Starting phenix.real_space_refine on Sat Apr 6 19:36:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pmd_17759/04_2024/8pmd_17759_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pmd_17759/04_2024/8pmd_17759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pmd_17759/04_2024/8pmd_17759.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pmd_17759/04_2024/8pmd_17759.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pmd_17759/04_2024/8pmd_17759_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pmd_17759/04_2024/8pmd_17759_updated.pdb" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 52 5.16 5 C 5651 2.51 5 N 1497 2.21 5 O 1636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A GLU 300": "OE1" <-> "OE2" Residue "A PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 404": "OD1" <-> "OD2" Residue "A GLU 476": "OE1" <-> "OE2" Residue "A GLU 521": "OE1" <-> "OE2" Residue "A GLU 534": "OE1" <-> "OE2" Residue "A PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 790": "OE1" <-> "OE2" Residue "A PHE 971": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1069": "OE1" <-> "OE2" Residue "A PHE 1111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1186": "OE1" <-> "OE2" Residue "A GLU 1209": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8844 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 8778 Classifications: {'peptide': 1129} Link IDs: {'PTRANS': 31, 'TRANS': 1097} Chain breaks: 5 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4, 'water': 2} Link IDs: {None: 5} Time building chain proxies: 5.55, per 1000 atoms: 0.63 Number of scatterers: 8844 At special positions: 0 Unit cell: (89.1, 79.2, 148.5, 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) S 52 16.00 P 6 15.00 Mg 2 11.99 O 1636 8.00 N 1497 7.00 C 5651 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.64 Conformation dependent library (CDL) restraints added in 1.8 seconds 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2080 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 4 sheets defined 63.0% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.58 Creating SS restraints... Processing helix chain 'A' and resid 47 through 49 No H-bonds generated for 'chain 'A' and resid 47 through 49' Processing helix chain 'A' and resid 56 through 99 removed outlier: 4.312A pdb=" N GLN A 76 " --> pdb=" O HIS A 72 " (cutoff:3.500A) Proline residue: A 77 - end of helix removed outlier: 4.260A pdb=" N GLU A 96 " --> pdb=" O ASP A 92 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A 97 " --> pdb=" O TYR A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 183 Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 195 through 213 removed outlier: 4.949A pdb=" N ILE A 206 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASN A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 213 " --> pdb=" O ILE A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 236 removed outlier: 4.304A pdb=" N GLY A 234 " --> pdb=" O GLY A 230 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE A 235 " --> pdb=" O PHE A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 286 Proline residue: A 250 - end of helix Processing helix chain 'A' and resid 288 through 293 Processing helix chain 'A' and resid 297 through 343 removed outlier: 3.904A pdb=" N ASN A 307 " --> pdb=" O ARG A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 397 removed outlier: 4.271A pdb=" N SER A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Proline residue: A 378 - end of helix removed outlier: 4.557A pdb=" N SER A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 468 Processing helix chain 'A' and resid 486 through 488 No H-bonds generated for 'chain 'A' and resid 486 through 488' Processing helix chain 'A' and resid 491 through 497 removed outlier: 3.780A pdb=" N GLN A 497 " --> pdb=" O TRP A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 518 Processing helix chain 'A' and resid 525 through 534 Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 554 through 556 No H-bonds generated for 'chain 'A' and resid 554 through 556' Processing helix chain 'A' and resid 561 through 573 Processing helix chain 'A' and resid 591 through 606 removed outlier: 4.695A pdb=" N HIS A 606 " --> pdb=" O SER A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 622 removed outlier: 4.951A pdb=" N ALA A 622 " --> pdb=" O SER A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 780 removed outlier: 3.819A pdb=" N ALA A 749 " --> pdb=" O LEU A 745 " (cutoff:3.500A) Proline residue: A 750 - end of helix Proline residue: A 753 - end of helix removed outlier: 4.402A pdb=" N THR A 769 " --> pdb=" O ASN A 765 " (cutoff:3.500A) Proline residue: A 770 - end of helix Processing helix chain 'A' and resid 794 through 840 removed outlier: 3.788A pdb=" N PHE A 811 " --> pdb=" O CYS A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 847 No H-bonds generated for 'chain 'A' and resid 844 through 847' Processing helix chain 'A' and resid 854 through 872 removed outlier: 4.211A pdb=" N ALA A 865 " --> pdb=" O LEU A 861 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA A 871 " --> pdb=" O GLN A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 894 Processing helix chain 'A' and resid 898 through 945 removed outlier: 4.543A pdb=" N PHE A 907 " --> pdb=" O VAL A 903 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N PHE A 908 " --> pdb=" O ILE A 904 " (cutoff:3.500A) Proline residue: A 909 - end of helix removed outlier: 4.243A pdb=" N ARG A 928 " --> pdb=" O GLY A 924 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLN A 931 " --> pdb=" O SER A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 953 Processing helix chain 'A' and resid 956 through 967 removed outlier: 3.546A pdb=" N ILE A 960 " --> pdb=" O GLU A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 1009 removed outlier: 4.159A pdb=" N THR A 973 " --> pdb=" O LYS A 969 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASN A 979 " --> pdb=" O ILE A 975 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 980 " --> pdb=" O GLN A 976 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE A 993 " --> pdb=" O GLN A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1027 Processing helix chain 'A' and resid 1030 through 1032 No H-bonds generated for 'chain 'A' and resid 1030 through 1032' Processing helix chain 'A' and resid 1038 through 1055 removed outlier: 3.615A pdb=" N ALA A1042 " --> pdb=" O THR A1038 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS A1043 " --> pdb=" O PRO A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1126 removed outlier: 3.556A pdb=" N ILE A1123 " --> pdb=" O LYS A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1155 removed outlier: 3.835A pdb=" N ASN A1155 " --> pdb=" O PHE A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1177 removed outlier: 4.524A pdb=" N GLY A1177 " --> pdb=" O ASN A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1194 Processing helix chain 'A' and resid 1198 through 1202 Processing helix chain 'A' and resid 1214 through 1216 No H-bonds generated for 'chain 'A' and resid 1214 through 1216' Processing helix chain 'A' and resid 1221 through 1235 removed outlier: 4.095A pdb=" N ARG A1235 " --> pdb=" O ARG A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1265 Processing helix chain 'A' and resid 1300 through 1306 Processing helix chain 'A' and resid 1309 through 1315 Processing sheet with id= A, first strand: chain 'A' and resid 634 through 636 removed outlier: 6.609A pdb=" N ILE A 610 " --> pdb=" O THR A 451 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N LEU A 453 " --> pdb=" O ILE A 610 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N SER A 612 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N GLY A 455 " --> pdb=" O SER A 612 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1078 through 1081 Processing sheet with id= C, first strand: chain 'A' and resid 1293 through 1298 removed outlier: 6.721A pdb=" N VAL A1288 " --> pdb=" O ILE A1295 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LYS A1297 " --> pdb=" O ILE A1286 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE A1286 " --> pdb=" O LYS A1297 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N CYS A1270 " --> pdb=" O LEU A1109 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N PHE A1111 " --> pdb=" O CYS A1270 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL A1272 " --> pdb=" O PHE A1111 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1083 through 1085 removed outlier: 8.029A pdb=" N PHE A1085 " --> pdb=" O ASN A1097 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ASN A1097 " --> pdb=" O PHE A1085 " (cutoff:3.500A) 528 hydrogen bonds defined for protein. 1569 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: 2.86 Time building geometry restraints manager: 3.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1440 1.32 - 1.44: 2403 1.44 - 1.56: 5073 1.56 - 1.69: 10 1.69 - 1.81: 85 Bond restraints: 9011 Sorted by residual: bond pdb=" C PHE A1111 " pdb=" O PHE A1111 " ideal model delta sigma weight residual 1.236 1.192 0.044 1.22e-02 6.72e+03 1.31e+01 bond pdb=" C LYS A 930 " pdb=" N GLN A 931 " ideal model delta sigma weight residual 1.335 1.297 0.037 1.36e-02 5.41e+03 7.58e+00 bond pdb=" C ALA A 773 " pdb=" N PHE A 774 " ideal model delta sigma weight residual 1.334 1.298 0.037 1.33e-02 5.65e+03 7.54e+00 bond pdb=" N ILE A1273 " pdb=" CA ILE A1273 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.20e-02 6.94e+03 7.00e+00 bond pdb=" C GLU A 504 " pdb=" N PRO A 505 " ideal model delta sigma weight residual 1.332 1.366 -0.034 1.30e-02 5.92e+03 6.81e+00 ... (remaining 9006 not shown) Histogram of bond angle deviations from ideal: 98.33 - 106.64: 209 106.64 - 114.96: 5346 114.96 - 123.27: 6354 123.27 - 131.58: 262 131.58 - 139.89: 18 Bond angle restraints: 12189 Sorted by residual: angle pdb=" N LEU A 332 " pdb=" CA LEU A 332 " pdb=" C LEU A 332 " ideal model delta sigma weight residual 111.03 104.70 6.33 1.11e+00 8.12e-01 3.26e+01 angle pdb=" CA ILE A 416 " pdb=" C ILE A 416 " pdb=" O ILE A 416 " ideal model delta sigma weight residual 121.23 115.36 5.87 1.07e+00 8.73e-01 3.01e+01 angle pdb=" CA PHE A 70 " pdb=" C PHE A 70 " pdb=" O PHE A 70 " ideal model delta sigma weight residual 120.55 115.55 5.00 1.06e+00 8.90e-01 2.22e+01 angle pdb=" CA TYR A 145 " pdb=" C TYR A 145 " pdb=" N ALA A 146 " ideal model delta sigma weight residual 117.63 122.64 -5.01 1.25e+00 6.40e-01 1.61e+01 angle pdb=" CA ILE A 416 " pdb=" C ILE A 416 " pdb=" N LYS A 417 " ideal model delta sigma weight residual 116.10 120.87 -4.77 1.20e+00 6.94e-01 1.58e+01 ... (remaining 12184 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 4544 17.11 - 34.21: 561 34.21 - 51.32: 224 51.32 - 68.42: 43 68.42 - 85.53: 17 Dihedral angle restraints: 5389 sinusoidal: 2153 harmonic: 3236 Sorted by residual: dihedral pdb=" CA ASP A 404 " pdb=" CB ASP A 404 " pdb=" CG ASP A 404 " pdb=" OD1 ASP A 404 " ideal model delta sinusoidal sigma weight residual -30.00 -89.80 59.80 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CG ARG A 575 " pdb=" CD ARG A 575 " pdb=" NE ARG A 575 " pdb=" CZ ARG A 575 " ideal model delta sinusoidal sigma weight residual -90.00 -134.34 44.34 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CG ARG A 487 " pdb=" CD ARG A 487 " pdb=" NE ARG A 487 " pdb=" CZ ARG A 487 " ideal model delta sinusoidal sigma weight residual 90.00 131.92 -41.92 2 1.50e+01 4.44e-03 9.52e+00 ... (remaining 5386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1095 0.051 - 0.102: 234 0.102 - 0.153: 48 0.153 - 0.204: 4 0.204 - 0.255: 1 Chirality restraints: 1382 Sorted by residual: chirality pdb=" CA ILE A 416 " pdb=" N ILE A 416 " pdb=" C ILE A 416 " pdb=" CB ILE A 416 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA LEU A 332 " pdb=" N LEU A 332 " pdb=" C LEU A 332 " pdb=" CB LEU A 332 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.97e-01 chirality pdb=" CG LEU A 827 " pdb=" CB LEU A 827 " pdb=" CD1 LEU A 827 " pdb=" CD2 LEU A 827 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.77e-01 ... (remaining 1379 not shown) Planarity restraints: 1544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 416 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.94e+00 pdb=" C ILE A 416 " -0.052 2.00e-02 2.50e+03 pdb=" O ILE A 416 " 0.019 2.00e-02 2.50e+03 pdb=" N LYS A 417 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 332 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.98e+00 pdb=" C LEU A 332 " 0.049 2.00e-02 2.50e+03 pdb=" O LEU A 332 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE A 333 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 216 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.18e+00 pdb=" C GLN A 216 " 0.046 2.00e-02 2.50e+03 pdb=" O GLN A 216 " -0.018 2.00e-02 2.50e+03 pdb=" N MET A 217 " -0.016 2.00e-02 2.50e+03 ... (remaining 1541 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.06: 7 2.06 - 2.77: 1746 2.77 - 3.48: 13100 3.48 - 4.19: 20733 4.19 - 4.90: 37468 Nonbonded interactions: 73054 Sorted by model distance: nonbonded pdb=" OE2 GLU A1127 " pdb=" CD1 ILE A1158 " model vdw 1.353 3.460 nonbonded pdb="MG MG A1503 " pdb=" O HOH A1601 " model vdw 1.962 2.170 nonbonded pdb=" OE1 GLN A1161 " pdb="MG MG A1503 " model vdw 1.981 2.170 nonbonded pdb=" OG SER A1120 " pdb="MG MG A1503 " model vdw 2.018 2.170 nonbonded pdb=" O3G ATP A1502 " pdb="MG MG A1504 " model vdw 2.027 2.170 ... (remaining 73049 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.93 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.310 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 28.670 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 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 : 0.004 0.044 9011 Z= 0.241 Angle : 0.658 6.699 12189 Z= 0.384 Chirality : 0.044 0.255 1382 Planarity : 0.004 0.054 1544 Dihedral : 18.209 85.530 3309 Min Nonbonded Distance : 1.353 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.21 % Allowed : 28.83 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.24), residues: 1117 helix: 1.42 (0.18), residues: 736 sheet: 0.56 (0.54), residues: 77 loop : -0.94 (0.32), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1071 HIS 0.003 0.001 HIS A 428 PHE 0.018 0.002 PHE A 747 TYR 0.025 0.002 TYR A 337 ARG 0.009 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 207 time to evaluate : 0.925 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 207 average time/residue: 1.1227 time to fit residues: 248.6918 Evaluate side-chains 187 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 186 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 776 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 5.9990 chunk 84 optimal weight: 0.3980 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 33 optimal weight: 0.0570 chunk 53 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 overall best weight: 1.2700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN A 598 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.0685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9011 Z= 0.216 Angle : 0.550 7.562 12189 Z= 0.297 Chirality : 0.042 0.145 1382 Planarity : 0.004 0.048 1544 Dihedral : 8.807 82.932 1285 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 6.32 % Allowed : 26.15 % Favored : 67.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.24), residues: 1117 helix: 1.54 (0.19), residues: 738 sheet: 0.80 (0.53), residues: 75 loop : -0.91 (0.32), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 163 HIS 0.003 0.001 HIS A 428 PHE 0.022 0.001 PHE A 383 TYR 0.020 0.001 TYR A 337 ARG 0.006 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 199 time to evaluate : 1.036 Fit side-chains revert: symmetry clash REVERT: A 80 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8052 (mt) REVERT: A 268 ASP cc_start: 0.8232 (t0) cc_final: 0.8018 (t0) REVERT: A 611 ILE cc_start: 0.8826 (mt) cc_final: 0.8540 (tt) REVERT: A 956 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7312 (mm-30) REVERT: A 1238 LYS cc_start: 0.7679 (mtpm) cc_final: 0.7409 (ttmt) outliers start: 59 outliers final: 27 residues processed: 234 average time/residue: 1.1156 time to fit residues: 280.0482 Evaluate side-chains 220 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 191 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 776 PHE Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1093 SER Chi-restraints excluded: chain A residue 1122 SER Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1183 ILE Chi-restraints excluded: chain A residue 1206 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN A 598 GLN ** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9011 Z= 0.196 Angle : 0.532 7.731 12189 Z= 0.286 Chirality : 0.041 0.138 1382 Planarity : 0.003 0.049 1544 Dihedral : 8.582 88.746 1285 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 6.65 % Allowed : 25.83 % Favored : 67.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.24), residues: 1117 helix: 1.60 (0.19), residues: 738 sheet: 0.67 (0.52), residues: 77 loop : -0.93 (0.32), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 163 HIS 0.004 0.001 HIS A 428 PHE 0.014 0.001 PHE A 811 TYR 0.024 0.001 TYR A 337 ARG 0.003 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 203 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: A 80 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8022 (mt) REVERT: A 268 ASP cc_start: 0.8219 (t0) cc_final: 0.7991 (t0) REVERT: A 399 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.6874 (ttt90) REVERT: A 450 MET cc_start: 0.7755 (OUTLIER) cc_final: 0.7379 (tmm) REVERT: A 956 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7316 (mm-30) REVERT: A 1001 ARG cc_start: 0.7525 (tpm170) cc_final: 0.7304 (tpm170) REVERT: A 1108 THR cc_start: 0.7562 (t) cc_final: 0.7271 (m) REVERT: A 1235 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.6570 (mtm180) outliers start: 62 outliers final: 29 residues processed: 241 average time/residue: 1.1274 time to fit residues: 291.2632 Evaluate side-chains 222 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 188 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 399 ARG Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1008 SER Chi-restraints excluded: chain A residue 1093 SER Chi-restraints excluded: chain A residue 1122 SER Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1206 GLU Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1235 ARG Chi-restraints excluded: chain A residue 1255 LYS Chi-restraints excluded: chain A residue 1262 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN ** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1009 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 9011 Z= 0.407 Angle : 0.681 6.854 12189 Z= 0.373 Chirality : 0.048 0.153 1382 Planarity : 0.005 0.052 1544 Dihedral : 8.880 89.384 1283 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 8.79 % Allowed : 24.44 % Favored : 66.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.23), residues: 1117 helix: 0.83 (0.18), residues: 733 sheet: 0.31 (0.51), residues: 77 loop : -1.35 (0.30), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 163 HIS 0.005 0.001 HIS A 428 PHE 0.030 0.002 PHE A 776 TYR 0.022 0.002 TYR A 337 ARG 0.005 0.001 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 210 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8031 (mt) REVERT: A 268 ASP cc_start: 0.8259 (t0) cc_final: 0.7973 (t70) REVERT: A 321 VAL cc_start: 0.7842 (OUTLIER) cc_final: 0.7601 (m) REVERT: A 399 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7137 (ttt90) REVERT: A 813 GLN cc_start: 0.8006 (tp40) cc_final: 0.7611 (mm-40) REVERT: A 956 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7348 (mm-30) REVERT: A 989 GLN cc_start: 0.7354 (OUTLIER) cc_final: 0.7053 (mt0) REVERT: A 1001 ARG cc_start: 0.7734 (tpm170) cc_final: 0.7456 (tpm170) REVERT: A 1296 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7364 (mt-10) outliers start: 82 outliers final: 39 residues processed: 266 average time/residue: 1.0455 time to fit residues: 298.9664 Evaluate side-chains 244 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 199 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 399 ARG Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 930 LYS Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 989 GLN Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1072 ASP Chi-restraints excluded: chain A residue 1093 SER Chi-restraints excluded: chain A residue 1122 SER Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1183 ILE Chi-restraints excluded: chain A residue 1206 GLU Chi-restraints excluded: chain A residue 1235 ARG Chi-restraints excluded: chain A residue 1255 LYS Chi-restraints excluded: chain A residue 1296 GLU Chi-restraints excluded: chain A residue 1315 THR Chi-restraints excluded: chain A residue 1316 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN A 598 GLN ** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9011 Z= 0.222 Angle : 0.571 6.451 12189 Z= 0.312 Chirality : 0.043 0.184 1382 Planarity : 0.004 0.050 1544 Dihedral : 8.423 86.305 1283 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 6.43 % Allowed : 28.08 % Favored : 65.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.24), residues: 1117 helix: 1.20 (0.18), residues: 733 sheet: 0.54 (0.54), residues: 77 loop : -1.19 (0.31), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1071 HIS 0.003 0.001 HIS A 428 PHE 0.021 0.001 PHE A 774 TYR 0.020 0.002 TYR A 337 ARG 0.003 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 196 time to evaluate : 0.992 Fit side-chains REVERT: A 80 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7958 (mt) REVERT: A 269 TYR cc_start: 0.7178 (m-10) cc_final: 0.6803 (m-10) REVERT: A 321 VAL cc_start: 0.7918 (OUTLIER) cc_final: 0.7667 (m) REVERT: A 399 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.6995 (ttt90) REVERT: A 496 ASP cc_start: 0.8932 (p0) cc_final: 0.8691 (p0) REVERT: A 573 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7915 (mp) REVERT: A 934 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7260 (mp0) REVERT: A 956 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7300 (mm-30) REVERT: A 1235 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.6523 (mtm180) REVERT: A 1291 GLN cc_start: 0.7757 (mt0) cc_final: 0.7325 (mt0) REVERT: A 1296 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7309 (mt-10) REVERT: A 1302 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7603 (mt-10) outliers start: 60 outliers final: 28 residues processed: 234 average time/residue: 1.1355 time to fit residues: 284.3932 Evaluate side-chains 227 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 190 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 399 ARG Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 776 PHE Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 930 LYS Chi-restraints excluded: chain A residue 934 GLU Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1093 SER Chi-restraints excluded: chain A residue 1122 SER Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1183 ILE Chi-restraints excluded: chain A residue 1235 ARG Chi-restraints excluded: chain A residue 1296 GLU Chi-restraints excluded: chain A residue 1302 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 63 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 108 optimal weight: 9.9990 chunk 89 optimal weight: 0.7980 chunk 50 optimal weight: 0.0370 chunk 9 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 overall best weight: 0.8862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN A 598 GLN ** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 ASN A1097 ASN ** A1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9011 Z= 0.189 Angle : 0.554 8.382 12189 Z= 0.298 Chirality : 0.041 0.163 1382 Planarity : 0.003 0.052 1544 Dihedral : 8.113 81.985 1283 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 6.65 % Allowed : 28.08 % Favored : 65.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.24), residues: 1117 helix: 1.40 (0.19), residues: 731 sheet: 0.86 (0.56), residues: 77 loop : -1.02 (0.31), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 163 HIS 0.003 0.001 HIS A 428 PHE 0.028 0.001 PHE A 70 TYR 0.020 0.001 TYR A 337 ARG 0.005 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 194 time to evaluate : 0.977 Fit side-chains revert: symmetry clash REVERT: A 80 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8111 (mt) REVERT: A 269 TYR cc_start: 0.7151 (m-10) cc_final: 0.6762 (m-10) REVERT: A 321 VAL cc_start: 0.7911 (OUTLIER) cc_final: 0.7650 (m) REVERT: A 399 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.6903 (ttt90) REVERT: A 450 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7022 (tmm) REVERT: A 496 ASP cc_start: 0.8830 (p0) cc_final: 0.8611 (p0) REVERT: A 591 ASN cc_start: 0.7730 (m-40) cc_final: 0.7458 (m110) REVERT: A 934 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7256 (mp0) REVERT: A 956 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7289 (mm-30) REVERT: A 972 LYS cc_start: 0.7240 (OUTLIER) cc_final: 0.7005 (mmtt) REVERT: A 1001 ARG cc_start: 0.7523 (tpm170) cc_final: 0.7313 (tpm170) REVERT: A 1235 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.6537 (mtm180) REVERT: A 1291 GLN cc_start: 0.7717 (mt0) cc_final: 0.7296 (mt0) REVERT: A 1296 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7272 (mt-10) REVERT: A 1302 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7580 (mt-10) outliers start: 62 outliers final: 35 residues processed: 235 average time/residue: 1.1461 time to fit residues: 288.0430 Evaluate side-chains 232 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 187 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 399 ARG Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 776 PHE Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 928 ARG Chi-restraints excluded: chain A residue 930 LYS Chi-restraints excluded: chain A residue 934 GLU Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 972 LYS Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1072 ASP Chi-restraints excluded: chain A residue 1093 SER Chi-restraints excluded: chain A residue 1122 SER Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1206 GLU Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1235 ARG Chi-restraints excluded: chain A residue 1262 ASP Chi-restraints excluded: chain A residue 1296 GLU Chi-restraints excluded: chain A residue 1302 GLU Chi-restraints excluded: chain A residue 1304 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN A 530 GLN A 598 GLN ** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9011 Z= 0.257 Angle : 0.596 6.635 12189 Z= 0.321 Chirality : 0.044 0.159 1382 Planarity : 0.004 0.051 1544 Dihedral : 8.204 81.224 1283 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 6.54 % Allowed : 28.30 % Favored : 65.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.24), residues: 1117 helix: 1.26 (0.18), residues: 731 sheet: 0.71 (0.56), residues: 78 loop : -1.09 (0.31), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 163 HIS 0.004 0.001 HIS A 428 PHE 0.022 0.002 PHE A 774 TYR 0.018 0.001 TYR A 337 ARG 0.005 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 187 time to evaluate : 1.094 Fit side-chains revert: symmetry clash REVERT: A 80 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8091 (mt) REVERT: A 224 MET cc_start: 0.8462 (mmp) cc_final: 0.8238 (mmm) REVERT: A 268 ASP cc_start: 0.8244 (t0) cc_final: 0.7912 (t70) REVERT: A 269 TYR cc_start: 0.7225 (m-10) cc_final: 0.6832 (m-10) REVERT: A 321 VAL cc_start: 0.7920 (OUTLIER) cc_final: 0.7662 (m) REVERT: A 399 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.6957 (ttt90) REVERT: A 450 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7067 (tmm) REVERT: A 496 ASP cc_start: 0.8866 (p0) cc_final: 0.8648 (p0) REVERT: A 591 ASN cc_start: 0.7813 (m-40) cc_final: 0.7566 (m110) REVERT: A 934 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7226 (mp0) REVERT: A 956 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7295 (mm-30) REVERT: A 972 LYS cc_start: 0.7285 (OUTLIER) cc_final: 0.7028 (mmtt) REVERT: A 989 GLN cc_start: 0.7205 (OUTLIER) cc_final: 0.6939 (mt0) REVERT: A 1001 ARG cc_start: 0.7622 (tpm170) cc_final: 0.7356 (tpm170) REVERT: A 1235 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.6584 (mtm180) REVERT: A 1291 GLN cc_start: 0.7733 (mt0) cc_final: 0.7311 (mt0) REVERT: A 1296 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7285 (mt-10) outliers start: 61 outliers final: 34 residues processed: 229 average time/residue: 1.1587 time to fit residues: 284.6582 Evaluate side-chains 226 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 182 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 399 ARG Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 776 PHE Chi-restraints excluded: chain A residue 853 SER Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 928 ARG Chi-restraints excluded: chain A residue 930 LYS Chi-restraints excluded: chain A residue 934 GLU Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 972 LYS Chi-restraints excluded: chain A residue 989 GLN Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1072 ASP Chi-restraints excluded: chain A residue 1093 SER Chi-restraints excluded: chain A residue 1122 SER Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1183 ILE Chi-restraints excluded: chain A residue 1206 GLU Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1235 ARG Chi-restraints excluded: chain A residue 1262 ASP Chi-restraints excluded: chain A residue 1296 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN A 598 GLN ** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 ASN ** A1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9011 Z= 0.221 Angle : 0.577 6.880 12189 Z= 0.311 Chirality : 0.043 0.155 1382 Planarity : 0.004 0.051 1544 Dihedral : 8.086 79.232 1283 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 6.43 % Allowed : 28.62 % Favored : 64.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.24), residues: 1117 helix: 1.32 (0.19), residues: 730 sheet: 0.80 (0.57), residues: 77 loop : -0.97 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 163 HIS 0.003 0.001 HIS A 428 PHE 0.031 0.002 PHE A 70 TYR 0.018 0.001 TYR A 337 ARG 0.005 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 187 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: A 224 MET cc_start: 0.8500 (mmp) cc_final: 0.8247 (mmm) REVERT: A 269 TYR cc_start: 0.7194 (m-10) cc_final: 0.6782 (m-10) REVERT: A 321 VAL cc_start: 0.7915 (OUTLIER) cc_final: 0.7657 (m) REVERT: A 399 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.6905 (ttt90) REVERT: A 450 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7014 (tmm) REVERT: A 934 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7199 (mp0) REVERT: A 956 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7299 (mm-30) REVERT: A 989 GLN cc_start: 0.7155 (OUTLIER) cc_final: 0.6895 (mt0) REVERT: A 1001 ARG cc_start: 0.7562 (tpm170) cc_final: 0.7311 (tpm170) REVERT: A 1235 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.6575 (mtm180) REVERT: A 1291 GLN cc_start: 0.7733 (mt0) cc_final: 0.7315 (mt0) REVERT: A 1296 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7286 (mt-10) REVERT: A 1302 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7566 (mt-10) outliers start: 60 outliers final: 35 residues processed: 226 average time/residue: 1.1371 time to fit residues: 275.0357 Evaluate side-chains 230 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 186 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 399 ARG Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 776 PHE Chi-restraints excluded: chain A residue 853 SER Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 928 ARG Chi-restraints excluded: chain A residue 930 LYS Chi-restraints excluded: chain A residue 934 GLU Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 989 GLN Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1072 ASP Chi-restraints excluded: chain A residue 1093 SER Chi-restraints excluded: chain A residue 1122 SER Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1206 GLU Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1235 ARG Chi-restraints excluded: chain A residue 1262 ASP Chi-restraints excluded: chain A residue 1296 GLU Chi-restraints excluded: chain A residue 1302 GLU Chi-restraints excluded: chain A residue 1304 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 30 optimal weight: 0.2980 chunk 90 optimal weight: 0.0270 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 0.0570 chunk 106 optimal weight: 3.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 GLN A 372 ASN A 490 ASN A 598 GLN ** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 ASN A1009 ASN A1300 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9011 Z= 0.166 Angle : 0.551 6.851 12189 Z= 0.294 Chirality : 0.041 0.161 1382 Planarity : 0.003 0.053 1544 Dihedral : 7.636 78.496 1283 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.54 % Allowed : 32.15 % Favored : 64.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.25), residues: 1117 helix: 1.61 (0.19), residues: 730 sheet: 0.92 (0.57), residues: 78 loop : -0.83 (0.32), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1071 HIS 0.002 0.000 HIS A 428 PHE 0.025 0.001 PHE A 774 TYR 0.018 0.001 TYR A 337 ARG 0.005 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 200 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 184 ARG cc_start: 0.7664 (ttt90) cc_final: 0.7459 (ttt90) REVERT: A 224 MET cc_start: 0.8480 (mmp) cc_final: 0.8199 (mmm) REVERT: A 268 ASP cc_start: 0.8246 (t0) cc_final: 0.8019 (t0) REVERT: A 269 TYR cc_start: 0.7113 (m-10) cc_final: 0.6793 (m-10) REVERT: A 956 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7214 (mm-30) REVERT: A 1291 GLN cc_start: 0.7698 (mt0) cc_final: 0.7288 (mt0) REVERT: A 1296 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7273 (mt-10) outliers start: 33 outliers final: 16 residues processed: 221 average time/residue: 1.0726 time to fit residues: 254.5209 Evaluate side-chains 201 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 183 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 776 PHE Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 899 LYS Chi-restraints excluded: chain A residue 928 ARG Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1296 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9980 chunk 50 optimal weight: 0.0980 chunk 73 optimal weight: 0.6980 chunk 111 optimal weight: 0.4980 chunk 102 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 GLN A 598 GLN ** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9011 Z= 0.179 Angle : 0.572 8.126 12189 Z= 0.303 Chirality : 0.041 0.162 1382 Planarity : 0.003 0.053 1544 Dihedral : 7.501 83.121 1283 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.57 % Allowed : 34.41 % Favored : 63.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.25), residues: 1117 helix: 1.65 (0.19), residues: 730 sheet: 0.98 (0.58), residues: 78 loop : -0.79 (0.32), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 163 HIS 0.002 0.000 HIS A 428 PHE 0.035 0.001 PHE A 70 TYR 0.018 0.001 TYR A 337 ARG 0.005 0.000 ARG A 184 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 190 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: A 224 MET cc_start: 0.8451 (mmp) cc_final: 0.8199 (mmm) REVERT: A 268 ASP cc_start: 0.8256 (t0) cc_final: 0.8020 (t0) REVERT: A 269 TYR cc_start: 0.7119 (m-10) cc_final: 0.6831 (m-10) REVERT: A 476 GLU cc_start: 0.8463 (mp0) cc_final: 0.7741 (pp20) REVERT: A 496 ASP cc_start: 0.8803 (p0) cc_final: 0.8464 (p0) REVERT: A 751 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7209 (mt-10) REVERT: A 935 MET cc_start: 0.8474 (tpp) cc_final: 0.8211 (tpt) REVERT: A 956 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7239 (mm-30) REVERT: A 1079 ASP cc_start: 0.7288 (p0) cc_final: 0.6961 (p0) REVERT: A 1291 GLN cc_start: 0.7706 (mt0) cc_final: 0.7288 (mt0) REVERT: A 1296 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7273 (mt-10) outliers start: 24 outliers final: 15 residues processed: 203 average time/residue: 1.1366 time to fit residues: 247.4194 Evaluate side-chains 204 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 187 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 776 PHE Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 899 LYS Chi-restraints excluded: chain A residue 928 ARG Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1296 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1009 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.143378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.131855 restraints weight = 10694.665| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.14 r_work: 0.3407 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3295 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 317 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 326 | |-----------------------------------------------------------------------------| r_final: 0.3284 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9011 Z= 0.291 Angle : 0.655 10.223 12189 Z= 0.346 Chirality : 0.045 0.176 1382 Planarity : 0.004 0.050 1544 Dihedral : 8.014 80.184 1283 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.00 % Allowed : 34.19 % Favored : 62.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.24), residues: 1117 helix: 1.31 (0.18), residues: 731 sheet: 0.88 (0.58), residues: 77 loop : -0.99 (0.31), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 342 HIS 0.003 0.001 HIS A 428 PHE 0.032 0.002 PHE A 202 TYR 0.018 0.002 TYR A 337 ARG 0.003 0.000 ARG A 830 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4453.87 seconds wall clock time: 79 minutes 55.12 seconds (4795.12 seconds total)