Starting phenix.real_space_refine on Fri Mar 15 19:08:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v5b_21051/03_2024/6v5b_21051.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v5b_21051/03_2024/6v5b_21051.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v5b_21051/03_2024/6v5b_21051.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v5b_21051/03_2024/6v5b_21051.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v5b_21051/03_2024/6v5b_21051.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v5b_21051/03_2024/6v5b_21051.pdb" } resolution = 3.7 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= 0.012 sd= 0.101 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: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 Zn 2 6.06 5 P 78 5.49 5 S 70 5.16 5 C 7670 2.51 5 N 2216 2.21 5 O 2526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 440": "NH1" <-> "NH2" Residue "A GLU 449": "OE1" <-> "OE2" Residue "A ARG 544": "NH1" <-> "NH2" Residue "A GLU 602": "OE1" <-> "OE2" Residue "A GLU 735": "OE1" <-> "OE2" Residue "A PHE 775": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 778": "NH1" <-> "NH2" Residue "A ARG 938": "NH1" <-> "NH2" Residue "A ARG 1020": "NH1" <-> "NH2" Residue "A ARG 1032": "NH1" <-> "NH2" Residue "A ARG 1131": "NH1" <-> "NH2" Residue "A ARG 1213": "NH1" <-> "NH2" Residue "A ARG 1248": "NH1" <-> "NH2" Residue "A ARG 1273": "NH1" <-> "NH2" Residue "A GLU 1278": "OE1" <-> "OE2" Residue "A ARG 1296": "NH1" <-> "NH2" Residue "C GLU 502": "OE1" <-> "OE2" Residue "C GLU 518": "OE1" <-> "OE2" Residue "C GLU 536": "OE1" <-> "OE2" Residue "C ASP 579": "OD1" <-> "OD2" Residue "C GLU 596": "OE1" <-> "OE2" Residue "C GLU 610": "OE1" <-> "OE2" Residue "C ARG 670": "NH1" <-> "NH2" Residue "C GLU 701": "OE1" <-> "OE2" Residue "C GLU 748": "OE1" <-> "OE2" Residue "C ARG 750": "NH1" <-> "NH2" Residue "B GLU 512": "OE1" <-> "OE2" Residue "B GLU 536": "OE1" <-> "OE2" Residue "B GLU 540": "OE1" <-> "OE2" Residue "B ARG 670": "NH1" <-> "NH2" Residue "B GLU 745": "OE1" <-> "OE2" Residue "B ARG 746": "NH1" <-> "NH2" 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: 12563 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 908, 7419 Classifications: {'peptide': 908} Link IDs: {'CIS': 2, 'PTRANS': 49, 'TRANS': 856} Chain breaks: 1 Chain: "C" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1750 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 8, 'TRANS': 208} Chain breaks: 4 Chain: "B" Number of atoms: 1739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1739 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 8, 'TRANS': 207} Chain breaks: 4 Chain: "D" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1652 Classifications: {'RNA': 78} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 36, 'rna3p_pyr': 38} Link IDs: {'rna2p': 4, 'rna3p': 73} Chain breaks: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 906 SG CYS A 561 50.511 93.376 40.445 1.00172.12 S ATOM 1864 SG CYS A 676 47.059 93.016 41.817 1.00178.36 S Time building chain proxies: 6.92, per 1000 atoms: 0.55 Number of scatterers: 12563 At special positions: 0 Unit cell: (92.22, 114.48, 167.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Ca 1 19.99 S 70 16.00 P 78 15.00 O 2526 8.00 N 2216 7.00 C 7670 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: 5.91 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1401 " pdb="ZN ZN A1401 " - pdb=" NE2 HIS A 609 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 561 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 676 " 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2540 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 7 sheets defined 45.8% alpha, 8.3% beta 27 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 4.15 Creating SS restraints... Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.067A pdb=" N GLN A 429 " --> pdb=" O PRO A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 449 Processing helix chain 'A' and resid 503 through 512 removed outlier: 3.700A pdb=" N ILE A 508 " --> pdb=" O VAL A 504 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS A 509 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 655 Processing helix chain 'A' and resid 698 through 709 removed outlier: 3.635A pdb=" N ILE A 702 " --> pdb=" O SER A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 723 removed outlier: 3.558A pdb=" N LEU A 723 " --> pdb=" O ALA A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 736 Processing helix chain 'A' and resid 787 through 805 removed outlier: 3.692A pdb=" N LEU A 793 " --> pdb=" O GLN A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 829 removed outlier: 3.751A pdb=" N ARG A 829 " --> pdb=" O LEU A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 876 Proline residue: A 864 - end of helix Processing helix chain 'A' and resid 877 through 884 removed outlier: 3.920A pdb=" N LYS A 881 " --> pdb=" O MET A 877 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU A 882 " --> pdb=" O HIS A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 897 removed outlier: 3.545A pdb=" N LEU A 895 " --> pdb=" O CYS A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 920 Processing helix chain 'A' and resid 944 through 950 Processing helix chain 'A' and resid 965 through 986 removed outlier: 3.839A pdb=" N ALA A 974 " --> pdb=" O PHE A 970 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU A 977 " --> pdb=" O ASP A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1004 removed outlier: 3.732A pdb=" N ILE A1003 " --> pdb=" O TYR A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1015 removed outlier: 3.562A pdb=" N LYS A1015 " --> pdb=" O MET A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1021 removed outlier: 5.973A pdb=" N ASP A1019 " --> pdb=" O LEU A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1055 Processing helix chain 'A' and resid 1056 through 1069 removed outlier: 3.707A pdb=" N ARG A1066 " --> pdb=" O GLN A1062 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE A1069 " --> pdb=" O GLY A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1080 Processing helix chain 'A' and resid 1084 through 1089 Processing helix chain 'A' and resid 1104 through 1115 removed outlier: 3.851A pdb=" N GLU A1109 " --> pdb=" O GLN A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1128 removed outlier: 3.931A pdb=" N LEU A1124 " --> pdb=" O HIS A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1166 removed outlier: 3.724A pdb=" N LEU A1149 " --> pdb=" O ARG A1145 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER A1152 " --> pdb=" O PHE A1148 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLN A1155 " --> pdb=" O ASP A1151 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N THR A1159 " --> pdb=" O GLN A1155 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE A1164 " --> pdb=" O GLU A1160 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE A1166 " --> pdb=" O LEU A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1182 Processing helix chain 'A' and resid 1185 through 1195 removed outlier: 3.585A pdb=" N VAL A1190 " --> pdb=" O THR A1186 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1200 Processing helix chain 'A' and resid 1213 through 1232 removed outlier: 3.578A pdb=" N ASP A1219 " --> pdb=" O LYS A1215 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A1220 " --> pdb=" O THR A1216 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A1221 " --> pdb=" O LEU A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1245 removed outlier: 4.303A pdb=" N VAL A1237 " --> pdb=" O ASP A1233 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A1243 " --> pdb=" O THR A1239 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1256 removed outlier: 4.521A pdb=" N LEU A1254 " --> pdb=" O LYS A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1270 removed outlier: 3.648A pdb=" N LEU A1270 " --> pdb=" O GLN A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1332 Processing helix chain 'A' and resid 1335 through 1348 removed outlier: 3.835A pdb=" N ARG A1346 " --> pdb=" O ARG A1342 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS A1347 " --> pdb=" O PHE A1343 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR A1348 " --> pdb=" O ILE A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1349 through 1356 removed outlier: 4.180A pdb=" N LYS A1353 " --> pdb=" O ARG A1349 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG A1356 " --> pdb=" O LEU A1352 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 521 removed outlier: 3.504A pdb=" N ILE C 515 " --> pdb=" O SER C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 577 Processing helix chain 'C' and resid 607 through 615 removed outlier: 3.771A pdb=" N LEU C 611 " --> pdb=" O ARG C 607 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N SER C 613 " --> pdb=" O TYR C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 629 Processing helix chain 'C' and resid 668 through 685 Processing helix chain 'C' and resid 691 through 699 Processing helix chain 'C' and resid 729 through 750 Processing helix chain 'B' and resid 511 through 523 removed outlier: 3.756A pdb=" N ILE B 515 " --> pdb=" O SER B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 575 Processing helix chain 'B' and resid 596 through 600 removed outlier: 4.163A pdb=" N ASN B 599 " --> pdb=" O GLU B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 609 removed outlier: 3.858A pdb=" N VAL B 608 " --> pdb=" O ASP B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 629 Processing helix chain 'B' and resid 668 through 685 Processing helix chain 'B' and resid 692 through 699 Processing helix chain 'B' and resid 728 through 745 removed outlier: 3.661A pdb=" N LEU B 732 " --> pdb=" O ASN B 728 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS B 734 " --> pdb=" O HIS B 730 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 591 through 594 removed outlier: 12.398A pdb=" N GLU A 602 " --> pdb=" O VAL A 578 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N VAL A 578 " --> pdb=" O GLU A 602 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N PHE A 604 " --> pdb=" O ILE A 576 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N CYS A 618 " --> pdb=" O ILE A 629 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 591 through 594 removed outlier: 5.373A pdb=" N PHE A 601 " --> pdb=" O VAL A 686 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL A 686 " --> pdb=" O PHE A 601 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N GLY A 603 " --> pdb=" O ARG A 684 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1284 through 1290 removed outlier: 5.087A pdb=" N TYR A1284 " --> pdb=" O TYR A1303 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N TYR A1303 " --> pdb=" O TYR A1284 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N THR A1286 " --> pdb=" O ALA A1301 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA A1301 " --> pdb=" O THR A1286 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL A1290 " --> pdb=" O THR A1297 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N TYR A1298 " --> pdb=" O LYS A1313 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS A1313 " --> pdb=" O TYR A1298 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL A1300 " --> pdb=" O CYS A1311 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N CYS A1311 " --> pdb=" O VAL A1300 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL A1302 " --> pdb=" O ILE A1309 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 532 through 534 Processing sheet with id=AA5, first strand: chain 'C' and resid 652 through 653 Processing sheet with id=AA6, first strand: chain 'B' and resid 529 through 534 removed outlier: 3.699A pdb=" N VAL B 546 " --> pdb=" O GLY B 554 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLY B 554 " --> pdb=" O VAL B 546 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE B 548 " --> pdb=" O THR B 552 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N THR B 552 " --> pdb=" O ILE B 548 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 651 through 657 removed outlier: 4.096A pdb=" N TYR B 653 " --> pdb=" O GLY B 664 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY B 664 " --> pdb=" O TYR B 653 " (cutoff:3.500A) 426 hydrogen bonds defined for protein. 1221 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 65 hydrogen bonds 122 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 3.91 Time building geometry restraints manager: 6.29 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: 3013 1.33 - 1.45: 3085 1.45 - 1.57: 6631 1.57 - 1.69: 157 1.69 - 1.82: 110 Bond restraints: 12996 Sorted by residual: bond pdb=" N TYR B 609 " pdb=" CA TYR B 609 " ideal model delta sigma weight residual 1.454 1.533 -0.079 1.34e-02 5.57e+03 3.51e+01 bond pdb=" CB TYR B 609 " pdb=" CG TYR B 609 " ideal model delta sigma weight residual 1.512 1.600 -0.088 2.20e-02 2.07e+03 1.60e+01 bond pdb=" N GLU B 610 " pdb=" CA GLU B 610 " ideal model delta sigma weight residual 1.457 1.509 -0.051 1.29e-02 6.01e+03 1.58e+01 bond pdb=" CA GLU B 610 " pdb=" C GLU B 610 " ideal model delta sigma weight residual 1.523 1.472 0.051 1.34e-02 5.57e+03 1.46e+01 bond pdb=" CA TYR C 609 " pdb=" C TYR C 609 " ideal model delta sigma weight residual 1.523 1.477 0.046 1.34e-02 5.57e+03 1.19e+01 ... (remaining 12991 not shown) Histogram of bond angle deviations from ideal: 95.29 - 103.06: 270 103.06 - 110.83: 4694 110.83 - 118.60: 5861 118.60 - 126.38: 6668 126.38 - 134.15: 404 Bond angle restraints: 17897 Sorted by residual: angle pdb=" CA GLU B 610 " pdb=" C GLU B 610 " pdb=" N LEU B 611 " ideal model delta sigma weight residual 116.84 103.81 13.03 1.71e+00 3.42e-01 5.81e+01 angle pdb=" N GLU B 610 " pdb=" CA GLU B 610 " pdb=" C GLU B 610 " ideal model delta sigma weight residual 110.80 95.29 15.51 2.13e+00 2.20e-01 5.30e+01 angle pdb=" O VAL B 608 " pdb=" C VAL B 608 " pdb=" N TYR B 609 " ideal model delta sigma weight residual 121.80 113.97 7.83 1.13e+00 7.83e-01 4.80e+01 angle pdb=" N ASP A1029 " pdb=" CA ASP A1029 " pdb=" CB ASP A1029 " ideal model delta sigma weight residual 114.17 106.61 7.56 1.14e+00 7.69e-01 4.39e+01 angle pdb=" CA VAL B 608 " pdb=" C VAL B 608 " pdb=" N TYR B 609 " ideal model delta sigma weight residual 117.69 125.24 -7.55 1.27e+00 6.20e-01 3.53e+01 ... (remaining 17892 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.64: 6790 18.64 - 37.28: 859 37.28 - 55.92: 202 55.92 - 74.57: 117 74.57 - 93.21: 13 Dihedral angle restraints: 7981 sinusoidal: 4063 harmonic: 3918 Sorted by residual: dihedral pdb=" CA GLY A 941 " pdb=" C GLY A 941 " pdb=" N ILE A 942 " pdb=" CA ILE A 942 " ideal model delta harmonic sigma weight residual 180.00 133.87 46.13 0 5.00e+00 4.00e-02 8.51e+01 dihedral pdb=" CA VAL A 714 " pdb=" C VAL A 714 " pdb=" N PRO A 715 " pdb=" CA PRO A 715 " ideal model delta harmonic sigma weight residual 180.00 136.29 43.71 0 5.00e+00 4.00e-02 7.64e+01 dihedral pdb=" CA LYS A 748 " pdb=" C LYS A 748 " pdb=" N PRO A 749 " pdb=" CA PRO A 749 " ideal model delta harmonic sigma weight residual -180.00 -147.40 -32.60 0 5.00e+00 4.00e-02 4.25e+01 ... (remaining 7978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1502 0.056 - 0.112: 397 0.112 - 0.168: 82 0.168 - 0.224: 21 0.224 - 0.280: 7 Chirality restraints: 2009 Sorted by residual: chirality pdb=" CB ILE A 656 " pdb=" CA ILE A 656 " pdb=" CG1 ILE A 656 " pdb=" CG2 ILE A 656 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" P U D 89 " pdb=" OP1 U D 89 " pdb=" OP2 U D 89 " pdb=" O5' U D 89 " both_signs ideal model delta sigma weight residual True 2.41 -2.17 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA TYR B 609 " pdb=" N TYR B 609 " pdb=" C TYR B 609 " pdb=" CB TYR B 609 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 2006 not shown) Planarity restraints: 2019 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 608 " -0.028 2.00e-02 2.50e+03 5.47e-02 2.99e+01 pdb=" C VAL C 608 " 0.095 2.00e-02 2.50e+03 pdb=" O VAL C 608 " -0.034 2.00e-02 2.50e+03 pdb=" N TYR C 609 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 714 " -0.053 5.00e-02 4.00e+02 7.93e-02 1.01e+01 pdb=" N PRO A 715 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO A 715 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 715 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A1246 " -0.052 5.00e-02 4.00e+02 7.79e-02 9.71e+00 pdb=" N PRO A1247 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO A1247 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A1247 " -0.044 5.00e-02 4.00e+02 ... (remaining 2016 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 168 2.56 - 3.14: 9356 3.14 - 3.73: 21723 3.73 - 4.31: 26961 4.31 - 4.90: 40927 Nonbonded interactions: 99135 Sorted by model distance: nonbonded pdb=" N GLU B 610 " pdb=" N LEU B 611 " model vdw 1.972 2.560 nonbonded pdb=" CE2 TYR C 609 " pdb=" OE1 GLN C 674 " model vdw 2.078 3.340 nonbonded pdb=" OG SER A 539 " pdb="ZN ZN A1402 " model vdw 2.147 2.230 nonbonded pdb=" N ALA A 542 " pdb="ZN ZN A1402 " model vdw 2.179 2.310 nonbonded pdb=" O VAL A 435 " pdb=" OG1 THR A 565 " model vdw 2.224 2.440 ... (remaining 99130 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = (chain 'C' and resid 493 through 749) } 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 group one per residue 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: 0.760 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: 4.280 Check model and map are aligned: 0.160 Set scattering table: 0.120 Process input model: 40.610 Find NCS groups from input model: 0.440 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 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 : 0.007 0.094 12996 Z= 0.489 Angle : 1.099 15.509 17897 Z= 0.605 Chirality : 0.057 0.280 2009 Planarity : 0.008 0.079 2019 Dihedral : 18.495 93.207 5441 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.69 % Favored : 88.15 % Rotamer: Outliers : 0.50 % Allowed : 11.76 % Favored : 87.74 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 3.08 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.89 (0.17), residues: 1317 helix: -2.70 (0.15), residues: 563 sheet: -3.42 (0.44), residues: 99 loop : -3.78 (0.20), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP C 691 HIS 0.011 0.002 HIS A 774 PHE 0.020 0.003 PHE C 503 TYR 0.029 0.003 TYR C 609 ARG 0.005 0.001 ARG A1126 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 257 time to evaluate : 1.282 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 GLN cc_start: 0.8523 (tp-100) cc_final: 0.7950 (pm20) REVERT: A 544 ARG cc_start: 0.8203 (ttm-80) cc_final: 0.7634 (mtm-85) REVERT: A 600 ILE cc_start: 0.9116 (mp) cc_final: 0.8764 (mt) REVERT: A 602 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8611 (mm-30) REVERT: A 646 GLU cc_start: 0.9052 (tp30) cc_final: 0.8761 (tt0) REVERT: A 659 LEU cc_start: 0.8153 (tp) cc_final: 0.7069 (tp) REVERT: A 662 TRP cc_start: 0.6055 (t-100) cc_final: 0.5118 (t-100) REVERT: A 681 PHE cc_start: 0.8157 (m-80) cc_final: 0.7838 (m-80) REVERT: A 736 GLU cc_start: 0.8652 (mp0) cc_final: 0.8128 (mp0) REVERT: A 740 MET cc_start: 0.9050 (pmm) cc_final: 0.8569 (pmm) REVERT: A 815 LYS cc_start: 0.7664 (mmmt) cc_final: 0.7377 (mttp) REVERT: A 852 ILE cc_start: 0.8639 (tt) cc_final: 0.8413 (tp) REVERT: A 864 PRO cc_start: 0.9189 (Cg_exo) cc_final: 0.8960 (Cg_endo) REVERT: A 1012 LEU cc_start: 0.9150 (tp) cc_final: 0.8891 (tp) REVERT: A 1068 LEU cc_start: 0.9329 (tp) cc_final: 0.9042 (tp) REVERT: A 1081 TYR cc_start: 0.8634 (p90) cc_final: 0.8265 (p90) REVERT: A 1086 LEU cc_start: 0.9101 (mt) cc_final: 0.8675 (mt) REVERT: A 1090 GLU cc_start: 0.8921 (mp0) cc_final: 0.8630 (mp0) REVERT: A 1192 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8234 (tm-30) REVERT: A 1208 ARG cc_start: 0.8326 (tpm170) cc_final: 0.8023 (tpp-160) REVERT: A 1261 PRO cc_start: 0.8808 (Cg_exo) cc_final: 0.8329 (Cg_endo) REVERT: A 1322 MET cc_start: 0.8971 (mtt) cc_final: 0.8401 (mmm) REVERT: C 617 LEU cc_start: 0.8798 (tp) cc_final: 0.8563 (mm) REVERT: C 681 LEU cc_start: 0.8210 (tp) cc_final: 0.7797 (mp) REVERT: C 691 TRP cc_start: 0.7902 (t-100) cc_final: 0.7414 (t60) REVERT: B 512 GLU cc_start: 0.8993 (mp0) cc_final: 0.8371 (mt-10) REVERT: B 535 CYS cc_start: 0.8888 (t) cc_final: 0.8531 (t) REVERT: B 553 TYR cc_start: 0.8353 (m-10) cc_final: 0.8075 (m-80) REVERT: B 573 LEU cc_start: 0.8885 (mm) cc_final: 0.8328 (tp) outliers start: 6 outliers final: 2 residues processed: 262 average time/residue: 0.2812 time to fit residues: 103.2441 Evaluate side-chains 185 residues out of total 1199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 183 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 612 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 108 optimal weight: 20.0000 chunk 42 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 126 optimal weight: 20.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 HIS ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 GLN A 888 GLN A 947 ASN ** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1092 ASN A1096 GLN A1143 ASN ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1266 GLN ** C 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 566 ASN C 599 ASN ** C 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 668 ASN ** C 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 ASN C 736 GLN B 625 HIS ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12996 Z= 0.192 Angle : 0.676 9.847 17897 Z= 0.343 Chirality : 0.040 0.159 2009 Planarity : 0.005 0.058 2019 Dihedral : 17.093 94.886 2651 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.96 % Favored : 90.96 % Rotamer: Outliers : 2.42 % Allowed : 19.60 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 1.54 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.21), residues: 1317 helix: -0.80 (0.21), residues: 579 sheet: -2.04 (0.59), residues: 77 loop : -3.51 (0.20), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 691 HIS 0.009 0.001 HIS C 625 PHE 0.012 0.001 PHE A 572 TYR 0.014 0.002 TYR A1303 ARG 0.005 0.000 ARG A 961 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 198 time to evaluate : 1.354 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 HIS cc_start: 0.9048 (m90) cc_final: 0.8722 (t-170) REVERT: A 519 HIS cc_start: 0.7670 (t-90) cc_final: 0.7029 (t-90) REVERT: A 544 ARG cc_start: 0.8409 (ttm-80) cc_final: 0.7842 (mtm-85) REVERT: A 594 TYR cc_start: 0.8198 (OUTLIER) cc_final: 0.7797 (t80) REVERT: A 600 ILE cc_start: 0.9134 (mp) cc_final: 0.7990 (mt) REVERT: A 602 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8331 (mp0) REVERT: A 646 GLU cc_start: 0.9092 (tp30) cc_final: 0.8751 (tt0) REVERT: A 659 LEU cc_start: 0.7936 (tp) cc_final: 0.7586 (tp) REVERT: A 736 GLU cc_start: 0.8668 (mp0) cc_final: 0.8245 (mp0) REVERT: A 740 MET cc_start: 0.8933 (pmm) cc_final: 0.8470 (pmm) REVERT: A 782 LEU cc_start: 0.8681 (tp) cc_final: 0.8475 (tt) REVERT: A 815 LYS cc_start: 0.7452 (mmmt) cc_final: 0.7088 (mttp) REVERT: A 848 TRP cc_start: 0.8594 (m100) cc_final: 0.7841 (m100) REVERT: A 852 ILE cc_start: 0.8632 (tt) cc_final: 0.8288 (tp) REVERT: A 908 MET cc_start: 0.6346 (mmp) cc_final: 0.6035 (mmt) REVERT: A 947 ASN cc_start: 0.9255 (OUTLIER) cc_final: 0.8876 (t0) REVERT: A 1068 LEU cc_start: 0.9408 (tp) cc_final: 0.9031 (tp) REVERT: A 1081 TYR cc_start: 0.8693 (p90) cc_final: 0.8389 (p90) REVERT: A 1147 GLU cc_start: 0.8788 (pp20) cc_final: 0.8240 (pp20) REVERT: A 1155 GLN cc_start: 0.9123 (pp30) cc_final: 0.8299 (pp30) REVERT: A 1192 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8220 (tm-30) REVERT: A 1196 MET cc_start: 0.8837 (mmm) cc_final: 0.8576 (mmm) REVERT: A 1208 ARG cc_start: 0.8356 (tpm170) cc_final: 0.8129 (tpp-160) REVERT: A 1259 ASN cc_start: 0.7109 (t0) cc_final: 0.6881 (t0) REVERT: A 1303 TYR cc_start: 0.8302 (m-80) cc_final: 0.8076 (m-10) REVERT: C 520 MET cc_start: 0.6704 (mmm) cc_final: 0.6087 (tpt) REVERT: C 521 GLN cc_start: 0.7270 (tm-30) cc_final: 0.7062 (tm-30) REVERT: C 617 LEU cc_start: 0.8878 (tp) cc_final: 0.8606 (mm) REVERT: B 512 GLU cc_start: 0.8984 (mp0) cc_final: 0.8701 (mp0) REVERT: B 535 CYS cc_start: 0.8763 (t) cc_final: 0.8500 (t) REVERT: B 597 TYR cc_start: 0.7846 (m-10) cc_final: 0.7582 (m-80) REVERT: B 601 ILE cc_start: 0.6639 (tp) cc_final: 0.6038 (tp) REVERT: B 613 SER cc_start: 0.8137 (t) cc_final: 0.7728 (m) REVERT: B 630 ARG cc_start: 0.7663 (mmt180) cc_final: 0.7275 (mpt-90) REVERT: B 671 VAL cc_start: 0.7584 (OUTLIER) cc_final: 0.7202 (t) REVERT: B 697 MET cc_start: 0.7014 (mmt) cc_final: 0.6434 (mmt) outliers start: 29 outliers final: 14 residues processed: 220 average time/residue: 0.2291 time to fit residues: 73.8801 Evaluate side-chains 191 residues out of total 1199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 174 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 594 TYR Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 947 ASN Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1223 SER Chi-restraints excluded: chain A residue 1269 CYS Chi-restraints excluded: chain C residue 749 THR Chi-restraints excluded: chain B residue 599 ASN Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 671 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 70 optimal weight: 0.7980 chunk 39 optimal weight: 0.0870 chunk 105 optimal weight: 0.1980 chunk 85 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 126 optimal weight: 20.0000 chunk 136 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 125 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 ASN A 680 HIS ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 GLN A 947 ASN ** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1336 GLN A1340 GLN ** C 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12996 Z= 0.171 Angle : 0.639 10.090 17897 Z= 0.318 Chirality : 0.039 0.142 2009 Planarity : 0.005 0.060 2019 Dihedral : 16.772 91.742 2651 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.25 % Favored : 89.67 % Rotamer: Outliers : 3.17 % Allowed : 21.18 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 1.54 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.23), residues: 1317 helix: -0.04 (0.22), residues: 584 sheet: -2.06 (0.53), residues: 98 loop : -3.32 (0.22), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 523 HIS 0.007 0.001 HIS A 934 PHE 0.010 0.001 PHE A 572 TYR 0.025 0.001 TYR C 609 ARG 0.004 0.000 ARG A1273 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 190 time to evaluate : 1.378 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: A 417 HIS cc_start: 0.9033 (OUTLIER) cc_final: 0.8711 (t-170) REVERT: A 519 HIS cc_start: 0.7742 (t-90) cc_final: 0.7242 (t-90) REVERT: A 544 ARG cc_start: 0.8446 (ttm-80) cc_final: 0.7801 (mtm-85) REVERT: A 600 ILE cc_start: 0.9174 (mp) cc_final: 0.8038 (mt) REVERT: A 602 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8433 (mp0) REVERT: A 646 GLU cc_start: 0.9138 (tp30) cc_final: 0.8806 (tt0) REVERT: A 736 GLU cc_start: 0.8616 (mp0) cc_final: 0.8182 (mp0) REVERT: A 740 MET cc_start: 0.8875 (pmm) cc_final: 0.8407 (pmm) REVERT: A 758 ASP cc_start: 0.7960 (t70) cc_final: 0.7405 (t70) REVERT: A 759 ARG cc_start: 0.8664 (mmp-170) cc_final: 0.8367 (mmm160) REVERT: A 815 LYS cc_start: 0.7487 (mmmt) cc_final: 0.7223 (mttp) REVERT: A 834 MET cc_start: 0.6854 (OUTLIER) cc_final: 0.6630 (ptp) REVERT: A 852 ILE cc_start: 0.8605 (tt) cc_final: 0.8273 (tp) REVERT: A 918 SER cc_start: 0.9406 (p) cc_final: 0.9190 (p) REVERT: A 1040 MET cc_start: 0.9174 (mmm) cc_final: 0.8966 (mmt) REVERT: A 1081 TYR cc_start: 0.8733 (p90) cc_final: 0.8439 (p90) REVERT: A 1147 GLU cc_start: 0.8819 (pp20) cc_final: 0.8260 (pp20) REVERT: A 1155 GLN cc_start: 0.9085 (pp30) cc_final: 0.8160 (pp30) REVERT: A 1192 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8136 (tm-30) REVERT: A 1196 MET cc_start: 0.8754 (mmm) cc_final: 0.8521 (mmm) REVERT: A 1208 ARG cc_start: 0.8323 (tpm170) cc_final: 0.8091 (tpp-160) REVERT: A 1273 ARG cc_start: 0.8549 (mmm160) cc_final: 0.8315 (mmm160) REVERT: A 1303 TYR cc_start: 0.8411 (m-80) cc_final: 0.8171 (m-10) REVERT: A 1322 MET cc_start: 0.8850 (mtt) cc_final: 0.8253 (mmm) REVERT: C 512 GLU cc_start: 0.8912 (tp30) cc_final: 0.8173 (tp30) REVERT: C 520 MET cc_start: 0.7022 (mmm) cc_final: 0.6535 (tpt) REVERT: C 617 LEU cc_start: 0.8853 (tp) cc_final: 0.8204 (mt) REVERT: C 681 LEU cc_start: 0.8104 (tp) cc_final: 0.7495 (mp) REVERT: C 691 TRP cc_start: 0.7487 (t60) cc_final: 0.6631 (t-100) REVERT: B 512 GLU cc_start: 0.8974 (mp0) cc_final: 0.8686 (mp0) REVERT: B 535 CYS cc_start: 0.8723 (t) cc_final: 0.8428 (t) REVERT: B 553 TYR cc_start: 0.7948 (m-80) cc_final: 0.7609 (m-80) REVERT: B 573 LEU cc_start: 0.8303 (mp) cc_final: 0.8078 (mp) REVERT: B 597 TYR cc_start: 0.7927 (m-10) cc_final: 0.7697 (m-80) REVERT: B 613 SER cc_start: 0.8265 (t) cc_final: 0.7919 (m) REVERT: B 671 VAL cc_start: 0.7535 (t) cc_final: 0.7330 (t) REVERT: B 697 MET cc_start: 0.6932 (mmt) cc_final: 0.6172 (mmm) outliers start: 38 outliers final: 20 residues processed: 217 average time/residue: 0.2514 time to fit residues: 80.1489 Evaluate side-chains 198 residues out of total 1199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 176 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 663 ASN Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 834 MET Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1223 SER Chi-restraints excluded: chain A residue 1233 ASP Chi-restraints excluded: chain A residue 1269 CYS Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 685 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 0.6980 chunk 95 optimal weight: 0.0270 chunk 65 optimal weight: 0.3980 chunk 13 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 126 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 36 optimal weight: 0.5980 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 GLN A 903 HIS ** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 ASN ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1267 GLN ** C 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 HIS ** C 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12996 Z= 0.181 Angle : 0.626 9.781 17897 Z= 0.311 Chirality : 0.038 0.141 2009 Planarity : 0.004 0.056 2019 Dihedral : 16.574 91.660 2651 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.72 % Favored : 90.21 % Rotamer: Outliers : 4.17 % Allowed : 22.52 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.23), residues: 1317 helix: 0.34 (0.23), residues: 581 sheet: -2.30 (0.51), residues: 101 loop : -3.14 (0.22), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 523 HIS 0.005 0.001 HIS A 774 PHE 0.013 0.001 PHE A 448 TYR 0.022 0.001 TYR C 609 ARG 0.003 0.000 ARG A 753 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 185 time to evaluate : 1.011 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 HIS cc_start: 0.9044 (OUTLIER) cc_final: 0.8709 (t-170) REVERT: A 544 ARG cc_start: 0.8508 (ttm-80) cc_final: 0.7790 (mtm-85) REVERT: A 600 ILE cc_start: 0.9213 (mp) cc_final: 0.8132 (mp) REVERT: A 602 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8509 (mp0) REVERT: A 635 MET cc_start: 0.8772 (ttm) cc_final: 0.8533 (ptm) REVERT: A 646 GLU cc_start: 0.9051 (tp30) cc_final: 0.8751 (tt0) REVERT: A 736 GLU cc_start: 0.8586 (mp0) cc_final: 0.8182 (mp0) REVERT: A 740 MET cc_start: 0.8801 (pmm) cc_final: 0.8385 (pmm) REVERT: A 815 LYS cc_start: 0.7487 (mmmt) cc_final: 0.7016 (mttp) REVERT: A 852 ILE cc_start: 0.8522 (tt) cc_final: 0.8201 (tp) REVERT: A 918 SER cc_start: 0.9413 (p) cc_final: 0.9189 (p) REVERT: A 1040 MET cc_start: 0.9212 (mmm) cc_final: 0.9007 (mmt) REVERT: A 1081 TYR cc_start: 0.8765 (p90) cc_final: 0.8471 (p90) REVERT: A 1155 GLN cc_start: 0.8954 (pp30) cc_final: 0.7843 (pp30) REVERT: A 1192 GLU cc_start: 0.8929 (tm-30) cc_final: 0.8173 (tm-30) REVERT: A 1196 MET cc_start: 0.8820 (mmm) cc_final: 0.8509 (mmm) REVERT: A 1208 ARG cc_start: 0.8344 (tpm170) cc_final: 0.8045 (tpp-160) REVERT: A 1252 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.8094 (t80) REVERT: A 1256 GLN cc_start: 0.7448 (mm110) cc_final: 0.7195 (tt0) REVERT: A 1273 ARG cc_start: 0.8569 (mmm160) cc_final: 0.8291 (mmm160) REVERT: A 1303 TYR cc_start: 0.8404 (m-80) cc_final: 0.8176 (m-10) REVERT: A 1322 MET cc_start: 0.8826 (mtt) cc_final: 0.8244 (mmm) REVERT: A 1334 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.7122 (p90) REVERT: C 512 GLU cc_start: 0.8893 (tp30) cc_final: 0.8095 (tp30) REVERT: C 520 MET cc_start: 0.6951 (mmm) cc_final: 0.6561 (tpt) REVERT: C 617 LEU cc_start: 0.8876 (tp) cc_final: 0.8331 (mt) REVERT: C 681 LEU cc_start: 0.8107 (tp) cc_final: 0.7446 (mt) REVERT: B 512 GLU cc_start: 0.9045 (mp0) cc_final: 0.8674 (mp0) REVERT: B 535 CYS cc_start: 0.8759 (t) cc_final: 0.8452 (t) REVERT: B 553 TYR cc_start: 0.7812 (m-80) cc_final: 0.7356 (m-80) REVERT: B 573 LEU cc_start: 0.8327 (mp) cc_final: 0.8120 (mp) REVERT: B 597 TYR cc_start: 0.7963 (m-10) cc_final: 0.7725 (m-80) REVERT: B 613 SER cc_start: 0.8349 (t) cc_final: 0.8001 (m) REVERT: B 655 MET cc_start: 0.7848 (tmm) cc_final: 0.7382 (ppp) REVERT: B 671 VAL cc_start: 0.7619 (t) cc_final: 0.7418 (t) outliers start: 50 outliers final: 32 residues processed: 221 average time/residue: 0.1829 time to fit residues: 61.1846 Evaluate side-chains 203 residues out of total 1199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 168 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 688 PHE Chi-restraints excluded: chain A residue 699 MET Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 791 GLN Chi-restraints excluded: chain A residue 814 ASP Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1223 SER Chi-restraints excluded: chain A residue 1233 ASP Chi-restraints excluded: chain A residue 1252 PHE Chi-restraints excluded: chain A residue 1269 CYS Chi-restraints excluded: chain A residue 1334 PHE Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 599 ASN Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 685 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 1 optimal weight: 0.6980 chunk 100 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 92 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 614 ASN A 639 ASN ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 GLN ** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1173 HIS ** A1340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 HIS ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12996 Z= 0.305 Angle : 0.719 9.669 17897 Z= 0.362 Chirality : 0.041 0.172 2009 Planarity : 0.005 0.053 2019 Dihedral : 16.647 93.188 2651 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.78 % Favored : 89.14 % Rotamer: Outliers : 4.42 % Allowed : 24.02 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.23), residues: 1317 helix: 0.45 (0.23), residues: 577 sheet: -2.67 (0.51), residues: 101 loop : -3.07 (0.22), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1258 HIS 0.008 0.001 HIS A 912 PHE 0.023 0.002 PHE B 580 TYR 0.027 0.002 TYR C 609 ARG 0.004 0.000 ARG A 829 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 170 time to evaluate : 1.607 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: symmetry clash revert: symmetry clash REVERT: A 526 ASP cc_start: 0.8858 (m-30) cc_final: 0.8631 (m-30) REVERT: A 544 ARG cc_start: 0.8517 (ttm-80) cc_final: 0.7955 (mtm-85) REVERT: A 600 ILE cc_start: 0.9241 (mp) cc_final: 0.8487 (mm) REVERT: A 602 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8604 (mp0) REVERT: A 646 GLU cc_start: 0.9174 (tp30) cc_final: 0.8858 (tt0) REVERT: A 731 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8417 (mp10) REVERT: A 736 GLU cc_start: 0.8584 (mp0) cc_final: 0.8193 (mp0) REVERT: A 740 MET cc_start: 0.8650 (pmm) cc_final: 0.8232 (pmm) REVERT: A 815 LYS cc_start: 0.7636 (mmmt) cc_final: 0.7199 (mttp) REVERT: A 852 ILE cc_start: 0.8275 (tt) cc_final: 0.7965 (tp) REVERT: A 1155 GLN cc_start: 0.8864 (pp30) cc_final: 0.8480 (pp30) REVERT: A 1192 GLU cc_start: 0.8949 (tm-30) cc_final: 0.8322 (tm-30) REVERT: A 1196 MET cc_start: 0.8925 (mmm) cc_final: 0.8455 (mmm) REVERT: A 1208 ARG cc_start: 0.8311 (tpm170) cc_final: 0.7995 (tpp-160) REVERT: A 1244 CYS cc_start: 0.7463 (t) cc_final: 0.7208 (t) REVERT: A 1252 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.8166 (t80) REVERT: A 1256 GLN cc_start: 0.7590 (mm110) cc_final: 0.7222 (mm110) REVERT: A 1273 ARG cc_start: 0.8676 (mmm160) cc_final: 0.8422 (mmm160) REVERT: C 512 GLU cc_start: 0.8914 (tp30) cc_final: 0.8154 (tp30) REVERT: C 520 MET cc_start: 0.7024 (mmm) cc_final: 0.6675 (tmm) REVERT: C 617 LEU cc_start: 0.8846 (tp) cc_final: 0.8243 (mt) REVERT: B 517 HIS cc_start: 0.8534 (OUTLIER) cc_final: 0.8117 (t70) REVERT: B 535 CYS cc_start: 0.8671 (t) cc_final: 0.8275 (t) REVERT: B 553 TYR cc_start: 0.7696 (m-80) cc_final: 0.6940 (m-80) REVERT: B 573 LEU cc_start: 0.8415 (mp) cc_final: 0.8210 (mp) REVERT: B 597 TYR cc_start: 0.8019 (m-10) cc_final: 0.7801 (m-80) REVERT: B 655 MET cc_start: 0.7949 (tmm) cc_final: 0.7591 (ppp) REVERT: B 665 TRP cc_start: 0.3445 (m-90) cc_final: 0.3025 (m-90) REVERT: B 697 MET cc_start: 0.7533 (mmt) cc_final: 0.6914 (mmp) outliers start: 53 outliers final: 38 residues processed: 209 average time/residue: 0.2142 time to fit residues: 67.5844 Evaluate side-chains 197 residues out of total 1199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 156 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 688 PHE Chi-restraints excluded: chain A residue 699 MET Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 731 GLN Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 814 ASP Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1136 ASN Chi-restraints excluded: chain A residue 1159 THR Chi-restraints excluded: chain A residue 1174 LEU Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1223 SER Chi-restraints excluded: chain A residue 1233 ASP Chi-restraints excluded: chain A residue 1252 PHE Chi-restraints excluded: chain A residue 1269 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain B residue 517 HIS Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 579 ASP Chi-restraints excluded: chain B residue 599 ASN Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 685 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 0.2980 chunk 120 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 78 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1340 GLN ** C 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 GLN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12996 Z= 0.222 Angle : 0.664 9.761 17897 Z= 0.330 Chirality : 0.040 0.148 2009 Planarity : 0.004 0.051 2019 Dihedral : 16.542 92.038 2651 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer: Outliers : 4.59 % Allowed : 24.44 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.91 (0.23), residues: 1317 helix: 0.63 (0.23), residues: 577 sheet: -2.49 (0.51), residues: 100 loop : -3.02 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 523 HIS 0.006 0.001 HIS C 625 PHE 0.027 0.002 PHE B 580 TYR 0.013 0.001 TYR A1236 ARG 0.002 0.000 ARG A1273 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 164 time to evaluate : 1.249 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 HIS cc_start: 0.8985 (m90) cc_final: 0.8671 (t-170) REVERT: A 544 ARG cc_start: 0.8524 (ttm-80) cc_final: 0.7936 (mtm-85) REVERT: A 548 ARG cc_start: 0.8603 (ttt-90) cc_final: 0.8317 (ttt-90) REVERT: A 600 ILE cc_start: 0.9191 (mp) cc_final: 0.8456 (mm) REVERT: A 646 GLU cc_start: 0.9170 (tp30) cc_final: 0.8876 (tt0) REVERT: A 731 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.8423 (mp10) REVERT: A 736 GLU cc_start: 0.8560 (mp0) cc_final: 0.8176 (mp0) REVERT: A 740 MET cc_start: 0.8767 (pmm) cc_final: 0.8258 (pmm) REVERT: A 774 HIS cc_start: 0.6075 (OUTLIER) cc_final: 0.5867 (m-70) REVERT: A 815 LYS cc_start: 0.7597 (mmmt) cc_final: 0.7135 (mttp) REVERT: A 852 ILE cc_start: 0.8178 (tt) cc_final: 0.7774 (tp) REVERT: A 918 SER cc_start: 0.9470 (p) cc_final: 0.9211 (p) REVERT: A 1192 GLU cc_start: 0.8979 (tm-30) cc_final: 0.8341 (tm-30) REVERT: A 1196 MET cc_start: 0.8842 (mmm) cc_final: 0.8424 (mmm) REVERT: A 1208 ARG cc_start: 0.8265 (tpm170) cc_final: 0.7940 (tpp-160) REVERT: A 1244 CYS cc_start: 0.7516 (t) cc_final: 0.7239 (t) REVERT: A 1252 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.8094 (t80) REVERT: A 1273 ARG cc_start: 0.8555 (mmm160) cc_final: 0.8282 (mmm160) REVERT: C 516 LEU cc_start: 0.9353 (tt) cc_final: 0.8971 (pp) REVERT: C 617 LEU cc_start: 0.8785 (tp) cc_final: 0.8519 (mm) REVERT: C 657 CYS cc_start: 0.5040 (OUTLIER) cc_final: 0.4638 (m) REVERT: B 517 HIS cc_start: 0.8573 (OUTLIER) cc_final: 0.8365 (t-170) REVERT: B 535 CYS cc_start: 0.8655 (t) cc_final: 0.8220 (t) REVERT: B 553 TYR cc_start: 0.7598 (m-80) cc_final: 0.6885 (m-80) REVERT: B 597 TYR cc_start: 0.8050 (m-10) cc_final: 0.7806 (m-80) REVERT: B 655 MET cc_start: 0.8003 (tmm) cc_final: 0.7801 (ppp) REVERT: B 697 MET cc_start: 0.7597 (mmt) cc_final: 0.7286 (mmt) outliers start: 55 outliers final: 36 residues processed: 206 average time/residue: 0.2126 time to fit residues: 66.2009 Evaluate side-chains 203 residues out of total 1199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 162 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 688 PHE Chi-restraints excluded: chain A residue 699 MET Chi-restraints excluded: chain A residue 731 GLN Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 774 HIS Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1136 ASN Chi-restraints excluded: chain A residue 1159 THR Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1223 SER Chi-restraints excluded: chain A residue 1233 ASP Chi-restraints excluded: chain A residue 1252 PHE Chi-restraints excluded: chain A residue 1258 TRP Chi-restraints excluded: chain A residue 1269 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain C residue 657 CYS Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain B residue 517 HIS Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 579 ASP Chi-restraints excluded: chain B residue 599 ASN Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 685 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 76 optimal weight: 0.0980 chunk 98 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 75 optimal weight: 0.2980 chunk 133 optimal weight: 6.9990 chunk 83 optimal weight: 0.0870 chunk 81 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 GLN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 12996 Z= 0.158 Angle : 0.631 10.002 17897 Z= 0.310 Chirality : 0.038 0.169 2009 Planarity : 0.004 0.052 2019 Dihedral : 16.376 90.298 2651 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 3.34 % Allowed : 25.85 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.80 (0.24), residues: 1317 helix: 0.70 (0.23), residues: 578 sheet: -2.27 (0.53), residues: 97 loop : -2.96 (0.22), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 523 HIS 0.004 0.001 HIS C 625 PHE 0.034 0.001 PHE B 580 TYR 0.010 0.001 TYR A1236 ARG 0.003 0.000 ARG B 570 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 169 time to evaluate : 1.149 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 602 GLU cc_start: 0.8425 (mp0) cc_final: 0.8088 (mp0) REVERT: A 635 MET cc_start: 0.8889 (ttp) cc_final: 0.8613 (ppp) REVERT: A 646 GLU cc_start: 0.9164 (tp30) cc_final: 0.8879 (tt0) REVERT: A 731 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8508 (mp10) REVERT: A 736 GLU cc_start: 0.8511 (mp0) cc_final: 0.8133 (mp0) REVERT: A 740 MET cc_start: 0.8811 (pmm) cc_final: 0.8340 (pmm) REVERT: A 747 THR cc_start: 0.7631 (t) cc_final: 0.7231 (t) REVERT: A 815 LYS cc_start: 0.7551 (mmmt) cc_final: 0.7042 (mttp) REVERT: A 852 ILE cc_start: 0.8107 (tt) cc_final: 0.7733 (tp) REVERT: A 1040 MET cc_start: 0.9069 (tpp) cc_final: 0.8702 (mmt) REVERT: A 1126 ARG cc_start: 0.7540 (ttt180) cc_final: 0.7320 (tpt-90) REVERT: A 1192 GLU cc_start: 0.8945 (tm-30) cc_final: 0.8295 (tm-30) REVERT: A 1196 MET cc_start: 0.8788 (mmm) cc_final: 0.8392 (mmm) REVERT: A 1208 ARG cc_start: 0.8227 (tpm170) cc_final: 0.7907 (tpp-160) REVERT: A 1241 MET cc_start: 0.9047 (tpt) cc_final: 0.8823 (mmm) REVERT: A 1244 CYS cc_start: 0.7471 (t) cc_final: 0.7216 (t) REVERT: A 1252 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.8063 (t80) REVERT: C 516 LEU cc_start: 0.9341 (tt) cc_final: 0.8920 (pp) REVERT: C 520 MET cc_start: 0.6902 (mmm) cc_final: 0.6428 (tmm) REVERT: C 657 CYS cc_start: 0.4854 (OUTLIER) cc_final: 0.4438 (m) REVERT: B 535 CYS cc_start: 0.8726 (t) cc_final: 0.8295 (t) REVERT: B 553 TYR cc_start: 0.7565 (m-80) cc_final: 0.7052 (m-80) REVERT: B 597 TYR cc_start: 0.8125 (m-10) cc_final: 0.7925 (m-80) REVERT: B 697 MET cc_start: 0.7616 (mmt) cc_final: 0.7044 (mmt) outliers start: 40 outliers final: 27 residues processed: 200 average time/residue: 0.2204 time to fit residues: 66.9110 Evaluate side-chains 188 residues out of total 1199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 158 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 688 PHE Chi-restraints excluded: chain A residue 699 MET Chi-restraints excluded: chain A residue 731 GLN Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1159 THR Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1223 SER Chi-restraints excluded: chain A residue 1252 PHE Chi-restraints excluded: chain A residue 1258 TRP Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain C residue 657 CYS Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain C residue 749 THR Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 649 GLN Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 685 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 105 optimal weight: 20.0000 chunk 121 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 GLN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 12996 Z= 0.403 Angle : 0.807 9.330 17897 Z= 0.404 Chirality : 0.045 0.204 2009 Planarity : 0.005 0.046 2019 Dihedral : 16.559 92.063 2651 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 20.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.16 % Favored : 88.76 % Rotamer: Outliers : 4.00 % Allowed : 25.85 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.97 (0.23), residues: 1317 helix: 0.55 (0.22), residues: 581 sheet: -2.37 (0.53), residues: 98 loop : -3.05 (0.22), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1258 HIS 0.014 0.002 HIS A 774 PHE 0.023 0.002 PHE A 448 TYR 0.025 0.003 TYR C 609 ARG 0.012 0.001 ARG A1273 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 150 time to evaluate : 1.412 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: A 548 ARG cc_start: 0.8606 (ttt-90) cc_final: 0.8293 (ttt-90) REVERT: A 635 MET cc_start: 0.9110 (ttp) cc_final: 0.8909 (ptm) REVERT: A 646 GLU cc_start: 0.9187 (tp30) cc_final: 0.8923 (tt0) REVERT: A 736 GLU cc_start: 0.8552 (mp0) cc_final: 0.8188 (mp0) REVERT: A 740 MET cc_start: 0.8683 (pmm) cc_final: 0.8191 (pmm) REVERT: A 815 LYS cc_start: 0.7664 (mmmt) cc_final: 0.7215 (mttp) REVERT: A 852 ILE cc_start: 0.8171 (tt) cc_final: 0.7844 (tp) REVERT: A 1192 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8191 (tm-30) REVERT: A 1196 MET cc_start: 0.8976 (mmm) cc_final: 0.8537 (mmm) REVERT: A 1208 ARG cc_start: 0.8244 (tpm170) cc_final: 0.7874 (tpp-160) REVERT: A 1252 PHE cc_start: 0.8627 (OUTLIER) cc_final: 0.8221 (t80) REVERT: A 1256 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7217 (mm110) REVERT: C 655 MET cc_start: 0.7824 (tpt) cc_final: 0.7522 (tmm) REVERT: C 737 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8620 (mp0) REVERT: B 522 ARG cc_start: 0.6680 (mmt180) cc_final: 0.6354 (mmt180) REVERT: B 535 CYS cc_start: 0.8761 (t) cc_final: 0.8284 (t) REVERT: B 553 TYR cc_start: 0.7260 (m-80) cc_final: 0.6466 (m-80) REVERT: B 597 TYR cc_start: 0.8137 (m-10) cc_final: 0.7914 (m-80) REVERT: B 649 GLN cc_start: 0.7341 (OUTLIER) cc_final: 0.6514 (pm20) REVERT: B 697 MET cc_start: 0.7702 (mmt) cc_final: 0.7316 (mmt) outliers start: 48 outliers final: 34 residues processed: 182 average time/residue: 0.2167 time to fit residues: 60.5481 Evaluate side-chains 183 residues out of total 1199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 146 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 688 PHE Chi-restraints excluded: chain A residue 699 MET Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 814 ASP Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1136 ASN Chi-restraints excluded: chain A residue 1159 THR Chi-restraints excluded: chain A residue 1164 ILE Chi-restraints excluded: chain A residue 1174 LEU Chi-restraints excluded: chain A residue 1183 ASN Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1223 SER Chi-restraints excluded: chain A residue 1233 ASP Chi-restraints excluded: chain A residue 1252 PHE Chi-restraints excluded: chain A residue 1256 GLN Chi-restraints excluded: chain A residue 1258 TRP Chi-restraints excluded: chain A residue 1269 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain C residue 749 THR Chi-restraints excluded: chain B residue 599 ASN Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 649 GLN Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 685 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 128 optimal weight: 3.9990 chunk 117 optimal weight: 9.9990 chunk 124 optimal weight: 0.8980 chunk 75 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 112 optimal weight: 0.0000 chunk 118 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 overall best weight: 2.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12996 Z= 0.259 Angle : 0.717 11.693 17897 Z= 0.354 Chirality : 0.042 0.337 2009 Planarity : 0.004 0.050 2019 Dihedral : 16.506 90.938 2651 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.40 % Favored : 89.60 % Rotamer: Outliers : 3.59 % Allowed : 26.61 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.88 (0.23), residues: 1317 helix: 0.66 (0.22), residues: 580 sheet: -2.30 (0.53), residues: 99 loop : -3.05 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 523 HIS 0.013 0.001 HIS A 774 PHE 0.017 0.002 PHE A1110 TYR 0.022 0.002 TYR C 609 ARG 0.007 0.000 ARG A1273 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 152 time to evaluate : 1.406 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: A 548 ARG cc_start: 0.8600 (ttt-90) cc_final: 0.8284 (ttt-90) REVERT: A 636 MET cc_start: 0.8710 (tmm) cc_final: 0.8394 (tmm) REVERT: A 646 GLU cc_start: 0.9154 (tp30) cc_final: 0.8903 (tt0) REVERT: A 682 MET cc_start: 0.8239 (tpp) cc_final: 0.7939 (tpp) REVERT: A 688 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7753 (t80) REVERT: A 731 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8316 (mp10) REVERT: A 736 GLU cc_start: 0.8507 (mp0) cc_final: 0.8148 (mp0) REVERT: A 815 LYS cc_start: 0.7601 (mmmt) cc_final: 0.7164 (mttp) REVERT: A 1040 MET cc_start: 0.9185 (tpp) cc_final: 0.8746 (mmt) REVERT: A 1192 GLU cc_start: 0.8912 (tm-30) cc_final: 0.8306 (tm-30) REVERT: A 1196 MET cc_start: 0.8906 (mmm) cc_final: 0.8467 (mmm) REVERT: A 1208 ARG cc_start: 0.8210 (tpm170) cc_final: 0.7833 (tpp-160) REVERT: A 1252 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.8103 (t80) REVERT: A 1273 ARG cc_start: 0.8706 (mmm160) cc_final: 0.8384 (mmm160) REVERT: C 520 MET cc_start: 0.6917 (mmm) cc_final: 0.6494 (tmm) REVERT: B 535 CYS cc_start: 0.8765 (t) cc_final: 0.8319 (t) REVERT: B 553 TYR cc_start: 0.7319 (m-80) cc_final: 0.6574 (m-80) REVERT: B 597 TYR cc_start: 0.8228 (m-10) cc_final: 0.8015 (m-80) REVERT: B 697 MET cc_start: 0.7667 (mmt) cc_final: 0.7387 (mmt) outliers start: 43 outliers final: 34 residues processed: 180 average time/residue: 0.2269 time to fit residues: 62.3964 Evaluate side-chains 186 residues out of total 1199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 149 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 688 PHE Chi-restraints excluded: chain A residue 699 MET Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 731 GLN Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 755 ASP Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1159 THR Chi-restraints excluded: chain A residue 1174 LEU Chi-restraints excluded: chain A residue 1183 ASN Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1223 SER Chi-restraints excluded: chain A residue 1252 PHE Chi-restraints excluded: chain A residue 1258 TRP Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 749 THR Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 599 ASN Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 685 HIS Chi-restraints excluded: chain B residue 698 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 91 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 87 optimal weight: 5.9990 chunk 117 optimal weight: 0.0060 overall best weight: 1.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 531 ASN ** C 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 GLN B 660 HIS ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12996 Z= 0.194 Angle : 0.686 10.986 17897 Z= 0.336 Chirality : 0.040 0.255 2009 Planarity : 0.004 0.051 2019 Dihedral : 16.401 89.089 2651 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.25 % Favored : 89.75 % Rotamer: Outliers : 3.42 % Allowed : 26.44 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.74 (0.24), residues: 1317 helix: 0.77 (0.23), residues: 580 sheet: -2.16 (0.54), residues: 98 loop : -2.98 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 523 HIS 0.010 0.001 HIS A 774 PHE 0.023 0.001 PHE A 448 TYR 0.019 0.001 TYR C 609 ARG 0.006 0.000 ARG A1273 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 159 time to evaluate : 1.228 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: A 548 ARG cc_start: 0.8572 (ttt-90) cc_final: 0.8247 (ttt-90) REVERT: A 636 MET cc_start: 0.8592 (tmm) cc_final: 0.8316 (tmm) REVERT: A 646 GLU cc_start: 0.9140 (tp30) cc_final: 0.8901 (tt0) REVERT: A 688 PHE cc_start: 0.8234 (OUTLIER) cc_final: 0.7841 (t80) REVERT: A 731 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8421 (mp10) REVERT: A 736 GLU cc_start: 0.8470 (mp0) cc_final: 0.8078 (mp0) REVERT: A 815 LYS cc_start: 0.7581 (mmmt) cc_final: 0.7146 (mttp) REVERT: A 1040 MET cc_start: 0.9121 (tpp) cc_final: 0.8680 (mmt) REVERT: A 1192 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8285 (tm-30) REVERT: A 1196 MET cc_start: 0.8872 (mmm) cc_final: 0.8432 (mmm) REVERT: A 1208 ARG cc_start: 0.8162 (tpm170) cc_final: 0.7790 (tpp-160) REVERT: A 1222 GLU cc_start: 0.9122 (OUTLIER) cc_final: 0.8676 (mm-30) REVERT: A 1241 MET cc_start: 0.9045 (tpt) cc_final: 0.8797 (mmm) REVERT: A 1252 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.8094 (t80) REVERT: A 1273 ARG cc_start: 0.8612 (mmm160) cc_final: 0.8262 (mmm160) REVERT: A 1322 MET cc_start: 0.8707 (mtm) cc_final: 0.7744 (mmm) REVERT: C 516 LEU cc_start: 0.9416 (tt) cc_final: 0.8920 (pp) REVERT: C 520 MET cc_start: 0.6886 (mmm) cc_final: 0.6233 (tmm) REVERT: B 522 ARG cc_start: 0.5979 (mmt180) cc_final: 0.5180 (mmt180) REVERT: B 535 CYS cc_start: 0.8730 (t) cc_final: 0.8280 (t) REVERT: B 553 TYR cc_start: 0.7317 (m-80) cc_final: 0.6797 (m-80) REVERT: B 597 TYR cc_start: 0.8222 (m-10) cc_final: 0.7979 (m-80) REVERT: B 697 MET cc_start: 0.7636 (mmt) cc_final: 0.7359 (mmt) outliers start: 41 outliers final: 35 residues processed: 185 average time/residue: 0.2241 time to fit residues: 62.1364 Evaluate side-chains 192 residues out of total 1199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 153 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 688 PHE Chi-restraints excluded: chain A residue 699 MET Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 731 GLN Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1159 THR Chi-restraints excluded: chain A residue 1174 LEU Chi-restraints excluded: chain A residue 1183 ASN Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1222 GLU Chi-restraints excluded: chain A residue 1223 SER Chi-restraints excluded: chain A residue 1252 PHE Chi-restraints excluded: chain A residue 1258 TRP Chi-restraints excluded: chain A residue 1269 CYS Chi-restraints excluded: chain C residue 531 ASN Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 749 THR Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 599 ASN Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 649 GLN Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 685 HIS Chi-restraints excluded: chain B residue 698 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 33 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 GLN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.114764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.080218 restraints weight = 35496.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.083111 restraints weight = 17392.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.085025 restraints weight = 10998.276| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.259 12996 Z= 0.298 Angle : 1.056 59.107 17897 Z= 0.611 Chirality : 0.043 0.615 2009 Planarity : 0.004 0.051 2019 Dihedral : 16.400 89.082 2651 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.17 % Favored : 89.83 % Rotamer: Outliers : 3.42 % Allowed : 26.61 % Favored : 69.97 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.73 (0.24), residues: 1317 helix: 0.78 (0.23), residues: 580 sheet: -2.20 (0.53), residues: 98 loop : -2.96 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 730 HIS 0.008 0.001 HIS C 625 PHE 0.019 0.001 PHE A1118 TYR 0.029 0.002 TYR C 609 ARG 0.005 0.000 ARG A1273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2432.34 seconds wall clock time: 45 minutes 31.56 seconds (2731.56 seconds total)