cc_final: -0.0295 (mpp) REVERT: A 239 ASN cc_start: 0.8284 (t0) cc_final: 0.7907 (t0) REVERT: A 245 ASP cc_start: 0.7589 (m-30) cc_final: 0.7264 (t0) REVERT: A 325 ILE cc_start: 0.8722 (mt) cc_final: 0.8431 (tp) REVERT: A 359 PHE cc_start: 0.8224 (t80) cc_final: 0.7944 (t80) REVERT: A 363 GLN cc_start: 0.7588 (pm20) cc_final: 0.7284 (mt0) REVERT: A 457 ASN cc_start: 0.7674 (m110) cc_final: 0.7378 (t0) REVERT: A 493 LYS cc_start: 0.7345 (mtmm) cc_final: 0.7011 (ptpt) REVERT: A 564 LEU cc_start: 0.7761 (mt) cc_final: 0.7477 (mt) REVERT: A 728 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7087 (mm-30) REVERT: A 819 GLU cc_start: 0.8122 (pp20) cc_final: 0.7710 (pp20) REVERT: A 867 LYS cc_start: 0.7546 (tptm) cc_final: 0.7140 (tptt) REVERT: A 892 ARG cc_start: 0.6516 (tpt170) cc_final: 0.6061 (mtt-85) REVERT: A 963 LYS cc_start: 0.7259 (tttp) cc_final: 0.6942 (ttpt) REVERT: A 1030 MET cc_start: 0.6971 (ptt) cc_final: 0.5704 (mmm) REVERT: A 1445 GLN cc_start: 0.8152 (mp10) cc_final: 0.7563 (mt0) REVERT: A 1483 ARG cc_start: 0.5752 (mmt180) cc_final: 0.5235 (tpp80) outliers start: 7 outliers final: 7 residues processed: 147 average time/residue: 0.2651 time to fit residues: 57.2899 Evaluate side-chains 143 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 136 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 613 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 139 optimal weight: 2.9990 chunk 127 optimal weight: 9.9990 chunk 135 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 128 optimal weight: 0.0870 chunk 89 optimal weight: 0.9980 chunk 143 optimal weight: 0.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1575 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12535 Z= 0.203 Angle : 0.486 8.831 16938 Z= 0.252 Chirality : 0.039 0.145 1883 Planarity : 0.003 0.040 2138 Dihedral : 3.468 18.769 1650 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.79 % Favored : 97.14 % Rotamer: Outliers : 1.11 % Allowed : 10.01 % Favored : 88.88 % 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: 1.71 (0.22), residues: 1509 helix: 2.00 (0.18), residues: 861 sheet: 0.95 (0.50), residues: 112 loop : -0.21 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1131 HIS 0.003 0.001 HIS A1365 PHE 0.017 0.001 PHE A 585 TYR 0.012 0.001 TYR A1382 ARG 0.008 0.000 ARG A1488 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 1.466 Fit side-chains revert: symmetry clash REVERT: A 94 MET cc_start: 0.0452 (ptt) cc_final: -0.0227 (mpp) REVERT: A 239 ASN cc_start: 0.8323 (t0) cc_final: 0.7938 (t0) REVERT: A 245 ASP cc_start: 0.7620 (m-30) cc_final: 0.7305 (t0) REVERT: A 325 ILE cc_start: 0.8743 (mt) cc_final: 0.8442 (tp) REVERT: A 359 PHE cc_start: 0.8256 (t80) cc_final: 0.7964 (t80) REVERT: A 363 GLN cc_start: 0.7604 (pm20) cc_final: 0.7341 (mt0) REVERT: A 457 ASN cc_start: 0.7713 (m110) cc_final: 0.7384 (t0) REVERT: A 541 ASP cc_start: 0.7915 (m-30) cc_final: 0.7399 (t0) REVERT: A 728 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7114 (mm-30) REVERT: A 819 GLU cc_start: 0.8154 (pp20) cc_final: 0.7771 (pp20) REVERT: A 867 LYS cc_start: 0.7547 (tptm) cc_final: 0.7134 (tptt) REVERT: A 892 ARG cc_start: 0.6512 (tpt170) cc_final: 0.5847 (mtp85) REVERT: A 963 LYS cc_start: 0.7362 (tttp) cc_final: 0.7041 (ttpt) REVERT: A 1030 MET cc_start: 0.6972 (ptt) cc_final: 0.5702 (mmm) REVERT: A 1128 HIS cc_start: 0.6759 (m170) cc_final: 0.6545 (m170) REVERT: A 1445 GLN cc_start: 0.8141 (mp10) cc_final: 0.7566 (mt0) REVERT: A 1483 ARG cc_start: 0.5966 (mmt180) cc_final: 0.5196 (tpp80) REVERT: A 1488 ARG cc_start: 0.6905 (mmt-90) cc_final: 0.6637 (mmt90) REVERT: A 1575 GLN cc_start: 0.6917 (tt0) cc_final: 0.6239 (mt0) REVERT: A 1593 MET cc_start: 0.8272 (tpp) cc_final: 0.7846 (tpp) outliers start: 15 outliers final: 12 residues processed: 141 average time/residue: 0.2546 time to fit residues: 53.2950 Evaluate side-chains 144 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1271 MET Chi-restraints excluded: chain A residue 1351 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 87 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 92 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12535 Z= 0.238 Angle : 0.514 12.443 16938 Z= 0.264 Chirality : 0.041 0.318 1883 Planarity : 0.003 0.040 2138 Dihedral : 3.567 18.689 1650 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.05 % Favored : 96.88 % Rotamer: Outliers : 0.82 % Allowed : 10.30 % Favored : 88.88 % 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: 1.62 (0.22), residues: 1509 helix: 1.93 (0.18), residues: 861 sheet: 0.91 (0.51), residues: 108 loop : -0.26 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1056 HIS 0.004 0.001 HIS A1365 PHE 0.018 0.001 PHE A 585 TYR 0.012 0.001 TYR A 912 ARG 0.006 0.000 ARG A1488 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 1.358 Fit side-chains revert: symmetry clash REVERT: A 94 MET cc_start: 0.1369 (ptt) cc_final: 0.0461 (mpp) REVERT: A 239 ASN cc_start: 0.8331 (t0) cc_final: 0.7951 (t0) REVERT: A 245 ASP cc_start: 0.7628 (m-30) cc_final: 0.7317 (t0) REVERT: A 325 ILE cc_start: 0.8737 (mt) cc_final: 0.8437 (tp) REVERT: A 359 PHE cc_start: 0.8252 (t80) cc_final: 0.8000 (t80) REVERT: A 363 GLN cc_start: 0.7628 (pm20) cc_final: 0.7400 (mt0) REVERT: A 457 ASN cc_start: 0.7759 (m110) cc_final: 0.7403 (t0) REVERT: A 564 LEU cc_start: 0.7734 (mt) cc_final: 0.7439 (mt) REVERT: A 728 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7372 (mm-30) REVERT: A 819 GLU cc_start: 0.8202 (pp20) cc_final: 0.7803 (pp20) REVERT: A 867 LYS cc_start: 0.7576 (tptm) cc_final: 0.7172 (tptt) REVERT: A 892 ARG cc_start: 0.6583 (tpt170) cc_final: 0.5909 (mtp85) REVERT: A 963 LYS cc_start: 0.7360 (tttp) cc_final: 0.7061 (ttpt) REVERT: A 1030 MET cc_start: 0.6966 (ptt) cc_final: 0.5712 (mmm) REVERT: A 1445 GLN cc_start: 0.8165 (mp10) cc_final: 0.7578 (mt0) REVERT: A 1483 ARG cc_start: 0.5951 (mmt180) cc_final: 0.5308 (tpp80) REVERT: A 1593 MET cc_start: 0.8336 (tpp) cc_final: 0.7945 (tpp) outliers start: 11 outliers final: 11 residues processed: 141 average time/residue: 0.2529 time to fit residues: 52.6106 Evaluate side-chains 142 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1271 MET Chi-restraints excluded: chain A residue 1351 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 36 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 123 optimal weight: 0.0870 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 0.2980 chunk 105 optimal weight: 0.0370 chunk 6 optimal weight: 6.9990 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1128 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.167292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.118094 restraints weight = 25223.959| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 3.54 r_work: 0.3058 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 12535 Z= 0.129 Angle : 0.471 12.759 16938 Z= 0.241 Chirality : 0.038 0.136 1883 Planarity : 0.003 0.038 2138 Dihedral : 3.392 18.426 1650 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.59 % Favored : 97.34 % Rotamer: Outliers : 0.67 % Allowed : 10.67 % Favored : 88.66 % 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: 1.83 (0.22), residues: 1509 helix: 2.12 (0.18), residues: 861 sheet: 0.80 (0.50), residues: 112 loop : -0.16 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1131 HIS 0.003 0.001 HIS A1128 PHE 0.013 0.001 PHE A 585 TYR 0.013 0.001 TYR A 713 ARG 0.006 0.000 ARG A 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2668.08 seconds wall clock time: 49 minutes 44.69 seconds (2984.69 seconds total)