Starting phenix.real_space_refine on Sat Mar 16 05:22:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yna_33956/03_2024/7yna_33956.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yna_33956/03_2024/7yna_33956.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yna_33956/03_2024/7yna_33956.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yna_33956/03_2024/7yna_33956.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yna_33956/03_2024/7yna_33956.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yna_33956/03_2024/7yna_33956.pdb" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 63 5.49 5 S 57 5.16 5 C 8468 2.51 5 N 2454 2.21 5 O 2742 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 10": "OE1" <-> "OE2" Residue "A GLU 82": "OE1" <-> "OE2" Residue "A GLU 93": "OE1" <-> "OE2" Residue "A ARG 97": "NH1" <-> "NH2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A ARG 108": "NH1" <-> "NH2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A GLU 350": "OE1" <-> "OE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A GLU 585": "OE1" <-> "OE2" Residue "A GLU 600": "OE1" <-> "OE2" Residue "A GLU 605": "OE1" <-> "OE2" Residue "A ARG 645": "NH1" <-> "NH2" Residue "A GLU 664": "OE1" <-> "OE2" Residue "A GLU 693": "OE1" <-> "OE2" Residue "A GLU 707": "OE1" <-> "OE2" Residue "A ARG 724": "NH1" <-> "NH2" Residue "A GLU 735": "OE1" <-> "OE2" Residue "A GLU 839": "OE1" <-> "OE2" Residue "A GLU 846": "OE1" <-> "OE2" Residue "A GLU 878": "OE1" <-> "OE2" Residue "A GLU 888": "OE1" <-> "OE2" Residue "A GLU 929": "OE1" <-> "OE2" Residue "A ARG 967": "NH1" <-> "NH2" Residue "A ARG 978": "NH1" <-> "NH2" Residue "A ARG 994": "NH1" <-> "NH2" Residue "A GLU 1028": "OE1" <-> "OE2" Residue "A GLU 1032": "OE1" <-> "OE2" Residue "A ARG 1066": "NH1" <-> "NH2" Residue "A ARG 1122": "NH1" <-> "NH2" Residue "A ARG 1125": "NH1" <-> "NH2" Residue "A TYR 1126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1135": "OE1" <-> "OE2" Residue "A GLU 1142": "OE1" <-> "OE2" Residue "A ARG 1184": "NH1" <-> "NH2" Residue "A GLU 1227": "OE1" <-> "OE2" Residue "A GLU 1232": "OE1" <-> "OE2" Residue "A GLU 1240": "OE1" <-> "OE2" Residue "A GLU 1254": "OE1" <-> "OE2" Residue "A ARG 1260": "NH1" <-> "NH2" Residue "A ARG 1356": "NH1" <-> "NH2" Residue "A ARG 1393": "NH1" <-> "NH2" Residue "A GLU 1501": "OE1" <-> "OE2" Residue "A GLU 1537": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13784 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 12447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1536, 12447 Classifications: {'peptide': 1536} Link IDs: {'PTRANS': 84, 'TRANS': 1451} Chain breaks: 4 Chain: "B" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 810 Classifications: {'RNA': 38} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 6, 'rna3p_pur': 7, 'rna3p_pyr': 11} Link IDs: {'rna2p': 20, 'rna3p': 17} Chain: "C" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 527 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 10, 'rna3p_pyr': 12} Link IDs: {'rna2p': 3, 'rna3p': 21} Time building chain proxies: 7.54, per 1000 atoms: 0.55 Number of scatterers: 13784 At special positions: 0 Unit cell: (92.02, 171.2, 132.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 P 63 15.00 O 2742 8.00 N 2454 7.00 C 8468 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: 5.79 Conformation dependent library (CDL) restraints added in 2.3 seconds 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2858 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 20 sheets defined 22.2% alpha, 15.3% beta 16 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 4.63 Creating SS restraints... Processing helix chain 'A' and resid 58 through 74 removed outlier: 3.510A pdb=" N THR A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 163 through 167 Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 261 through 276 Processing helix chain 'A' and resid 281 through 290 Processing helix chain 'A' and resid 291 through 295 removed outlier: 4.037A pdb=" N ARG A 294 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 302 removed outlier: 3.945A pdb=" N LEU A 302 " --> pdb=" O VAL A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 336 Processing helix chain 'A' and resid 344 through 365 removed outlier: 4.080A pdb=" N ASP A 365 " --> pdb=" O LEU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 459 removed outlier: 3.613A pdb=" N VAL A 447 " --> pdb=" O PRO A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 554 Processing helix chain 'A' and resid 562 through 566 Processing helix chain 'A' and resid 587 through 594 removed outlier: 3.562A pdb=" N ASN A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 607 Processing helix chain 'A' and resid 642 through 649 Processing helix chain 'A' and resid 675 through 688 removed outlier: 3.651A pdb=" N PHE A 679 " --> pdb=" O LYS A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 713 Processing helix chain 'A' and resid 780 through 784 Processing helix chain 'A' and resid 787 through 801 Processing helix chain 'A' and resid 809 through 813 removed outlier: 3.650A pdb=" N GLY A 813 " --> pdb=" O SER A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 962 removed outlier: 3.986A pdb=" N LEU A 950 " --> pdb=" O PRO A 946 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR A 962 " --> pdb=" O TYR A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1109 removed outlier: 4.178A pdb=" N GLU A1106 " --> pdb=" O ASN A1102 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N LYS A1107 " --> pdb=" O PHE A1103 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A1108 " --> pdb=" O ASP A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1246 removed outlier: 3.980A pdb=" N ARG A1235 " --> pdb=" O PRO A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1265 Processing helix chain 'A' and resid 1300 through 1305 removed outlier: 4.132A pdb=" N MET A1305 " --> pdb=" O GLY A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1420 through 1427 removed outlier: 3.975A pdb=" N ILE A1424 " --> pdb=" O ALA A1420 " (cutoff:3.500A) Processing helix chain 'A' and resid 1466 through 1476 removed outlier: 3.646A pdb=" N GLN A1476 " --> pdb=" O ILE A1472 " (cutoff:3.500A) Processing helix chain 'A' and resid 1515 through 1517 No H-bonds generated for 'chain 'A' and resid 1515 through 1517' Processing helix chain 'A' and resid 1518 through 1534 Processing helix chain 'A' and resid 1538 through 1548 Processing helix chain 'A' and resid 1565 through 1569 removed outlier: 4.032A pdb=" N ASP A1568 " --> pdb=" O ARG A1565 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP A1569 " --> pdb=" O LYS A1566 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1565 through 1569' Processing helix chain 'A' and resid 1575 through 1580 Processing helix chain 'A' and resid 1588 through 1595 removed outlier: 3.569A pdb=" N THR A1594 " --> pdb=" O GLN A1590 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 148 through 150 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 removed outlier: 3.709A pdb=" N MET A 17 " --> pdb=" O TYR A 190 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR A 190 " --> pdb=" O MET A 17 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG A 171 " --> pdb=" O ALA A 189 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 44 Processing sheet with id=AA4, first strand: chain 'A' and resid 483 through 484 removed outlier: 3.630A pdb=" N TYR A 577 " --> pdb=" O ASN A 611 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN A 611 " --> pdb=" O TYR A 577 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 527 through 529 Processing sheet with id=AA6, first strand: chain 'A' and resid 497 through 504 removed outlier: 3.742A pdb=" N GLU A 497 " --> pdb=" O VAL A 521 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG A 503 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ALA A 515 " --> pdb=" O ARG A 503 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 723 through 724 removed outlier: 3.743A pdb=" N VAL A 630 " --> pdb=" O GLY A 774 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ASN A 629 " --> pdb=" O ILE A 822 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE A 822 " --> pdb=" O ASN A 629 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N SER A 631 " --> pdb=" O LEU A 820 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU A 820 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLU A 633 " --> pdb=" O LYS A 818 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 659 through 660 removed outlier: 3.518A pdb=" N LEU A 728 " --> pdb=" O TYR A 674 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 739 through 744 removed outlier: 3.594A pdb=" N PHE A 757 " --> pdb=" O HIS A 741 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LYS A 755 " --> pdb=" O ALA A 743 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 861 through 862 Processing sheet with id=AB2, first strand: chain 'A' and resid 944 through 945 removed outlier: 3.603A pdb=" N SER A1363 " --> pdb=" O SER A1455 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 944 through 945 removed outlier: 3.603A pdb=" N SER A1363 " --> pdb=" O SER A1455 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 976 through 978 Processing sheet with id=AB5, first strand: chain 'A' and resid 991 through 993 removed outlier: 4.035A pdb=" N VAL A1275 " --> pdb=" O GLY A 993 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TYR A1276 " --> pdb=" O ILE A1287 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ILE A1287 " --> pdb=" O TYR A1276 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LYS A1278 " --> pdb=" O GLU A1285 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1001 through 1011 removed outlier: 8.390A pdb=" N ALA A1129 " --> pdb=" O THR A1008 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ARG A1010 " --> pdb=" O ALA A1129 " (cutoff:3.500A) removed outlier: 19.405A pdb=" N CYS A1143 " --> pdb=" O LYS A1223 " (cutoff:3.500A) removed outlier: 14.370A pdb=" N LYS A1223 " --> pdb=" O CYS A1143 " (cutoff:3.500A) removed outlier: 9.178A pdb=" N GLU A1145 " --> pdb=" O ASP A1221 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP A1221 " --> pdb=" O GLU A1145 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE A1220 " --> pdb=" O GLU A1007 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLU A1007 " --> pdb=" O PHE A1220 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU A1222 " --> pdb=" O PHE A1005 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N PHE A1005 " --> pdb=" O LEU A1222 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N GLU A1224 " --> pdb=" O GLN A1003 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N GLN A1003 " --> pdb=" O GLU A1224 " (cutoff:3.500A) removed outlier: 10.121A pdb=" N GLU A1226 " --> pdb=" O HIS A1001 " (cutoff:3.500A) removed outlier: 8.960A pdb=" N HIS A1001 " --> pdb=" O GLU A1226 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1044 through 1047 Processing sheet with id=AB8, first strand: chain 'A' and resid 1070 through 1071 Processing sheet with id=AB9, first strand: chain 'A' and resid 1081 through 1086 removed outlier: 3.670A pdb=" N LEU A1096 " --> pdb=" O PHE A1083 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A1085 " --> pdb=" O PHE A1094 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1200 through 1202 Processing sheet with id=AC2, first strand: chain 'A' and resid 1385 through 1387 307 hydrogen bonds defined for protein. 825 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 80 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 6.21 Time building geometry restraints manager: 6.32 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: 3596 1.33 - 1.45: 2944 1.45 - 1.57: 7491 1.57 - 1.69: 124 1.69 - 1.81: 82 Bond restraints: 14237 Sorted by residual: bond pdb=" C CYS A1560 " pdb=" N TYR A1561 " ideal model delta sigma weight residual 1.331 1.267 0.064 2.07e-02 2.33e+03 9.42e+00 bond pdb=" N CYS A 965 " pdb=" CA CYS A 965 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.22e-02 6.72e+03 7.06e+00 bond pdb=" N CYS A 706 " pdb=" CA CYS A 706 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.30e-02 5.92e+03 6.87e+00 bond pdb=" N CYS A 711 " pdb=" CA CYS A 711 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.29e-02 6.01e+03 6.68e+00 bond pdb=" N CYS A 708 " pdb=" CA CYS A 708 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.25e-02 6.40e+03 6.19e+00 ... (remaining 14232 not shown) Histogram of bond angle deviations from ideal: 99.44 - 106.36: 747 106.36 - 113.29: 7648 113.29 - 120.21: 5217 120.21 - 127.13: 5580 127.13 - 134.06: 292 Bond angle restraints: 19484 Sorted by residual: angle pdb=" N SER A1080 " pdb=" CA SER A1080 " pdb=" C SER A1080 " ideal model delta sigma weight residual 108.34 113.35 -5.01 1.31e+00 5.83e-01 1.46e+01 angle pdb=" N LYS A1586 " pdb=" CA LYS A1586 " pdb=" C LYS A1586 " ideal model delta sigma weight residual 114.75 110.41 4.34 1.26e+00 6.30e-01 1.18e+01 angle pdb=" CA CYS A 708 " pdb=" C CYS A 708 " pdb=" O CYS A 708 " ideal model delta sigma weight residual 121.55 118.02 3.53 1.06e+00 8.90e-01 1.11e+01 angle pdb=" N GLN A 884 " pdb=" CA GLN A 884 " pdb=" C GLN A 884 " ideal model delta sigma weight residual 110.80 103.99 6.81 2.13e+00 2.20e-01 1.02e+01 angle pdb=" C SER A1403 " pdb=" N ASP A1404 " pdb=" CA ASP A1404 " ideal model delta sigma weight residual 121.54 115.60 5.94 1.91e+00 2.74e-01 9.69e+00 ... (remaining 19479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.14: 8376 34.14 - 68.28: 289 68.28 - 102.42: 35 102.42 - 136.56: 2 136.56 - 170.70: 1 Dihedral angle restraints: 8703 sinusoidal: 4272 harmonic: 4431 Sorted by residual: dihedral pdb=" CA HIS A 383 " pdb=" C HIS A 383 " pdb=" N GLY A 384 " pdb=" CA GLY A 384 " ideal model delta harmonic sigma weight residual -180.00 -156.48 -23.52 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA LEU A 173 " pdb=" C LEU A 173 " pdb=" N ASN A 174 " pdb=" CA ASN A 174 " ideal model delta harmonic sigma weight residual -180.00 -159.20 -20.80 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" C4' U B -14 " pdb=" C3' U B -14 " pdb=" O3' U B -14 " pdb=" P G B -13 " ideal model delta sinusoidal sigma weight residual -110.00 60.70 -170.70 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 8700 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1524 0.048 - 0.097: 440 0.097 - 0.145: 103 0.145 - 0.193: 13 0.193 - 0.241: 4 Chirality restraints: 2084 Sorted by residual: chirality pdb=" C3' U B -14 " pdb=" C4' U B -14 " pdb=" O3' U B -14 " pdb=" C2' U B -14 " both_signs ideal model delta sigma weight residual False -2.74 -2.50 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" C1' A B 13 " pdb=" O4' A B 13 " pdb=" C2' A B 13 " pdb=" N9 A B 13 " both_signs ideal model delta sigma weight residual False 2.46 2.25 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA CYS A1342 " pdb=" N CYS A1342 " pdb=" C CYS A1342 " pdb=" CB CYS A1342 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 2081 not shown) Planarity restraints: 2315 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 863 " -0.052 5.00e-02 4.00e+02 7.89e-02 9.96e+00 pdb=" N PRO A 864 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO A 864 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 864 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G B 9 " -0.037 2.00e-02 2.50e+03 1.69e-02 8.56e+00 pdb=" N9 G B 9 " 0.043 2.00e-02 2.50e+03 pdb=" C8 G B 9 " 0.001 2.00e-02 2.50e+03 pdb=" N7 G B 9 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G B 9 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G B 9 " -0.006 2.00e-02 2.50e+03 pdb=" O6 G B 9 " -0.007 2.00e-02 2.50e+03 pdb=" N1 G B 9 " -0.005 2.00e-02 2.50e+03 pdb=" C2 G B 9 " 0.005 2.00e-02 2.50e+03 pdb=" N2 G B 9 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G B 9 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G B 9 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A1311 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.87e+00 pdb=" C PRO A1311 " 0.045 2.00e-02 2.50e+03 pdb=" O PRO A1311 " -0.017 2.00e-02 2.50e+03 pdb=" N CYS A1312 " -0.015 2.00e-02 2.50e+03 ... (remaining 2312 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 609 2.69 - 3.25: 13133 3.25 - 3.80: 20329 3.80 - 4.35: 25821 4.35 - 4.90: 44074 Nonbonded interactions: 103966 Sorted by model distance: nonbonded pdb=" O2' A B 11 " pdb=" O4' C B 12 " model vdw 2.143 2.440 nonbonded pdb=" OG SER A 445 " pdb=" OP1 A B -2 " model vdw 2.186 2.440 nonbonded pdb=" NZ LYS A1004 " pdb=" O PHE A1005 " model vdw 2.229 2.520 nonbonded pdb=" NE2 HIS A 931 " pdb=" OG1 THR A1444 " model vdw 2.241 2.520 nonbonded pdb=" NH1 ARG A 974 " pdb=" O ASP A1298 " model vdw 2.241 2.520 ... (remaining 103961 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.340 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: 7.810 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 43.550 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 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 0.064 14237 Z= 0.429 Angle : 0.729 11.132 19484 Z= 0.406 Chirality : 0.048 0.241 2084 Planarity : 0.005 0.079 2315 Dihedral : 16.960 170.704 5845 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 16.06 % Favored : 83.81 % Rotamer: Outliers : 0.60 % Allowed : 7.22 % Favored : 92.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.75 (0.17), residues: 1526 helix: -1.14 (0.28), residues: 300 sheet: -3.22 (0.26), residues: 281 loop : -4.07 (0.15), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1600 HIS 0.005 0.002 HIS A1473 PHE 0.015 0.002 PHE A 528 TYR 0.021 0.002 TYR A 863 ARG 0.005 0.000 ARG A 444 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 1.648 Fit side-chains REVERT: A 311 ASP cc_start: 0.8125 (t0) cc_final: 0.7676 (t70) REVERT: A 1065 ARG cc_start: 0.8012 (mmm160) cc_final: 0.7252 (ttm170) REVERT: A 1211 MET cc_start: 0.7960 (tmm) cc_final: 0.7123 (tmm) REVERT: A 1270 LYS cc_start: 0.7649 (mmmt) cc_final: 0.7339 (mttm) REVERT: A 1342 CYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7846 (p) outliers start: 8 outliers final: 3 residues processed: 74 average time/residue: 0.3640 time to fit residues: 37.8601 Evaluate side-chains 48 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 1342 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 123 optimal weight: 8.9990 chunk 47 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN A 456 GLN A 586 ASN A 589 ASN A1027 GLN ** A1095 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1136 ASN A1207 ASN ** A1246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1247 ASN A1417 HIS A1419 HIS A1452 ASN A1483 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14237 Z= 0.162 Angle : 0.581 11.636 19484 Z= 0.303 Chirality : 0.043 0.222 2084 Planarity : 0.005 0.059 2315 Dihedral : 16.237 174.945 2639 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.55 % Favored : 89.45 % Rotamer: Outliers : 0.37 % Allowed : 11.38 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.19), residues: 1526 helix: 0.35 (0.31), residues: 310 sheet: -2.54 (0.28), residues: 274 loop : -3.74 (0.16), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 595 HIS 0.006 0.001 HIS A1149 PHE 0.010 0.001 PHE A 776 TYR 0.011 0.001 TYR A1081 ARG 0.005 0.000 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 62 time to evaluate : 1.607 Fit side-chains REVERT: A 305 ASP cc_start: 0.7218 (t0) cc_final: 0.6467 (t0) REVERT: A 410 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7706 (pp) REVERT: A 989 ASP cc_start: 0.8099 (t70) cc_final: 0.7896 (t0) REVERT: A 1065 ARG cc_start: 0.7890 (mmm160) cc_final: 0.7202 (ttm170) REVERT: A 1211 MET cc_start: 0.7909 (tmm) cc_final: 0.7198 (tmm) REVERT: A 1270 LYS cc_start: 0.7621 (mmmt) cc_final: 0.7395 (mttm) outliers start: 5 outliers final: 3 residues processed: 67 average time/residue: 0.2941 time to fit residues: 29.7914 Evaluate side-chains 55 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 1479 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 119 optimal weight: 0.7980 chunk 97 optimal weight: 0.0060 chunk 39 optimal weight: 0.4980 chunk 143 optimal weight: 0.6980 chunk 155 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1095 HIS A1105 GLN A1246 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14237 Z= 0.149 Angle : 0.532 11.648 19484 Z= 0.275 Chirality : 0.041 0.212 2084 Planarity : 0.004 0.052 2315 Dihedral : 16.073 174.001 2637 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.88 % Favored : 89.12 % Rotamer: Outliers : 0.89 % Allowed : 12.87 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.20), residues: 1526 helix: 1.02 (0.32), residues: 312 sheet: -1.85 (0.30), residues: 266 loop : -3.44 (0.16), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1600 HIS 0.005 0.001 HIS A1473 PHE 0.010 0.001 PHE A 776 TYR 0.010 0.001 TYR A 313 ARG 0.004 0.000 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 53 time to evaluate : 1.497 Fit side-chains REVERT: A 60 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8764 (tt) REVERT: A 410 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7914 (pt) REVERT: A 1065 ARG cc_start: 0.7854 (mmm160) cc_final: 0.7104 (ttp-170) REVERT: A 1211 MET cc_start: 0.7857 (tmm) cc_final: 0.7432 (tmm) REVERT: A 1270 LYS cc_start: 0.7569 (mmmt) cc_final: 0.7286 (mttm) outliers start: 12 outliers final: 8 residues processed: 65 average time/residue: 0.3006 time to fit residues: 29.2110 Evaluate side-chains 55 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 45 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1479 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 4.9990 chunk 108 optimal weight: 0.0670 chunk 74 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 136 optimal weight: 0.0030 chunk 41 optimal weight: 2.9990 overall best weight: 1.3732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14237 Z= 0.191 Angle : 0.545 11.577 19484 Z= 0.280 Chirality : 0.041 0.221 2084 Planarity : 0.004 0.054 2315 Dihedral : 15.998 175.238 2637 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.07 % Favored : 88.93 % Rotamer: Outliers : 1.64 % Allowed : 14.43 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.20), residues: 1526 helix: 1.29 (0.32), residues: 310 sheet: -1.63 (0.30), residues: 271 loop : -3.35 (0.16), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1600 HIS 0.005 0.001 HIS A1473 PHE 0.012 0.001 PHE A 382 TYR 0.011 0.001 TYR A 863 ARG 0.004 0.000 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 48 time to evaluate : 1.638 Fit side-chains REVERT: A 60 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8798 (tt) REVERT: A 410 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7442 (pp) REVERT: A 1065 ARG cc_start: 0.7863 (mmm160) cc_final: 0.7213 (ttp-170) REVERT: A 1211 MET cc_start: 0.7859 (tmm) cc_final: 0.7293 (tmm) REVERT: A 1270 LYS cc_start: 0.7568 (mmmt) cc_final: 0.7311 (mttm) outliers start: 22 outliers final: 17 residues processed: 69 average time/residue: 0.2657 time to fit residues: 28.5430 Evaluate side-chains 64 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 45 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1479 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 HIS A 985 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 14237 Z= 0.455 Angle : 0.698 10.578 19484 Z= 0.361 Chirality : 0.047 0.262 2084 Planarity : 0.005 0.069 2315 Dihedral : 16.127 178.794 2637 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.61 % Favored : 85.39 % Rotamer: Outliers : 2.38 % Allowed : 15.70 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.20), residues: 1526 helix: 1.01 (0.31), residues: 308 sheet: -1.74 (0.29), residues: 280 loop : -3.43 (0.17), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1600 HIS 0.007 0.002 HIS A1149 PHE 0.019 0.002 PHE A1540 TYR 0.022 0.002 TYR A 863 ARG 0.004 0.000 ARG A 444 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 43 time to evaluate : 1.485 Fit side-chains REVERT: A 410 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.7904 (pp) REVERT: A 1065 ARG cc_start: 0.7984 (mmm160) cc_final: 0.7350 (ttm170) REVERT: A 1211 MET cc_start: 0.7909 (tmm) cc_final: 0.7258 (tmm) REVERT: A 1270 LYS cc_start: 0.7616 (mmmt) cc_final: 0.7403 (mttm) REVERT: A 1533 TRP cc_start: 0.8406 (OUTLIER) cc_final: 0.7920 (m-10) outliers start: 32 outliers final: 22 residues processed: 73 average time/residue: 0.2605 time to fit residues: 29.5084 Evaluate side-chains 65 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 41 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1103 PHE Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1533 TRP Chi-restraints excluded: chain A residue 1600 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 0.6980 chunk 137 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 89 optimal weight: 0.4980 chunk 37 optimal weight: 0.7980 chunk 152 optimal weight: 3.9990 chunk 126 optimal weight: 0.0040 chunk 70 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14237 Z= 0.147 Angle : 0.539 11.587 19484 Z= 0.277 Chirality : 0.041 0.200 2084 Planarity : 0.004 0.050 2315 Dihedral : 15.970 173.460 2637 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 1.64 % Allowed : 17.26 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.21), residues: 1526 helix: 1.41 (0.32), residues: 318 sheet: -1.39 (0.31), residues: 266 loop : -3.21 (0.17), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1600 HIS 0.004 0.001 HIS A1473 PHE 0.008 0.001 PHE A1407 TYR 0.010 0.001 TYR A 313 ARG 0.005 0.000 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 45 time to evaluate : 1.786 Fit side-chains REVERT: A 410 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7910 (pt) REVERT: A 1065 ARG cc_start: 0.7898 (mmm160) cc_final: 0.7232 (ttp-170) REVERT: A 1211 MET cc_start: 0.7855 (tmm) cc_final: 0.7217 (tmm) REVERT: A 1270 LYS cc_start: 0.7548 (mmmt) cc_final: 0.7272 (mttm) outliers start: 22 outliers final: 15 residues processed: 65 average time/residue: 0.3085 time to fit residues: 30.8531 Evaluate side-chains 60 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 44 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1103 PHE Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1600 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 14237 Z= 0.422 Angle : 0.669 10.822 19484 Z= 0.345 Chirality : 0.046 0.251 2084 Planarity : 0.005 0.065 2315 Dihedral : 16.059 179.369 2637 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.15 % Favored : 85.85 % Rotamer: Outliers : 2.08 % Allowed : 17.41 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.20), residues: 1526 helix: 1.28 (0.32), residues: 308 sheet: -1.54 (0.30), residues: 280 loop : -3.32 (0.17), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1600 HIS 0.006 0.001 HIS A1149 PHE 0.017 0.002 PHE A 528 TYR 0.019 0.002 TYR A 863 ARG 0.003 0.000 ARG A 444 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 41 time to evaluate : 1.691 Fit side-chains REVERT: A 410 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.7869 (pp) REVERT: A 1065 ARG cc_start: 0.7981 (mmm160) cc_final: 0.7348 (ttm170) REVERT: A 1211 MET cc_start: 0.7902 (tmm) cc_final: 0.7213 (tmm) REVERT: A 1533 TRP cc_start: 0.8304 (OUTLIER) cc_final: 0.7829 (m-10) outliers start: 28 outliers final: 18 residues processed: 66 average time/residue: 0.2851 time to fit residues: 29.0318 Evaluate side-chains 59 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 39 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1103 PHE Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1533 TRP Chi-restraints excluded: chain A residue 1600 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 119 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14237 Z= 0.201 Angle : 0.570 11.575 19484 Z= 0.292 Chirality : 0.042 0.217 2084 Planarity : 0.005 0.057 2315 Dihedral : 15.974 175.751 2637 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.88 % Favored : 89.12 % Rotamer: Outliers : 1.93 % Allowed : 17.56 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.21), residues: 1526 helix: 1.42 (0.32), residues: 316 sheet: -1.42 (0.32), residues: 267 loop : -3.18 (0.17), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1600 HIS 0.006 0.001 HIS A1149 PHE 0.011 0.001 PHE A 776 TYR 0.011 0.001 TYR A 313 ARG 0.005 0.000 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 43 time to evaluate : 1.643 Fit side-chains REVERT: A 410 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7921 (pt) REVERT: A 473 MET cc_start: 0.8364 (mmm) cc_final: 0.8117 (mmm) REVERT: A 480 MET cc_start: 0.8702 (mtp) cc_final: 0.8487 (mmt) REVERT: A 1065 ARG cc_start: 0.7895 (mmm160) cc_final: 0.7188 (ttp-170) REVERT: A 1211 MET cc_start: 0.7912 (tmm) cc_final: 0.7517 (tmm) REVERT: A 1473 HIS cc_start: 0.8293 (OUTLIER) cc_final: 0.7882 (t-90) outliers start: 26 outliers final: 19 residues processed: 68 average time/residue: 0.2593 time to fit residues: 27.6818 Evaluate side-chains 63 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 42 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1103 PHE Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1367 ASP Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1473 HIS Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1600 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 128 optimal weight: 0.0970 chunk 134 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 150 optimal weight: 5.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14237 Z= 0.235 Angle : 0.576 11.338 19484 Z= 0.295 Chirality : 0.042 0.221 2084 Planarity : 0.005 0.063 2315 Dihedral : 15.949 175.643 2637 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.93 % Favored : 88.07 % Rotamer: Outliers : 2.23 % Allowed : 17.41 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.21), residues: 1526 helix: 1.47 (0.32), residues: 316 sheet: -1.37 (0.30), residues: 282 loop : -3.15 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1600 HIS 0.005 0.001 HIS A1473 PHE 0.012 0.001 PHE A 776 TYR 0.012 0.001 TYR A 863 ARG 0.005 0.000 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 42 time to evaluate : 1.579 Fit side-chains REVERT: A 410 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7526 (pp) REVERT: A 480 MET cc_start: 0.8745 (mtp) cc_final: 0.8514 (mmt) REVERT: A 1065 ARG cc_start: 0.7898 (mmm160) cc_final: 0.7194 (ttp-170) REVERT: A 1211 MET cc_start: 0.7949 (tmm) cc_final: 0.7353 (tmm) REVERT: A 1283 TYR cc_start: 0.7712 (OUTLIER) cc_final: 0.7274 (m-10) REVERT: A 1473 HIS cc_start: 0.8327 (OUTLIER) cc_final: 0.7878 (t-90) outliers start: 30 outliers final: 26 residues processed: 70 average time/residue: 0.2360 time to fit residues: 26.5506 Evaluate side-chains 71 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 42 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1103 PHE Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1283 TYR Chi-restraints excluded: chain A residue 1367 ASP Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain A residue 1473 HIS Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1491 MET Chi-restraints excluded: chain A residue 1600 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 144 optimal weight: 0.9980 chunk 125 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 99 optimal weight: 10.0000 chunk 133 optimal weight: 0.1980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14237 Z= 0.144 Angle : 0.525 11.669 19484 Z= 0.268 Chirality : 0.040 0.201 2084 Planarity : 0.004 0.055 2315 Dihedral : 15.870 172.014 2637 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 1.86 % Allowed : 17.71 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.21), residues: 1526 helix: 1.72 (0.32), residues: 316 sheet: -1.19 (0.32), residues: 267 loop : -2.95 (0.18), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1466 HIS 0.005 0.001 HIS A1473 PHE 0.010 0.001 PHE A1407 TYR 0.010 0.001 TYR A 313 ARG 0.005 0.000 ARG A 393 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 46 time to evaluate : 1.590 Fit side-chains REVERT: A 1065 ARG cc_start: 0.7853 (mmm160) cc_final: 0.7180 (ttp-170) REVERT: A 1211 MET cc_start: 0.7860 (tmm) cc_final: 0.7213 (tmm) REVERT: A 1473 HIS cc_start: 0.8254 (OUTLIER) cc_final: 0.7782 (t-90) outliers start: 25 outliers final: 21 residues processed: 67 average time/residue: 0.3027 time to fit residues: 31.4295 Evaluate side-chains 65 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 43 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1103 PHE Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1305 MET Chi-restraints excluded: chain A residue 1367 ASP Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1473 HIS Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1491 MET Chi-restraints excluded: chain A residue 1600 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 34 optimal weight: 0.0060 chunk 125 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 15 optimal weight: 0.0040 chunk 23 optimal weight: 0.9990 chunk 110 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.5812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.084917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.065802 restraints weight = 36261.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.067797 restraints weight = 20067.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.069078 restraints weight = 14045.608| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14237 Z= 0.134 Angle : 0.524 11.778 19484 Z= 0.265 Chirality : 0.040 0.199 2084 Planarity : 0.004 0.055 2315 Dihedral : 15.787 170.926 2636 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer: Outliers : 1.64 % Allowed : 18.23 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.21), residues: 1526 helix: 1.83 (0.32), residues: 316 sheet: -1.00 (0.31), residues: 282 loop : -2.83 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1180 HIS 0.005 0.001 HIS A1473 PHE 0.009 0.001 PHE A1407 TYR 0.009 0.001 TYR A 313 ARG 0.004 0.000 ARG A 393 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2169.61 seconds wall clock time: 40 minutes 39.05 seconds (2439.05 seconds total)