Starting phenix.real_space_refine (version: dev) on Fri Apr 8 04:06:47 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a22_6337/04_2022/5a22_6337_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a22_6337/04_2022/5a22_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_6337/04_2022/5a22_6337.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a22_6337/04_2022/5a22_6337.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a22_6337/04_2022/5a22_6337_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a22_6337/04_2022/5a22_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 Convert atoms to be neutral 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-dev-4553/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: {'undetermined': 2, 'peptide': 2002} 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: 15.32, per 1000 atoms: 0.48 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: 27.58 Conformation dependent library (CDL) restraints added in 2.7 seconds Dynamic metal coordination Zn2+ tetrahedral 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: 1.25 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: 16.24 Time building geometry restraints manager: 28.34 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 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. 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: 0.070 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: 0.490 Extract box with map and model: 3.680 Check model and map are aligned: 0.510 Convert atoms to be neutral: 0.280 Process input model: 111.370 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 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 : 14.01 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 : 2.694 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: 0.7367 time to fit residues: 568.0036 Evaluate side-chains 345 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 310 time to evaluate : 2.532 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: 0.3988 time to fit residues: 28.0231 ------------------------------------------------------------------------------- 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: 10.0000 chunk 102 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 181 optimal weight: 8.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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: 0.8189 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 16456 Z= 0.277 Angle : 0.797 8.196 22270 Z= 0.430 Chirality : 0.044 0.196 2460 Planarity : 0.006 0.117 2828 Dihedral : 7.587 37.275 2186 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 1.20 % Allowed : 12.84 % Favored : 85.96 % Rotamer Outliers : 2.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.26 % 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: -3.53 (0.16), residues: 1994 helix: -1.38 (0.14), residues: 1012 sheet: -1.94 (0.40), residues: 113 loop : -3.62 (0.18), residues: 869 *********************** 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 388 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 346 time to evaluate : 2.518 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 outliers start: 42 outliers final: 30 residues processed: 375 average time/residue: 0.6403 time to fit residues: 360.5076 Evaluate side-chains 311 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 281 time to evaluate : 2.551 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 3 residues processed: 30 average time/residue: 0.3749 time to fit residues: 23.8573 ------------------------------------------------------------------------------- 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: 20.0000 chunk 56 optimal weight: 10.0000 chunk 151 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 181 optimal weight: 20.0000 chunk 196 optimal weight: 9.9990 chunk 162 optimal weight: 9.9990 chunk 180 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 145 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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 613 GLN A 618 ASN ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2045 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.062 16456 Z= 0.390 Angle : 0.792 8.624 22270 Z= 0.431 Chirality : 0.044 0.173 2460 Planarity : 0.006 0.109 2828 Dihedral : 7.149 37.909 2186 Min Nonbonded Distance : 1.678 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 1.20 % Allowed : 15.35 % Favored : 83.45 % Rotamer Outliers : 3.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.21 % 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: -2.95 (0.17), residues: 1994 helix: -0.67 (0.15), residues: 1006 sheet: -2.09 (0.41), residues: 114 loop : -3.61 (0.18), residues: 874 *********************** 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 355 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 299 time to evaluate : 2.578 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: 56 outliers final: 31 residues processed: 344 average time/residue: 0.6382 time to fit residues: 327.8516 Evaluate side-chains 296 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 265 time to evaluate : 2.780 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 3 residues processed: 31 average time/residue: 0.3735 time to fit residues: 24.7828 ------------------------------------------------------------------------------- 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: 5.9990 chunk 136 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 182 optimal weight: 10.0000 chunk 193 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 chunk 173 optimal weight: 20.0000 chunk 52 optimal weight: 0.6980 overall best weight: 3.7186 ------------------------------------------------------------------------------- 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** A2045 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 16456 Z= 0.253 Angle : 0.705 7.998 22270 Z= 0.378 Chirality : 0.041 0.155 2460 Planarity : 0.005 0.112 2828 Dihedral : 6.811 35.857 2186 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 1.20 % Allowed : 13.34 % Favored : 85.46 % Rotamer Outliers : 2.01 % 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: -2.43 (0.18), residues: 1994 helix: -0.16 (0.16), residues: 1003 sheet: -1.93 (0.43), residues: 113 loop : -3.44 (0.19), residues: 878 *********************** 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 339 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 303 time to evaluate : 2.729 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 outliers start: 36 outliers final: 20 residues processed: 327 average time/residue: 0.6305 time to fit residues: 311.6197 Evaluate side-chains 291 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 271 time to evaluate : 2.608 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: 0.4067 time to fit residues: 17.6177 ------------------------------------------------------------------------------- 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: 5.9990 chunk 2 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 chunk 164 optimal weight: 0.9980 chunk 133 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 98 optimal weight: 20.0000 chunk 173 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- 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 618 ASN A 712 GLN ** 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: 0.8193 moved from start: 0.5330 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= 0.242 Angle : 0.688 8.666 22270 Z= 0.367 Chirality : 0.041 0.174 2460 Planarity : 0.005 0.113 2828 Dihedral : 6.545 36.969 2186 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 1.10 % Allowed : 13.79 % Favored : 85.11 % Rotamer Outliers : 1.73 % 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: -2.11 (0.18), residues: 1994 helix: 0.12 (0.16), residues: 1009 sheet: -1.83 (0.44), residues: 121 loop : -3.32 (0.19), residues: 864 *********************** 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 318 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 287 time to evaluate : 2.758 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: 31 outliers final: 25 residues processed: 306 average time/residue: 0.6403 time to fit residues: 297.0273 Evaluate side-chains 287 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 262 time to evaluate : 2.815 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 4 residues processed: 25 average time/residue: 0.4135 time to fit residues: 22.3279 ------------------------------------------------------------------------------- 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: 7.9990 chunk 174 optimal weight: 30.0000 chunk 38 optimal weight: 0.0980 chunk 113 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 193 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 101 optimal weight: 20.0000 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 ASN A 712 GLN A2045 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.5593 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= 0.254 Angle : 0.680 8.191 22270 Z= 0.364 Chirality : 0.041 0.160 2460 Planarity : 0.006 0.114 2828 Dihedral : 6.428 36.118 2186 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 1.10 % Allowed : 13.49 % Favored : 85.41 % Rotamer Outliers : 1.51 % 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: -1.95 (0.18), residues: 1994 helix: 0.29 (0.16), residues: 1012 sheet: -1.79 (0.43), residues: 124 loop : -3.29 (0.19), residues: 858 *********************** 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 313 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 286 time to evaluate : 2.565 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: 27 outliers final: 15 residues processed: 300 average time/residue: 0.6350 time to fit residues: 287.5095 Evaluate side-chains 276 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 261 time to evaluate : 2.668 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 4 residues processed: 15 average time/residue: 0.4187 time to fit residues: 14.2816 ------------------------------------------------------------------------------- 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: 9.9990 chunk 21 optimal weight: 8.9990 chunk 110 optimal weight: 0.8980 chunk 141 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 chunk 162 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 192 optimal weight: 0.9980 chunk 120 optimal weight: 10.0000 chunk 117 optimal weight: 20.0000 chunk 88 optimal weight: 10.0000 overall best weight: 4.5786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2045 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.5798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 16456 Z= 0.267 Angle : 0.684 8.092 22270 Z= 0.365 Chirality : 0.041 0.161 2460 Planarity : 0.006 0.114 2828 Dihedral : 6.355 36.363 2186 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 1.10 % Allowed : 14.09 % Favored : 84.80 % Rotamer Outliers : 1.67 % 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: -1.90 (0.18), residues: 1994 helix: 0.33 (0.16), residues: 1012 sheet: -1.73 (0.40), residues: 137 loop : -3.30 (0.20), residues: 845 *********************** 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 289 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 259 time to evaluate : 2.609 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 outliers start: 30 outliers final: 25 residues processed: 276 average time/residue: 0.6274 time to fit residues: 263.1514 Evaluate side-chains 273 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 248 time to evaluate : 2.709 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 5 residues processed: 25 average time/residue: 0.3827 time to fit residues: 21.0095 ------------------------------------------------------------------------------- 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: 9.9990 chunk 76 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 122 optimal weight: 9.9990 chunk 131 optimal weight: 9.9990 chunk 95 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 151 optimal weight: 3.9990 chunk 175 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8200 moved from start: 0.5981 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= 0.265 Angle : 0.685 7.699 22270 Z= 0.366 Chirality : 0.041 0.152 2460 Planarity : 0.006 0.114 2828 Dihedral : 6.262 35.996 2186 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 1.10 % Allowed : 13.94 % Favored : 84.95 % Rotamer Outliers : 1.23 % 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: -1.84 (0.19), residues: 1994 helix: 0.35 (0.16), residues: 1019 sheet: -1.62 (0.41), residues: 137 loop : -3.28 (0.20), residues: 838 *********************** 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 283 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 261 time to evaluate : 3.016 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 outliers start: 22 outliers final: 13 residues processed: 276 average time/residue: 0.6427 time to fit residues: 268.1962 Evaluate side-chains 261 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 248 time to evaluate : 2.642 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 13 average time/residue: 0.4143 time to fit residues: 12.6401 ------------------------------------------------------------------------------- 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: 7.9990 chunk 168 optimal weight: 7.9990 chunk 179 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 141 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 chunk 162 optimal weight: 10.0000 chunk 169 optimal weight: 7.9990 chunk 117 optimal weight: 20.0000 chunk 189 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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** ** A1633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.6057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 1.089 16456 Z= 0.872 Angle : 0.997 94.674 22270 Z= 0.469 Chirality : 0.043 0.299 2460 Planarity : 0.006 0.122 2828 Dihedral : 6.286 35.444 2186 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 20.94 Ramachandran Plot: Outliers : 1.10 % Allowed : 14.34 % Favored : 84.55 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % 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: -1.90 (0.19), residues: 1994 helix: 0.33 (0.16), residues: 1012 sheet: -1.60 (0.41), residues: 135 loop : -3.32 (0.20), residues: 847 *********************** 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 272 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 252 time to evaluate : 2.599 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 outliers start: 20 outliers final: 17 residues processed: 260 average time/residue: 0.6404 time to fit residues: 251.3070 Evaluate side-chains 262 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 245 time to evaluate : 3.630 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 5 residues processed: 17 average time/residue: 0.4084 time to fit residues: 15.5100 ------------------------------------------------------------------------------- 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: 3.9990 chunk 90 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 199 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 158 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 chunk 169 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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** ** A1633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.6123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 1.112 16456 Z= 0.847 Angle : 0.968 95.884 22270 Z= 0.437 Chirality : 0.042 0.307 2460 Planarity : 0.006 0.114 2828 Dihedral : 6.255 36.041 2186 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 19.45 Ramachandran Plot: Outliers : 1.10 % Allowed : 13.69 % Favored : 85.21 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.05 % 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: -1.80 (0.19), residues: 1994 helix: 0.37 (0.16), residues: 1017 sheet: -1.55 (0.41), residues: 135 loop : -3.25 (0.20), residues: 842 ********************** 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 272 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 262 time to evaluate : 3.301 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 outliers start: 10 outliers final: 9 residues processed: 265 average time/residue: 0.6357 time to fit residues: 254.6471 Evaluate side-chains 256 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 247 time to evaluate : 2.542 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 9 average time/residue: 0.4086 time to fit residues: 9.7605 ------------------------------------------------------------------------------- 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: 0.9990 chunk 23 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 158 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 163 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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** ** A1633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1692 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.163265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.141103 restraints weight = 83133.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.147142 restraints weight = 35501.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.150882 restraints weight = 19779.450| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.6158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 1.149 16456 Z= 0.848 Angle : 1.013 103.825 22270 Z= 0.456 Chirality : 0.042 0.308 2460 Planarity : 0.006 0.114 2828 Dihedral : 6.250 35.926 2186 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 1.10 % Allowed : 13.59 % Favored : 85.31 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.05 % 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: -1.79 (0.19), residues: 1994 helix: 0.39 (0.16), residues: 1017 sheet: -1.53 (0.41), residues: 135 loop : -3.25 (0.20), residues: 842 =============================================================================== Job complete usr+sys time: 6666.82 seconds wall clock time: 119 minutes 33.46 seconds (7173.46 seconds total)