Starting phenix.real_space_refine (version: 1.21rc1) on Sat Jul 15 05:19:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a22_6337/07_2023/5a22_6337_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a22_6337/07_2023/5a22_6337.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a22_6337/07_2023/5a22_6337.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a22_6337/07_2023/5a22_6337.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a22_6337/07_2023/5a22_6337_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a22_6337/07_2023/5a22_6337_neut.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.052 sd= 0.385 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 S 89 5.16 5 C 10249 2.51 5 N 2803 2.21 5 O 2934 1.98 5 H 16110 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 115": "OE1" <-> "OE2" Residue "A ASP 414": "OD1" <-> "OD2" Residue "A TYR 991": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 32187 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 32187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2004, 32187 Unusual residues: {' ZN': 2} Classifications: {'peptide': 2002, 'undetermined': 2} Link IDs: {'PTRANS': 93, 'TRANS': 1908, None: 2} Not linked: pdbres="ASP A2109 " pdbres=" ZN A3000 " Not linked: pdbres=" ZN A3000 " pdbres=" ZN A3001 " Chain breaks: 3 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 17047 SG CYS A1081 70.220 68.005 80.519 1.00193.79 S ATOM 20418 SG CYS A1299 67.983 67.609 80.307 1.00220.85 S ATOM 20461 SG CYS A1302 67.501 70.395 78.910 1.00140.37 S ATOM 17656 SG CYS A1120 68.106 51.296 71.661 1.00172.55 S ATOM 17690 SG CYS A1123 67.624 52.782 73.640 1.00217.61 S Time building chain proxies: 13.54, per 1000 atoms: 0.42 Number of scatterers: 32187 At special positions: 0 Unit cell: (123.7, 134.833, 98.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 89 16.00 O 2934 8.00 N 2803 7.00 C 10249 6.00 H 16110 1.00 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: 27.81 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3000 " pdb="ZN ZN A3000 " - pdb=" SG CYS A1302 " pdb="ZN ZN A3000 " - pdb=" SG CYS A1299 " pdb="ZN ZN A3000 " - pdb=" SG CYS A1081 " pdb=" ZN A3001 " pdb="ZN ZN A3001 " - pdb=" ND1 HIS A1294 " pdb="ZN ZN A3001 " - pdb=" NE2 HIS A1296 " pdb="ZN ZN A3001 " - pdb=" SG CYS A1120 " pdb="ZN ZN A3001 " - pdb=" SG CYS A1123 " Number of angles added : 2 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3762 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 8 sheets defined 55.2% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 47 through 58 Processing helix chain 'A' and resid 65 through 69 removed outlier: 3.949A pdb=" N SER A 68 " --> pdb=" O MET A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 81 Processing helix chain 'A' and resid 88 through 99 Processing helix chain 'A' and resid 106 through 135 removed outlier: 3.534A pdb=" N TYR A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 172 Processing helix chain 'A' and resid 175 through 186 Processing helix chain 'A' and resid 228 through 250 removed outlier: 4.601A pdb=" N CYS A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 278 Processing helix chain 'A' and resid 279 through 281 No H-bonds generated for 'chain 'A' and resid 279 through 281' Processing helix chain 'A' and resid 282 through 304 Proline residue: A 291 - end of helix Processing helix chain 'A' and resid 311 through 329 removed outlier: 4.341A pdb=" N GLU A 315 " --> pdb=" O PHE A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 342 Processing helix chain 'A' and resid 344 through 355 removed outlier: 3.815A pdb=" N THR A 348 " --> pdb=" O THR A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 378 Processing helix chain 'A' and resid 384 through 406 Processing helix chain 'A' and resid 420 through 428 Processing helix chain 'A' and resid 433 through 440 Processing helix chain 'A' and resid 460 through 464 removed outlier: 4.126A pdb=" N ILE A 463 " --> pdb=" O ASP A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 483 Processing helix chain 'A' and resid 493 through 501 Processing helix chain 'A' and resid 505 through 517 Processing helix chain 'A' and resid 519 through 522 Processing helix chain 'A' and resid 545 through 563 Processing helix chain 'A' and resid 564 through 567 Processing helix chain 'A' and resid 576 through 584 Processing helix chain 'A' and resid 593 through 595 No H-bonds generated for 'chain 'A' and resid 593 through 595' Processing helix chain 'A' and resid 608 through 613 Processing helix chain 'A' and resid 614 through 629 Proline residue: A 620 - end of helix Processing helix chain 'A' and resid 634 through 636 No H-bonds generated for 'chain 'A' and resid 634 through 636' Processing helix chain 'A' and resid 637 through 645 Processing helix chain 'A' and resid 652 through 656 removed outlier: 3.818A pdb=" N LEU A 655 " --> pdb=" O ARG A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 700 Processing helix chain 'A' and resid 730 through 758 removed outlier: 3.596A pdb=" N GLN A 734 " --> pdb=" O VAL A 730 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 758 " --> pdb=" O GLY A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 797 Processing helix chain 'A' and resid 807 through 826 removed outlier: 4.007A pdb=" N MET A 812 " --> pdb=" O CYS A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 850 Processing helix chain 'A' and resid 870 through 880 Processing helix chain 'A' and resid 902 through 918 Processing helix chain 'A' and resid 921 through 932 Processing helix chain 'A' and resid 939 through 949 Processing helix chain 'A' and resid 960 through 976 Processing helix chain 'A' and resid 982 through 1005 removed outlier: 6.194A pdb=" N ASP A 997 " --> pdb=" O TYR A 993 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ARG A 998 " --> pdb=" O HIS A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1021 Processing helix chain 'A' and resid 1023 through 1033 removed outlier: 3.689A pdb=" N PHE A1033 " --> pdb=" O LEU A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1042 Processing helix chain 'A' and resid 1043 through 1045 No H-bonds generated for 'chain 'A' and resid 1043 through 1045' Processing helix chain 'A' and resid 1048 through 1070 removed outlier: 4.106A pdb=" N ASP A1052 " --> pdb=" O HIS A1048 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1094 removed outlier: 4.152A pdb=" N HIS A1085 " --> pdb=" O CYS A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1111 removed outlier: 3.863A pdb=" N MET A1109 " --> pdb=" O HIS A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1186 Processing helix chain 'A' and resid 1195 through 1209 Processing helix chain 'A' and resid 1243 through 1250 removed outlier: 4.057A pdb=" N LEU A1247 " --> pdb=" O SER A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1268 through 1285 Processing helix chain 'A' and resid 1323 through 1331 removed outlier: 3.871A pdb=" N ASN A1331 " --> pdb=" O LYS A1327 " (cutoff:3.500A) Processing helix chain 'A' and resid 1359 through 1377 Processing helix chain 'A' and resid 1397 through 1420 Processing helix chain 'A' and resid 1427 through 1446 Processing helix chain 'A' and resid 1446 through 1455 removed outlier: 3.644A pdb=" N LEU A1450 " --> pdb=" O SER A1446 " (cutoff:3.500A) Processing helix chain 'A' and resid 1457 through 1465 removed outlier: 3.722A pdb=" N GLU A1461 " --> pdb=" O PRO A1457 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE A1465 " --> pdb=" O GLU A1461 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1498 Processing helix chain 'A' and resid 1515 through 1533 removed outlier: 4.606A pdb=" N ILE A1519 " --> pdb=" O SER A1515 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY A1520 " --> pdb=" O ILE A1516 " (cutoff:3.500A) Proline residue: A1521 - end of helix Processing helix chain 'A' and resid 1540 through 1556 removed outlier: 3.755A pdb=" N GLU A1544 " --> pdb=" O LYS A1540 " (cutoff:3.500A) Processing helix chain 'A' and resid 1633 through 1640 removed outlier: 4.464A pdb=" N SER A1637 " --> pdb=" O ASN A1633 " (cutoff:3.500A) Processing helix chain 'A' and resid 1647 through 1659 Processing helix chain 'A' and resid 1674 through 1684 Processing helix chain 'A' and resid 1710 through 1717 removed outlier: 3.663A pdb=" N LEU A1716 " --> pdb=" O LEU A1713 " (cutoff:3.500A) Processing helix chain 'A' and resid 1728 through 1732 removed outlier: 3.842A pdb=" N TYR A1732 " --> pdb=" O CYS A1729 " (cutoff:3.500A) Processing helix chain 'A' and resid 1740 through 1753 Processing helix chain 'A' and resid 1767 through 1782 Processing helix chain 'A' and resid 1783 through 1785 No H-bonds generated for 'chain 'A' and resid 1783 through 1785' Processing helix chain 'A' and resid 1797 through 1804 removed outlier: 4.186A pdb=" N SER A1804 " --> pdb=" O TYR A1800 " (cutoff:3.500A) Processing helix chain 'A' and resid 1806 through 1811 Processing helix chain 'A' and resid 1850 through 1862 Processing helix chain 'A' and resid 1867 through 1881 Processing helix chain 'A' and resid 1896 through 1906 Processing helix chain 'A' and resid 1909 through 1923 Processing helix chain 'A' and resid 1927 through 1944 Processing helix chain 'A' and resid 1958 through 1980 Processing helix chain 'A' and resid 1981 through 1994 removed outlier: 3.795A pdb=" N TYR A1985 " --> pdb=" O ASP A1981 " (cutoff:3.500A) Processing helix chain 'A' and resid 2029 through 2045 Processing helix chain 'A' and resid 2053 through 2065 Processing helix chain 'A' and resid 2069 through 2075 Processing helix chain 'A' and resid 2079 through 2083 Processing sheet with id= AA, first strand: chain 'A' and resid 189 through 193 Processing sheet with id= AB, first strand: chain 'A' and resid 541 through 543 Processing sheet with id= AC, first strand: chain 'A' and resid 706 through 712 Processing sheet with id= AD, first strand: chain 'A' and resid 657 through 659 Processing sheet with id= AE, first strand: chain 'A' and resid 774 through 776 Processing sheet with id= AF, first strand: chain 'A' and resid 1114 through 1115 Processing sheet with id= AG, first strand: chain 'A' and resid 1608 through 1613 removed outlier: 3.595A pdb=" N THR A1608 " --> pdb=" O VAL A1822 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL A1822 " --> pdb=" O THR A1608 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'A' and resid 2012 through 2014 848 hydrogen bonds defined for protein. 2439 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.80 Time building geometry restraints manager: 28.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 16083 1.04 - 1.24: 1860 1.24 - 1.44: 5254 1.44 - 1.64: 9223 1.64 - 1.84: 146 Bond restraints: 32566 Sorted by residual: bond pdb=" CA VAL A 289 " pdb=" CB VAL A 289 " ideal model delta sigma weight residual 1.540 1.613 -0.073 1.11e-02 8.12e+03 4.36e+01 bond pdb=" CA ILE A 865 " pdb=" CB ILE A 865 " ideal model delta sigma weight residual 1.537 1.603 -0.065 1.29e-02 6.01e+03 2.58e+01 bond pdb=" C GLN A 721 " pdb=" O GLN A 721 " ideal model delta sigma weight residual 1.235 1.286 -0.051 1.18e-02 7.18e+03 1.89e+01 bond pdb=" CA THR A 817 " pdb=" CB THR A 817 " ideal model delta sigma weight residual 1.529 1.591 -0.062 1.58e-02 4.01e+03 1.54e+01 bond pdb=" C ILE A 122 " pdb=" O ILE A 122 " ideal model delta sigma weight residual 1.236 1.280 -0.043 1.11e-02 8.12e+03 1.52e+01 ... (remaining 32561 not shown) Histogram of bond angle deviations from ideal: 97.43 - 105.40: 395 105.40 - 113.38: 38379 113.38 - 121.36: 13303 121.36 - 129.34: 6621 129.34 - 137.32: 171 Bond angle restraints: 58869 Sorted by residual: angle pdb=" C GLN A1165 " pdb=" N PRO A1166 " pdb=" CA PRO A1166 " ideal model delta sigma weight residual 119.84 107.78 12.06 1.25e+00 6.40e-01 9.31e+01 angle pdb=" N PRO A1447 " pdb=" CA PRO A1447 " pdb=" C PRO A1447 " ideal model delta sigma weight residual 110.70 120.60 -9.90 1.22e+00 6.72e-01 6.59e+01 angle pdb=" C ASN A1954 " pdb=" N PRO A1955 " pdb=" CA PRO A1955 " ideal model delta sigma weight residual 120.38 112.22 8.16 1.03e+00 9.43e-01 6.27e+01 angle pdb=" C ILE A 62 " pdb=" N PRO A 63 " pdb=" CA PRO A 63 " ideal model delta sigma weight residual 119.84 110.49 9.35 1.25e+00 6.40e-01 5.59e+01 angle pdb=" N ILE A 332 " pdb=" CA ILE A 332 " pdb=" C ILE A 332 " ideal model delta sigma weight residual 110.62 103.24 7.38 1.02e+00 9.61e-01 5.23e+01 ... (remaining 58864 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.14: 11737 18.14 - 36.27: 925 36.27 - 54.41: 192 54.41 - 72.55: 247 72.55 - 90.68: 12 Dihedral angle restraints: 13113 sinusoidal: 6170 harmonic: 6943 Sorted by residual: dihedral pdb=" CA GLU A 766 " pdb=" C GLU A 766 " pdb=" N THR A 767 " pdb=" CA THR A 767 " ideal model delta harmonic sigma weight residual -180.00 -134.47 -45.53 0 5.00e+00 4.00e-02 8.29e+01 dihedral pdb=" CA ALA A1151 " pdb=" C ALA A1151 " pdb=" N TYR A1152 " pdb=" CA TYR A1152 " ideal model delta harmonic sigma weight residual 180.00 137.82 42.18 0 5.00e+00 4.00e-02 7.12e+01 dihedral pdb=" CA TRP A1167 " pdb=" C TRP A1167 " pdb=" N GLU A1168 " pdb=" CA GLU A1168 " ideal model delta harmonic sigma weight residual -180.00 -141.33 -38.67 0 5.00e+00 4.00e-02 5.98e+01 ... (remaining 13110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1945 0.068 - 0.137: 438 0.137 - 0.205: 69 0.205 - 0.274: 7 0.274 - 0.342: 1 Chirality restraints: 2460 Sorted by residual: chirality pdb=" CA TYR A 879 " pdb=" N TYR A 879 " pdb=" C TYR A 879 " pdb=" CB TYR A 879 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CA HIS A2067 " pdb=" N HIS A2067 " pdb=" C HIS A2067 " pdb=" CB HIS A2067 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA ILE A2083 " pdb=" N ILE A2083 " pdb=" C ILE A2083 " pdb=" CB ILE A2083 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 2457 not shown) Planarity restraints: 4734 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A1955 " -0.066 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO A1956 " 0.173 5.00e-02 4.00e+02 pdb=" CA PRO A1956 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A1956 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A1954 " 0.048 5.00e-02 4.00e+02 7.30e-02 8.54e+00 pdb=" N PRO A1955 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO A1955 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A1955 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 609 " -0.014 2.00e-02 2.50e+03 2.87e-02 8.25e+00 pdb=" C TRP A 609 " 0.050 2.00e-02 2.50e+03 pdb=" O TRP A 609 " -0.019 2.00e-02 2.50e+03 pdb=" N ASN A 610 " -0.016 2.00e-02 2.50e+03 ... (remaining 4731 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.11: 1296 2.11 - 2.73: 58423 2.73 - 3.35: 96523 3.35 - 3.98: 122110 3.98 - 4.60: 192250 Nonbonded interactions: 470602 Sorted by model distance: nonbonded pdb=" O TRP A2013 " pdb=" HG1 THR A2077 " model vdw 1.482 1.850 nonbonded pdb=" H SER A 471 " pdb=" O MET A 544 " model vdw 1.491 1.850 nonbonded pdb=" O SER A 354 " pdb=" H ARG A 356 " model vdw 1.539 1.850 nonbonded pdb=" O LEU A 629 " pdb=" H TYR A 631 " model vdw 1.546 1.850 nonbonded pdb=" O THR A1254 " pdb=" H MET A1257 " model vdw 1.557 1.850 ... (remaining 470597 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: 0.110 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: 0.470 Extract box with map and model: 3.470 Check model and map are aligned: 0.440 Set scattering table: 0.300 Process input model: 112.680 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 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 : 0.009 0.081 16456 Z= 0.606 Angle : 1.490 12.317 22270 Z= 0.976 Chirality : 0.058 0.342 2460 Planarity : 0.008 0.100 2828 Dihedral : 15.754 90.682 6145 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 1.96 % Allowed : 13.89 % Favored : 84.15 % Rotamer Outliers : 5.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.26 % Twisted General : 0.58 % 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: -5.08 (0.13), residues: 1994 helix: -3.24 (0.11), residues: 959 sheet: -1.56 (0.41), residues: 113 loop : -3.75 (0.15), residues: 922 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 457 time to evaluate : 2.510 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: 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: 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: 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 outliers start: 100 outliers final: 35 residues processed: 530 average time/residue: 0.7827 time to fit residues: 595.5766 Evaluate side-chains 345 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 310 time to evaluate : 2.520 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 4 residues processed: 35 average time/residue: 0.4361 time to fit residues: 30.4348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 7.9990 chunk 151 optimal weight: 8.9990 chunk 84 optimal weight: 0.8980 chunk 51 optimal weight: 9.9990 chunk 102 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 chunk 181 optimal weight: 8.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 GLN A 425 HIS A 618 ASN A 856 GLN A 954 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 16456 Z= 0.288 Angle : 0.803 8.256 22270 Z= 0.433 Chirality : 0.044 0.195 2460 Planarity : 0.006 0.108 2828 Dihedral : 7.563 37.770 2186 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 1.20 % Allowed : 12.94 % Favored : 85.86 % Rotamer Outliers : 2.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.26 % Twisted General : 0.37 % 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: -3.47 (0.16), residues: 1994 helix: -1.30 (0.14), residues: 1003 sheet: -1.95 (0.40), residues: 113 loop : -3.61 (0.18), residues: 878 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 346 time to evaluate : 2.608 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: 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: 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 outliers start: 48 outliers final: 33 residues processed: 379 average time/residue: 0.6617 time to fit residues: 375.0141 Evaluate side-chains 313 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 280 time to evaluate : 2.304 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 3 residues processed: 33 average time/residue: 0.3898 time to fit residues: 26.3438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 151 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 181 optimal weight: 20.0000 chunk 196 optimal weight: 0.9980 chunk 162 optimal weight: 9.9990 chunk 180 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 145 optimal weight: 9.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS A 473 ASN ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 ASN A2045 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 16456 Z= 0.316 Angle : 0.754 8.460 22270 Z= 0.406 Chirality : 0.043 0.174 2460 Planarity : 0.006 0.109 2828 Dihedral : 7.131 38.427 2186 Min Nonbonded Distance : 1.694 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 1.15 % Allowed : 14.34 % Favored : 84.50 % Rotamer Outliers : 2.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.31 % 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: -2.83 (0.17), residues: 1994 helix: -0.60 (0.15), residues: 1014 sheet: -1.98 (0.43), residues: 113 loop : -3.54 (0.18), residues: 867 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 295 time to evaluate : 2.560 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 24 residues processed: 328 average time/residue: 0.7252 time to fit residues: 353.3482 Evaluate side-chains 291 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 267 time to evaluate : 2.372 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 2 residues processed: 24 average time/residue: 0.3803 time to fit residues: 19.6677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 6.9990 chunk 136 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 182 optimal weight: 9.9990 chunk 193 optimal weight: 9.9990 chunk 95 optimal weight: 0.8980 chunk 173 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A1633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2045 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 16456 Z= 0.294 Angle : 0.719 8.243 22270 Z= 0.387 Chirality : 0.042 0.157 2460 Planarity : 0.006 0.111 2828 Dihedral : 6.848 37.166 2186 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 1.20 % Allowed : 13.94 % Favored : 84.85 % Rotamer Outliers : 2.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.26 % 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: -2.51 (0.18), residues: 1994 helix: -0.23 (0.16), residues: 1008 sheet: -2.00 (0.43), residues: 113 loop : -3.48 (0.18), residues: 873 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 292 time to evaluate : 2.642 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 23 residues processed: 318 average time/residue: 0.6873 time to fit residues: 324.1721 Evaluate side-chains 285 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 262 time to evaluate : 2.572 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 2 residues processed: 23 average time/residue: 0.4625 time to fit residues: 21.3259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 143 optimal weight: 9.9990 chunk 79 optimal weight: 0.9980 chunk 164 optimal weight: 8.9990 chunk 133 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 173 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 ASN A 618 ASN A2045 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.5268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 16456 Z= 0.240 Angle : 0.683 8.552 22270 Z= 0.365 Chirality : 0.041 0.149 2460 Planarity : 0.005 0.112 2828 Dihedral : 6.570 37.353 2186 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 1.10 % Allowed : 13.79 % Favored : 85.11 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % 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: -2.16 (0.18), residues: 1994 helix: 0.08 (0.16), residues: 1013 sheet: -1.89 (0.44), residues: 123 loop : -3.36 (0.19), residues: 858 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 290 time to evaluate : 2.629 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: 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: 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 outliers start: 29 outliers final: 21 residues processed: 308 average time/residue: 0.7015 time to fit residues: 327.2177 Evaluate side-chains 286 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 265 time to evaluate : 2.498 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 3 residues processed: 21 average time/residue: 0.3928 time to fit residues: 18.1336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 6.9990 chunk 174 optimal weight: 20.0000 chunk 38 optimal weight: 0.0670 chunk 113 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 193 optimal weight: 8.9990 chunk 160 optimal weight: 0.4980 chunk 89 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 overall best weight: 4.3124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN A 618 ASN ** A1633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2045 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.5548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 16456 Z= 0.258 Angle : 0.682 8.272 22270 Z= 0.366 Chirality : 0.041 0.174 2460 Planarity : 0.005 0.112 2828 Dihedral : 6.456 36.732 2186 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 1.15 % Allowed : 13.94 % Favored : 84.90 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.09 % 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: -2.04 (0.18), residues: 1994 helix: 0.22 (0.16), residues: 1011 sheet: -1.91 (0.43), residues: 126 loop : -3.34 (0.19), residues: 857 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 280 time to evaluate : 2.808 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: 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: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 20 residues processed: 298 average time/residue: 0.6661 time to fit residues: 300.4377 Evaluate side-chains 276 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 256 time to evaluate : 2.830 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 3 residues processed: 20 average time/residue: 0.4263 time to fit residues: 18.7488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 110 optimal weight: 0.0970 chunk 141 optimal weight: 0.9990 chunk 109 optimal weight: 7.9990 chunk 162 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 192 optimal weight: 0.6980 chunk 120 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1048 HIS ** A1633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.5811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 16456 Z= 0.204 Angle : 0.658 7.022 22270 Z= 0.348 Chirality : 0.040 0.152 2460 Planarity : 0.005 0.112 2828 Dihedral : 6.229 36.257 2186 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 1.10 % Allowed : 12.09 % Favored : 86.81 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.05 % 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: -1.75 (0.19), residues: 1994 helix: 0.47 (0.16), residues: 1011 sheet: -1.63 (0.42), residues: 137 loop : -3.25 (0.20), residues: 846 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 297 time to evaluate : 2.501 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 14 residues processed: 308 average time/residue: 0.6522 time to fit residues: 305.5145 Evaluate side-chains 280 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 266 time to evaluate : 2.707 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 14 average time/residue: 0.3980 time to fit residues: 13.3618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 20.0000 chunk 76 optimal weight: 9.9990 chunk 115 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 131 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 151 optimal weight: 1.9990 chunk 175 optimal weight: 9.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.6001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 16456 Z= 0.247 Angle : 0.671 7.499 22270 Z= 0.358 Chirality : 0.041 0.175 2460 Planarity : 0.005 0.111 2828 Dihedral : 6.189 36.149 2186 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 1.05 % Allowed : 13.64 % Favored : 85.31 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.19), residues: 1994 helix: 0.52 (0.16), residues: 1010 sheet: -1.61 (0.42), residues: 135 loop : -3.23 (0.20), residues: 849 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 269 time to evaluate : 2.614 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: 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: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 17 residues processed: 283 average time/residue: 0.6644 time to fit residues: 283.9354 Evaluate side-chains 280 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 263 time to evaluate : 2.530 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 6 residues processed: 17 average time/residue: 0.5009 time to fit residues: 17.3208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 0.9990 chunk 168 optimal weight: 9.9990 chunk 179 optimal weight: 9.9990 chunk 108 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 141 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 162 optimal weight: 9.9990 chunk 169 optimal weight: 8.9990 chunk 117 optimal weight: 20.0000 chunk 189 optimal weight: 9.9990 overall best weight: 3.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 ASN ** A1633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.6136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 16456 Z= 0.244 Angle : 0.672 8.550 22270 Z= 0.358 Chirality : 0.040 0.144 2460 Planarity : 0.005 0.112 2828 Dihedral : 6.142 35.871 2186 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 1.05 % Allowed : 13.29 % Favored : 85.66 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.19), residues: 1994 helix: 0.58 (0.16), residues: 1009 sheet: -1.60 (0.42), residues: 135 loop : -3.22 (0.20), residues: 850 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 270 time to evaluate : 2.580 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: 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 outliers start: 15 outliers final: 10 residues processed: 280 average time/residue: 0.6696 time to fit residues: 281.1698 Evaluate side-chains 271 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 261 time to evaluate : 2.478 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 10 average time/residue: 0.4533 time to fit residues: 11.1683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 132 optimal weight: 9.9990 chunk 199 optimal weight: 9.9990 chunk 183 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 122 optimal weight: 20.0000 chunk 97 optimal weight: 0.9980 chunk 126 optimal weight: 0.5980 chunk 169 optimal weight: 10.0000 overall best weight: 3.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 ASN ** A2076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.6306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 16456 Z= 0.224 Angle : 0.661 7.842 22270 Z= 0.351 Chirality : 0.040 0.151 2460 Planarity : 0.005 0.111 2828 Dihedral : 6.065 35.556 2186 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 1.05 % Allowed : 12.89 % Favored : 86.06 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.19), residues: 1994 helix: 0.65 (0.16), residues: 1010 sheet: -1.50 (0.42), residues: 135 loop : -3.19 (0.20), residues: 849 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 273 time to evaluate : 2.472 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: 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 outliers start: 12 outliers final: 11 residues processed: 280 average time/residue: 0.6726 time to fit residues: 285.6694 Evaluate side-chains 272 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 261 time to evaluate : 2.521 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 11 average time/residue: 0.4344 time to fit residues: 11.6979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 10.0000 chunk 146 optimal weight: 0.0470 chunk 23 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 158 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 163 optimal weight: 0.0970 chunk 20 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 139 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 overall best weight: 1.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN A 618 ASN ** A2076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.163888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.143262 restraints weight = 83374.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.148884 restraints weight = 35767.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.152321 restraints weight = 19823.987| |-----------------------------------------------------------------------------| r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.6441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 16456 Z= 0.196 Angle : 0.644 7.374 22270 Z= 0.340 Chirality : 0.040 0.156 2460 Planarity : 0.005 0.112 2828 Dihedral : 5.923 35.019 2186 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 1.00 % Allowed : 12.14 % Favored : 86.86 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.19), residues: 1994 helix: 0.80 (0.17), residues: 1013 sheet: -1.31 (0.43), residues: 135 loop : -3.12 (0.20), residues: 846 =============================================================================== Job complete usr+sys time: 6976.00 seconds wall clock time: 124 minutes 54.98 seconds (7494.98 seconds total)