Starting phenix.real_space_refine on Wed Sep 17 13:27:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nfm_49370/09_2025/9nfm_49370_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nfm_49370/09_2025/9nfm_49370.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nfm_49370/09_2025/9nfm_49370_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nfm_49370/09_2025/9nfm_49370_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nfm_49370/09_2025/9nfm_49370.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nfm_49370/09_2025/9nfm_49370.map" } resolution = 3.89 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 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= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 48 5.16 5 Cl 5 4.86 5 C 5670 2.51 5 N 1499 2.21 5 O 1628 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8850 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1142, 8831 Classifications: {'peptide': 1142} Link IDs: {'PTRANS': 31, 'TRANS': 1110} Chain breaks: 4 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'6WT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.27, per 1000 atoms: 0.26 Number of scatterers: 8850 At special positions: 0 Unit cell: (74.8, 114.07, 141.185, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 5 17.00 S 48 16.00 O 1628 8.00 N 1499 7.00 C 5670 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 - 3.00 Amino acid : True - 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: 0.94 Conformation dependent library (CDL) restraints added in 350.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2110 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 5 sheets defined 70.9% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 47 through 52 removed outlier: 3.505A pdb=" N PHE A 52 " --> pdb=" O PRO A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 98 removed outlier: 3.972A pdb=" N LEU A 77 " --> pdb=" O HIS A 73 " (cutoff:3.500A) Proline residue: A 78 - end of helix Processing helix chain 'A' and resid 117 through 170 Processing helix chain 'A' and resid 171 through 198 removed outlier: 4.478A pdb=" N VAL A 177 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN A 178 " --> pdb=" O TRP A 174 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N THR A 180 " --> pdb=" O ASP A 176 " (cutoff:3.500A) removed outlier: 8.905A pdb=" N GLY A 181 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU A 182 " --> pdb=" O ASN A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 233 removed outlier: 3.998A pdb=" N GLY A 203 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N LYS A 225 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LEU A 226 " --> pdb=" O LYS A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 272 removed outlier: 3.838A pdb=" N LEU A 237 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 279 Processing helix chain 'A' and resid 283 through 336 Processing helix chain 'A' and resid 339 through 383 Proline residue: A 362 - end of helix removed outlier: 3.849A pdb=" N GLN A 365 " --> pdb=" O SER A 361 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 366 " --> pdb=" O PRO A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 453 removed outlier: 3.568A pdb=" N GLN A 453 " --> pdb=" O ILE A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 468 removed outlier: 3.568A pdb=" N THR A 467 " --> pdb=" O SER A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 473 Processing helix chain 'A' and resid 474 through 481 Processing helix chain 'A' and resid 495 through 502 Processing helix chain 'A' and resid 509 through 516 removed outlier: 3.548A pdb=" N GLN A 514 " --> pdb=" O GLN A 510 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA A 516 " --> pdb=" O ILE A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 519 No H-bonds generated for 'chain 'A' and resid 517 through 519' Processing helix chain 'A' and resid 521 through 526 Processing helix chain 'A' and resid 544 through 557 Processing helix chain 'A' and resid 574 through 590 removed outlier: 3.894A pdb=" N LEU A 590 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 606 Processing helix chain 'A' and resid 623 through 630 Processing helix chain 'A' and resid 714 through 723 removed outlier: 4.177A pdb=" N LEU A 721 " --> pdb=" O LYS A 717 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASN A 722 " --> pdb=" O VAL A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 756 removed outlier: 3.535A pdb=" N MET A 729 " --> pdb=" O GLU A 725 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 731 " --> pdb=" O PRO A 727 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN A 743 " --> pdb=" O ASN A 739 " (cutoff:3.500A) Proline residue: A 744 - end of helix Processing helix chain 'A' and resid 757 through 759 No H-bonds generated for 'chain 'A' and resid 757 through 759' Processing helix chain 'A' and resid 761 through 816 Processing helix chain 'A' and resid 817 through 822 removed outlier: 4.135A pdb=" N PHE A 821 " --> pdb=" O ASP A 817 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP A 822 " --> pdb=" O LEU A 818 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 817 through 822' Processing helix chain 'A' and resid 823 through 826 Processing helix chain 'A' and resid 827 through 842 removed outlier: 3.802A pdb=" N ALA A 839 " --> pdb=" O LEU A 835 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ALA A 840 " --> pdb=" O ALA A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 846 removed outlier: 3.696A pdb=" N THR A 846 " --> pdb=" O GLN A 843 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 843 through 846' Processing helix chain 'A' and resid 847 through 888 removed outlier: 7.984A pdb=" N GLU A 873 " --> pdb=" O VAL A 869 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N LEU A 874 " --> pdb=" O TYR A 870 " (cutoff:3.500A) Proline residue: A 883 - end of helix removed outlier: 4.132A pdb=" N ALA A 886 " --> pdb=" O VAL A 882 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A 888 " --> pdb=" O ILE A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 920 removed outlier: 3.996A pdb=" N GLN A 892 " --> pdb=" O ALA A 888 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY A 898 " --> pdb=" O GLN A 894 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS A 899 " --> pdb=" O LEU A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 927 Processing helix chain 'A' and resid 929 through 984 removed outlier: 4.524A pdb=" N VAL A 943 " --> pdb=" O GLU A 939 " (cutoff:3.500A) Proline residue: A 944 - end of helix removed outlier: 4.141A pdb=" N ILE A 966 " --> pdb=" O SER A 962 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR A 967 " --> pdb=" O GLN A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 1008 removed outlier: 3.824A pdb=" N VAL A 991 " --> pdb=" O ASP A 987 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N TYR A 992 " --> pdb=" O ALA A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1030 Processing helix chain 'A' and resid 1092 through 1101 removed outlier: 3.831A pdb=" N THR A1096 " --> pdb=" O GLY A1092 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE A1097 " --> pdb=" O LYS A1093 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLN A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1129 Processing helix chain 'A' and resid 1143 through 1151 removed outlier: 4.146A pdb=" N GLY A1151 " --> pdb=" O ASN A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1158 through 1169 Processing helix chain 'A' and resid 1171 through 1176 Processing helix chain 'A' and resid 1194 through 1208 Processing helix chain 'A' and resid 1224 through 1239 Processing helix chain 'A' and resid 1250 through 1255 Processing helix chain 'A' and resid 1274 through 1281 Processing sheet with id=AA1, first strand: chain 'A' and resid 407 through 410 removed outlier: 5.194A pdb=" N ASN A 408 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N SER A 462 " --> pdb=" O ASN A 408 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 435 through 436 Processing sheet with id=AA3, first strand: chain 'A' and resid 482 through 485 removed outlier: 6.023A pdb=" N GLY A 483 " --> pdb=" O LEU A 565 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ASP A 567 " --> pdb=" O GLY A 483 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL A 485 " --> pdb=" O ASP A 567 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU A 564 " --> pdb=" O ILE A 595 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N VAL A 597 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LEU A 566 " --> pdb=" O VAL A 597 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 1084 through 1085 removed outlier: 3.846A pdb=" N VAL A1262 " --> pdb=" O GLU A1270 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLU A1270 " --> pdb=" O VAL A1262 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1131 through 1132 removed outlier: 6.653A pdb=" N LEU A1214 " --> pdb=" O ILE A1245 " (cutoff:3.500A) 588 hydrogen bonds defined for protein. 1743 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: 1.40 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2882 1.34 - 1.46: 1826 1.46 - 1.58: 4209 1.58 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 9009 Sorted by residual: bond pdb=" C09 6WT A1401 " pdb=" C10 6WT A1401 " ideal model delta sigma weight residual 1.392 1.533 -0.141 2.00e-02 2.50e+03 4.97e+01 bond pdb=" C04 6WT A1401 " pdb=" C05 6WT A1401 " ideal model delta sigma weight residual 1.386 1.527 -0.141 2.00e-02 2.50e+03 4.97e+01 bond pdb=" C01 6WT A1401 " pdb=" C06 6WT A1401 " ideal model delta sigma weight residual 1.392 1.533 -0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C11 6WT A1401 " pdb=" C12 6WT A1401 " ideal model delta sigma weight residual 1.385 1.525 -0.140 2.00e-02 2.50e+03 4.88e+01 bond pdb=" C02 6WT A1401 " pdb=" C03 6WT A1401 " ideal model delta sigma weight residual 1.386 1.525 -0.139 2.00e-02 2.50e+03 4.82e+01 ... (remaining 9004 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 11996 2.30 - 4.61: 150 4.61 - 6.91: 18 6.91 - 9.22: 7 9.22 - 11.52: 1 Bond angle restraints: 12172 Sorted by residual: angle pdb=" OG1 THR A 188 " pdb=" CB THR A 188 " pdb=" CG2 THR A 188 " ideal model delta sigma weight residual 109.30 120.82 -11.52 2.00e+00 2.50e-01 3.32e+01 angle pdb=" N GLU A 533 " pdb=" CA GLU A 533 " pdb=" C GLU A 533 " ideal model delta sigma weight residual 110.91 116.52 -5.61 1.17e+00 7.31e-01 2.30e+01 angle pdb=" CA THR A 188 " pdb=" CB THR A 188 " pdb=" CG2 THR A 188 " ideal model delta sigma weight residual 110.50 118.38 -7.88 1.70e+00 3.46e-01 2.15e+01 angle pdb=" C GLU A 179 " pdb=" CA GLU A 179 " pdb=" CB GLU A 179 " ideal model delta sigma weight residual 115.79 110.75 5.04 1.19e+00 7.06e-01 1.79e+01 angle pdb=" CA THR A 188 " pdb=" CB THR A 188 " pdb=" OG1 THR A 188 " ideal model delta sigma weight residual 109.60 115.85 -6.25 1.50e+00 4.44e-01 1.74e+01 ... (remaining 12167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 4609 17.90 - 35.79: 574 35.79 - 53.69: 172 53.69 - 71.58: 24 71.58 - 89.48: 9 Dihedral angle restraints: 5388 sinusoidal: 2109 harmonic: 3279 Sorted by residual: dihedral pdb=" CA PHE A 532 " pdb=" C PHE A 532 " pdb=" N GLU A 533 " pdb=" CA GLU A 533 " ideal model delta harmonic sigma weight residual 180.00 157.24 22.76 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA GLU A 179 " pdb=" C GLU A 179 " pdb=" N THR A 180 " pdb=" CA THR A 180 " ideal model delta harmonic sigma weight residual -180.00 -158.46 -21.54 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA GLU A 533 " pdb=" C GLU A 533 " pdb=" N THR A 534 " pdb=" CA THR A 534 " ideal model delta harmonic sigma weight residual 180.00 160.21 19.79 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 5385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.285: 1397 0.285 - 0.570: 1 0.570 - 0.855: 0 0.855 - 1.139: 0 1.139 - 1.424: 1 Chirality restraints: 1399 Sorted by residual: chirality pdb=" CB THR A 188 " pdb=" CA THR A 188 " pdb=" OG1 THR A 188 " pdb=" CG2 THR A 188 " both_signs ideal model delta sigma weight residual False 2.55 1.13 1.42 2.00e-01 2.50e+01 5.07e+01 chirality pdb=" CA MET A 986 " pdb=" N MET A 986 " pdb=" C MET A 986 " pdb=" CB MET A 986 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CA ILE A1130 " pdb=" N ILE A1130 " pdb=" C ILE A1130 " pdb=" CB ILE A1130 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.32e-01 ... (remaining 1396 not shown) Planarity restraints: 1549 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 820 " 0.017 2.00e-02 2.50e+03 1.37e-02 4.66e+00 pdb=" CG TRP A 820 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP A 820 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 820 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 820 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 820 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 820 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 820 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 820 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 820 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 147 " 0.016 2.00e-02 2.50e+03 1.48e-02 3.83e+00 pdb=" CG PHE A 147 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE A 147 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 147 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 147 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 147 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 147 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 187 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.24e+00 pdb=" C LEU A 187 " -0.031 2.00e-02 2.50e+03 pdb=" O LEU A 187 " 0.012 2.00e-02 2.50e+03 pdb=" N THR A 188 " 0.011 2.00e-02 2.50e+03 ... (remaining 1546 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 131 2.60 - 3.17: 9010 3.17 - 3.75: 14466 3.75 - 4.32: 18762 4.32 - 4.90: 30458 Nonbonded interactions: 72827 Sorted by model distance: nonbonded pdb=" OD1 ASP A 838 " pdb=" OG SER A1021 " model vdw 2.021 3.040 nonbonded pdb=" O LEU A 248 " pdb=" OG1 THR A 252 " model vdw 2.051 3.040 nonbonded pdb=" O GLY A1181 " pdb=" OG1 THR A1184 " model vdw 2.147 3.040 nonbonded pdb=" N GLU A 182 " pdb=" OE1 GLU A 182 " model vdw 2.154 3.120 nonbonded pdb=" O THR A 339 " pdb=" OG1 THR A 342 " model vdw 2.196 3.040 ... (remaining 72822 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.510 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: 0.020 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.140 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 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 : 0.006 0.141 9009 Z= 0.284 Angle : 0.676 11.522 12172 Z= 0.377 Chirality : 0.054 1.424 1399 Planarity : 0.004 0.045 1549 Dihedral : 17.425 89.481 3278 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.76 % Allowed : 24.65 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.25), residues: 1132 helix: 1.52 (0.19), residues: 737 sheet: -2.96 (0.71), residues: 42 loop : -2.15 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1031 TYR 0.021 0.002 TYR A 328 PHE 0.034 0.002 PHE A 147 TRP 0.037 0.002 TRP A 820 HIS 0.006 0.001 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00579 ( 9009) covalent geometry : angle 0.67602 (12172) hydrogen bonds : bond 0.10545 ( 588) hydrogen bonds : angle 5.15682 ( 1743) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 289 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 GLN cc_start: 0.7631 (tp40) cc_final: 0.7352 (tp40) REVERT: A 174 TRP cc_start: 0.8446 (t60) cc_final: 0.8127 (t60) REVERT: A 190 ASP cc_start: 0.8083 (m-30) cc_final: 0.7775 (m-30) REVERT: A 299 MET cc_start: 0.7488 (tpp) cc_final: 0.7180 (tpp) REVERT: A 333 ILE cc_start: 0.6791 (mt) cc_final: 0.6559 (mt) REVERT: A 501 LYS cc_start: 0.6002 (tptp) cc_final: 0.5771 (tptp) REVERT: A 794 PHE cc_start: 0.7022 (m-80) cc_final: 0.6770 (m-80) REVERT: A 838 ASP cc_start: 0.8032 (m-30) cc_final: 0.7736 (m-30) REVERT: A 961 PHE cc_start: 0.7254 (t80) cc_final: 0.6896 (t80) REVERT: A 999 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8831 (mm) REVERT: A 1020 MET cc_start: 0.7238 (tpp) cc_final: 0.6967 (tpp) REVERT: A 1027 MET cc_start: 0.8351 (tmm) cc_final: 0.7908 (tmm) REVERT: A 1077 VAL cc_start: 0.7519 (t) cc_final: 0.7280 (t) outliers start: 26 outliers final: 14 residues processed: 304 average time/residue: 0.0972 time to fit residues: 40.3909 Evaluate side-chains 203 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 188 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 776 PHE Chi-restraints excluded: chain A residue 799 GLU Chi-restraints excluded: chain A residue 822 ASP Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 868 PHE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 899 HIS Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1233 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 ASN ** A 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 ASN A 920 ASN A 938 GLN A1129 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.150882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.118957 restraints weight = 24650.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.122714 restraints weight = 14187.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.125136 restraints weight = 9449.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.126885 restraints weight = 7008.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.128030 restraints weight = 5629.242| |-----------------------------------------------------------------------------| r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9009 Z= 0.173 Angle : 0.727 12.203 12172 Z= 0.371 Chirality : 0.045 0.275 1399 Planarity : 0.004 0.045 1549 Dihedral : 7.429 83.875 1253 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 4.46 % Allowed : 26.35 % Favored : 69.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.25), residues: 1132 helix: 1.42 (0.18), residues: 757 sheet: -3.15 (0.51), residues: 56 loop : -1.89 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1127 TYR 0.026 0.002 TYR A 870 PHE 0.023 0.002 PHE A1059 TRP 0.025 0.003 TRP A1125 HIS 0.012 0.001 HIS A 624 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 9009) covalent geometry : angle 0.72653 (12172) hydrogen bonds : bond 0.04754 ( 588) hydrogen bonds : angle 4.65083 ( 1743) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 216 time to evaluate : 0.355 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: A 174 TRP cc_start: 0.8483 (t60) cc_final: 0.8086 (t60) REVERT: A 190 ASP cc_start: 0.8328 (m-30) cc_final: 0.8034 (m-30) REVERT: A 294 GLU cc_start: 0.8062 (tp30) cc_final: 0.7724 (mm-30) REVERT: A 299 MET cc_start: 0.8104 (tpp) cc_final: 0.7425 (tpp) REVERT: A 311 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8280 (mpp) REVERT: A 333 ILE cc_start: 0.7145 (mt) cc_final: 0.6725 (mt) REVERT: A 365 GLN cc_start: 0.8764 (pt0) cc_final: 0.8531 (mm110) REVERT: A 505 PRO cc_start: 0.6820 (Cg_exo) cc_final: 0.6582 (Cg_endo) REVERT: A 563 ILE cc_start: 0.9190 (mm) cc_final: 0.8990 (mm) REVERT: A 776 PHE cc_start: 0.7800 (OUTLIER) cc_final: 0.7487 (m-80) REVERT: A 794 PHE cc_start: 0.7834 (m-80) cc_final: 0.7515 (m-80) REVERT: A 801 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8967 (tp) REVERT: A 882 VAL cc_start: 0.9076 (t) cc_final: 0.8782 (m) REVERT: A 906 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8073 (mm-30) REVERT: A 908 GLU cc_start: 0.8734 (tp30) cc_final: 0.8279 (pt0) REVERT: A 1020 MET cc_start: 0.8295 (tpp) cc_final: 0.8023 (tpp) REVERT: A 1027 MET cc_start: 0.8982 (tmm) cc_final: 0.8417 (tmm) REVERT: A 1125 TRP cc_start: 0.8824 (t-100) cc_final: 0.8547 (t-100) REVERT: A 1129 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.7997 (tp40) REVERT: A 1245 ILE cc_start: 0.8844 (mm) cc_final: 0.8447 (tp) outliers start: 42 outliers final: 15 residues processed: 238 average time/residue: 0.0858 time to fit residues: 29.5347 Evaluate side-chains 209 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 190 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 776 PHE Chi-restraints excluded: chain A residue 799 GLU Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 868 PHE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 899 HIS Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain A residue 1129 GLN Chi-restraints excluded: chain A residue 1142 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 46 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 106 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 107 optimal weight: 20.0000 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1037 ASN A1147 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.135992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.103420 restraints weight = 24537.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.106764 restraints weight = 14102.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.108979 restraints weight = 9545.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.110507 restraints weight = 7228.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.111553 restraints weight = 5919.676| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.5372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 9009 Z= 0.255 Angle : 0.768 8.748 12172 Z= 0.401 Chirality : 0.046 0.179 1399 Planarity : 0.005 0.048 1549 Dihedral : 6.947 82.066 1241 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 6.48 % Allowed : 25.72 % Favored : 67.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.25), residues: 1132 helix: 0.93 (0.18), residues: 758 sheet: -3.22 (0.48), residues: 54 loop : -1.69 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 605 TYR 0.018 0.002 TYR A 328 PHE 0.026 0.003 PHE A 794 TRP 0.022 0.003 TRP A1125 HIS 0.008 0.002 HIS A 899 Details of bonding type rmsd covalent geometry : bond 0.00574 ( 9009) covalent geometry : angle 0.76775 (12172) hydrogen bonds : bond 0.05018 ( 588) hydrogen bonds : angle 4.86913 ( 1743) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 199 time to evaluate : 0.308 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: A 150 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.9298 (mp) REVERT: A 190 ASP cc_start: 0.8540 (m-30) cc_final: 0.8179 (m-30) REVERT: A 200 ASP cc_start: 0.8459 (m-30) cc_final: 0.7789 (m-30) REVERT: A 295 ASP cc_start: 0.8270 (m-30) cc_final: 0.7955 (t70) REVERT: A 299 MET cc_start: 0.8228 (tpp) cc_final: 0.7613 (tpp) REVERT: A 425 MET cc_start: 0.7770 (mmm) cc_final: 0.7509 (mmm) REVERT: A 543 MET cc_start: 0.6969 (mpp) cc_final: 0.6569 (mpp) REVERT: A 738 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.9007 (tp) REVERT: A 764 ILE cc_start: 0.7341 (mt) cc_final: 0.7110 (mt) REVERT: A 838 ASP cc_start: 0.8760 (m-30) cc_final: 0.8448 (m-30) REVERT: A 882 VAL cc_start: 0.9228 (t) cc_final: 0.9009 (m) REVERT: A 906 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8070 (mm-30) REVERT: A 1020 MET cc_start: 0.8252 (tpp) cc_final: 0.7956 (tpp) REVERT: A 1027 MET cc_start: 0.8928 (tmm) cc_final: 0.8333 (tmm) REVERT: A 1125 TRP cc_start: 0.8988 (t-100) cc_final: 0.8482 (t-100) REVERT: A 1129 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.8068 (mm-40) outliers start: 61 outliers final: 33 residues processed: 237 average time/residue: 0.0803 time to fit residues: 27.9759 Evaluate side-chains 208 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 726 TRP Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 776 PHE Chi-restraints excluded: chain A residue 799 GLU Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 868 PHE Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 899 HIS Chi-restraints excluded: chain A residue 903 ASP Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain A residue 1129 GLN Chi-restraints excluded: chain A residue 1134 SER Chi-restraints excluded: chain A residue 1142 CYS Chi-restraints excluded: chain A residue 1251 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 1 optimal weight: 1.9990 chunk 95 optimal weight: 20.0000 chunk 60 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 30 optimal weight: 0.2980 chunk 108 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 GLN ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 920 ASN A1129 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.134269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.102040 restraints weight = 24498.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.105422 restraints weight = 13659.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.107662 restraints weight = 9097.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.109223 restraints weight = 6811.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.110267 restraints weight = 5560.276| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.6155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9009 Z= 0.164 Angle : 0.677 11.501 12172 Z= 0.341 Chirality : 0.043 0.219 1399 Planarity : 0.004 0.051 1549 Dihedral : 6.863 82.080 1241 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 5.21 % Allowed : 27.74 % Favored : 67.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.25), residues: 1132 helix: 1.16 (0.19), residues: 758 sheet: -2.57 (0.62), residues: 44 loop : -1.79 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 766 TYR 0.012 0.001 TYR A 955 PHE 0.016 0.002 PHE A 734 TRP 0.015 0.002 TRP A1125 HIS 0.004 0.001 HIS A 468 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 9009) covalent geometry : angle 0.67731 (12172) hydrogen bonds : bond 0.04444 ( 588) hydrogen bonds : angle 4.63557 ( 1743) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 196 time to evaluate : 0.243 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: A 147 PHE cc_start: 0.8954 (m-10) cc_final: 0.8718 (m-10) REVERT: A 190 ASP cc_start: 0.8354 (m-30) cc_final: 0.7969 (m-30) REVERT: A 192 TYR cc_start: 0.8639 (t80) cc_final: 0.8345 (t80) REVERT: A 196 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7733 (mm-30) REVERT: A 207 GLN cc_start: 0.8610 (tt0) cc_final: 0.8386 (tt0) REVERT: A 295 ASP cc_start: 0.8282 (m-30) cc_final: 0.7956 (t70) REVERT: A 299 MET cc_start: 0.8182 (tpp) cc_final: 0.7692 (tpp) REVERT: A 327 TRP cc_start: 0.8095 (t60) cc_final: 0.7661 (t60) REVERT: A 334 MET cc_start: 0.7901 (mmm) cc_final: 0.7673 (mmm) REVERT: A 365 GLN cc_start: 0.8664 (mm110) cc_final: 0.8399 (pp30) REVERT: A 445 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8229 (mttp) REVERT: A 480 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7963 (mm-30) REVERT: A 543 MET cc_start: 0.7295 (mpp) cc_final: 0.6970 (mpp) REVERT: A 820 TRP cc_start: 0.8879 (t60) cc_final: 0.8529 (t60) REVERT: A 838 ASP cc_start: 0.8707 (m-30) cc_final: 0.8388 (m-30) REVERT: A 841 GLN cc_start: 0.8802 (mm-40) cc_final: 0.8385 (mm-40) REVERT: A 846 THR cc_start: 0.9154 (OUTLIER) cc_final: 0.8912 (t) REVERT: A 876 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8685 (mt) REVERT: A 882 VAL cc_start: 0.9281 (t) cc_final: 0.9037 (m) REVERT: A 885 MET cc_start: 0.6368 (ttm) cc_final: 0.6050 (tmm) REVERT: A 906 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7900 (mm-30) REVERT: A 908 GLU cc_start: 0.8706 (tp30) cc_final: 0.8193 (pt0) REVERT: A 929 ARG cc_start: 0.8118 (mmm-85) cc_final: 0.7827 (mmt90) REVERT: A 1020 MET cc_start: 0.8354 (tpp) cc_final: 0.8055 (tpp) REVERT: A 1027 MET cc_start: 0.8940 (tmm) cc_final: 0.8316 (tmm) REVERT: A 1125 TRP cc_start: 0.9102 (t-100) cc_final: 0.8238 (t-100) REVERT: A 1129 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8467 (mm110) outliers start: 49 outliers final: 28 residues processed: 224 average time/residue: 0.0806 time to fit residues: 26.0898 Evaluate side-chains 203 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 171 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 359 GLN Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 726 TRP Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 776 PHE Chi-restraints excluded: chain A residue 799 GLU Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 868 PHE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 899 HIS Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain A residue 1061 TYR Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain A residue 1129 GLN Chi-restraints excluded: chain A residue 1214 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 27 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN A 560 ASN A 631 GLN ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.128694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.094635 restraints weight = 24958.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.097829 restraints weight = 14211.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.099901 restraints weight = 9692.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.101356 restraints weight = 7461.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.102338 restraints weight = 6214.204| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.7298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9009 Z= 0.231 Angle : 0.727 14.972 12172 Z= 0.376 Chirality : 0.044 0.225 1399 Planarity : 0.005 0.051 1549 Dihedral : 6.819 84.209 1241 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 6.70 % Allowed : 27.52 % Favored : 65.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.25), residues: 1132 helix: 0.93 (0.19), residues: 759 sheet: -2.60 (0.58), residues: 44 loop : -1.77 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 806 TYR 0.018 0.002 TYR A 992 PHE 0.022 0.002 PHE A 794 TRP 0.017 0.002 TRP A 872 HIS 0.004 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00505 ( 9009) covalent geometry : angle 0.72742 (12172) hydrogen bonds : bond 0.04805 ( 588) hydrogen bonds : angle 4.87515 ( 1743) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 184 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 MET cc_start: 0.8515 (tpp) cc_final: 0.8112 (tpp) REVERT: A 196 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7883 (mm-30) REVERT: A 237 LEU cc_start: 0.8813 (pp) cc_final: 0.8470 (pp) REVERT: A 295 ASP cc_start: 0.8716 (m-30) cc_final: 0.8202 (t70) REVERT: A 299 MET cc_start: 0.8289 (tpp) cc_final: 0.7762 (tpp) REVERT: A 316 LEU cc_start: 0.9488 (tp) cc_final: 0.9263 (tp) REVERT: A 327 TRP cc_start: 0.8515 (t60) cc_final: 0.7999 (t60) REVERT: A 365 GLN cc_start: 0.8736 (mm110) cc_final: 0.8457 (pp30) REVERT: A 480 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8121 (mm-30) REVERT: A 501 LYS cc_start: 0.7368 (tptp) cc_final: 0.6466 (tptt) REVERT: A 543 MET cc_start: 0.7580 (mpp) cc_final: 0.7136 (mpp) REVERT: A 784 PHE cc_start: 0.9013 (t80) cc_final: 0.8585 (t80) REVERT: A 820 TRP cc_start: 0.9007 (t60) cc_final: 0.8429 (t60) REVERT: A 838 ASP cc_start: 0.8777 (m-30) cc_final: 0.8477 (m-30) REVERT: A 841 GLN cc_start: 0.8955 (mm-40) cc_final: 0.8562 (mm-40) REVERT: A 846 THR cc_start: 0.9189 (OUTLIER) cc_final: 0.8950 (t) REVERT: A 885 MET cc_start: 0.6645 (ttm) cc_final: 0.6274 (tmm) REVERT: A 906 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7854 (mm-30) REVERT: A 965 MET cc_start: 0.8113 (mmm) cc_final: 0.7827 (mmm) REVERT: A 1020 MET cc_start: 0.8417 (tpp) cc_final: 0.8115 (tpp) REVERT: A 1027 MET cc_start: 0.8863 (tmm) cc_final: 0.8220 (tmm) REVERT: A 1074 ASN cc_start: 0.7978 (p0) cc_final: 0.7325 (m-40) REVERT: A 1103 PHE cc_start: 0.8224 (m-80) cc_final: 0.7976 (m-80) REVERT: A 1125 TRP cc_start: 0.9016 (t-100) cc_final: 0.8761 (t-100) REVERT: A 1129 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8504 (tp40) REVERT: A 1146 GLU cc_start: 0.8459 (pt0) cc_final: 0.8259 (pt0) REVERT: A 1150 TYR cc_start: 0.7936 (OUTLIER) cc_final: 0.7476 (t80) REVERT: A 1277 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.7068 (tp) outliers start: 63 outliers final: 39 residues processed: 220 average time/residue: 0.0819 time to fit residues: 26.2716 Evaluate side-chains 212 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 169 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 726 TRP Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 776 PHE Chi-restraints excluded: chain A residue 799 GLU Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 899 HIS Chi-restraints excluded: chain A residue 903 ASP Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain A residue 1061 TYR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain A residue 1129 GLN Chi-restraints excluded: chain A residue 1142 CYS Chi-restraints excluded: chain A residue 1150 TYR Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1277 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 110 optimal weight: 30.0000 chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 107 optimal weight: 8.9990 chunk 92 optimal weight: 8.9990 chunk 47 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 GLN A1147 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.127355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.095500 restraints weight = 24840.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.098621 restraints weight = 13841.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.100650 restraints weight = 9339.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.102017 restraints weight = 7107.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.102861 restraints weight = 5887.981| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.7678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 9009 Z= 0.180 Angle : 0.703 13.656 12172 Z= 0.354 Chirality : 0.044 0.316 1399 Planarity : 0.004 0.051 1549 Dihedral : 6.663 84.848 1239 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 5.63 % Allowed : 29.01 % Favored : 65.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.25), residues: 1132 helix: 1.07 (0.19), residues: 757 sheet: -2.38 (0.61), residues: 44 loop : -1.79 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 929 TYR 0.022 0.002 TYR A 378 PHE 0.022 0.002 PHE A 147 TRP 0.015 0.002 TRP A 872 HIS 0.004 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 9009) covalent geometry : angle 0.70316 (12172) hydrogen bonds : bond 0.04492 ( 588) hydrogen bonds : angle 4.73302 ( 1743) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 179 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ASP cc_start: 0.8423 (m-30) cc_final: 0.8133 (m-30) REVERT: A 192 TYR cc_start: 0.8891 (t80) cc_final: 0.8515 (t80) REVERT: A 196 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7966 (mm-30) REVERT: A 295 ASP cc_start: 0.8687 (m-30) cc_final: 0.8200 (t70) REVERT: A 299 MET cc_start: 0.8352 (tpp) cc_final: 0.7836 (tpp) REVERT: A 327 TRP cc_start: 0.8494 (t60) cc_final: 0.8006 (t60) REVERT: A 365 GLN cc_start: 0.8731 (mm110) cc_final: 0.8436 (pp30) REVERT: A 425 MET cc_start: 0.7185 (mmm) cc_final: 0.6912 (mmm) REVERT: A 454 ARG cc_start: 0.8907 (tpt-90) cc_final: 0.8611 (tpt-90) REVERT: A 455 PHE cc_start: 0.8092 (m-10) cc_final: 0.7742 (m-10) REVERT: A 480 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8000 (mm-30) REVERT: A 501 LYS cc_start: 0.7335 (tptp) cc_final: 0.6619 (tptt) REVERT: A 505 PRO cc_start: 0.6918 (Cg_endo) cc_final: 0.6600 (Cg_exo) REVERT: A 543 MET cc_start: 0.7368 (mpp) cc_final: 0.6998 (mpp) REVERT: A 745 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8585 (tp) REVERT: A 784 PHE cc_start: 0.9070 (t80) cc_final: 0.8511 (t80) REVERT: A 814 MET cc_start: 0.7532 (mtm) cc_final: 0.7181 (mtm) REVERT: A 820 TRP cc_start: 0.8913 (t60) cc_final: 0.8482 (t60) REVERT: A 838 ASP cc_start: 0.8725 (m-30) cc_final: 0.8427 (m-30) REVERT: A 841 GLN cc_start: 0.8925 (mm-40) cc_final: 0.8558 (mm-40) REVERT: A 846 THR cc_start: 0.9135 (OUTLIER) cc_final: 0.8925 (t) REVERT: A 876 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8769 (mm) REVERT: A 885 MET cc_start: 0.6607 (ttm) cc_final: 0.6256 (tmm) REVERT: A 906 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8009 (mm-30) REVERT: A 1020 MET cc_start: 0.8357 (tpp) cc_final: 0.8049 (tpp) REVERT: A 1027 MET cc_start: 0.8813 (tmm) cc_final: 0.8169 (tmm) REVERT: A 1074 ASN cc_start: 0.7939 (p0) cc_final: 0.7428 (m110) REVERT: A 1103 PHE cc_start: 0.8192 (m-80) cc_final: 0.7970 (m-80) REVERT: A 1125 TRP cc_start: 0.8999 (t-100) cc_final: 0.8617 (t-100) REVERT: A 1129 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8394 (tp40) REVERT: A 1170 ASN cc_start: 0.7752 (t0) cc_final: 0.7355 (p0) REVERT: A 1277 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7128 (tp) outliers start: 53 outliers final: 29 residues processed: 214 average time/residue: 0.0879 time to fit residues: 27.3259 Evaluate side-chains 203 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 169 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 726 TRP Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 799 GLU Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 899 HIS Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1061 TYR Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain A residue 1129 GLN Chi-restraints excluded: chain A residue 1142 CYS Chi-restraints excluded: chain A residue 1147 ASN Chi-restraints excluded: chain A residue 1277 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 25 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 chunk 38 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 32 optimal weight: 0.0970 chunk 48 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 ASN ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.128119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.096567 restraints weight = 24633.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.099736 restraints weight = 13668.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.101869 restraints weight = 9167.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.103129 restraints weight = 6907.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.104212 restraints weight = 5738.693| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.7927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9009 Z= 0.153 Angle : 0.702 13.678 12172 Z= 0.348 Chirality : 0.043 0.209 1399 Planarity : 0.004 0.049 1549 Dihedral : 6.250 87.797 1235 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.89 % Allowed : 29.22 % Favored : 65.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.25), residues: 1132 helix: 1.21 (0.19), residues: 750 sheet: -2.38 (0.61), residues: 44 loop : -1.73 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 284 TYR 0.042 0.002 TYR A 378 PHE 0.020 0.002 PHE A1059 TRP 0.014 0.002 TRP A 872 HIS 0.005 0.001 HIS A 410 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 9009) covalent geometry : angle 0.70208 (12172) hydrogen bonds : bond 0.04413 ( 588) hydrogen bonds : angle 4.67418 ( 1743) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 181 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 TYR cc_start: 0.8843 (t80) cc_final: 0.8455 (t80) REVERT: A 196 GLU cc_start: 0.8321 (mm-30) cc_final: 0.8035 (mm-30) REVERT: A 295 ASP cc_start: 0.8635 (m-30) cc_final: 0.8196 (t70) REVERT: A 299 MET cc_start: 0.8321 (tpp) cc_final: 0.7853 (tpp) REVERT: A 316 LEU cc_start: 0.9460 (tp) cc_final: 0.9221 (tp) REVERT: A 327 TRP cc_start: 0.8455 (t60) cc_final: 0.7972 (t60) REVERT: A 334 MET cc_start: 0.7882 (mmm) cc_final: 0.7502 (mmm) REVERT: A 365 GLN cc_start: 0.8710 (mm110) cc_final: 0.8454 (pp30) REVERT: A 378 TYR cc_start: 0.9243 (m-80) cc_final: 0.8698 (m-80) REVERT: A 425 MET cc_start: 0.7601 (mmm) cc_final: 0.7297 (mmm) REVERT: A 454 ARG cc_start: 0.8845 (tpt-90) cc_final: 0.8565 (tpt-90) REVERT: A 455 PHE cc_start: 0.7988 (m-10) cc_final: 0.7720 (m-80) REVERT: A 480 GLU cc_start: 0.8403 (mm-30) cc_final: 0.7880 (mm-30) REVERT: A 501 LYS cc_start: 0.7293 (tptp) cc_final: 0.6978 (tptt) REVERT: A 543 MET cc_start: 0.7487 (mpp) cc_final: 0.7088 (mpp) REVERT: A 745 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8641 (tp) REVERT: A 784 PHE cc_start: 0.9057 (t80) cc_final: 0.8378 (t80) REVERT: A 820 TRP cc_start: 0.8910 (t60) cc_final: 0.8514 (t60) REVERT: A 838 ASP cc_start: 0.8708 (m-30) cc_final: 0.8395 (m-30) REVERT: A 841 GLN cc_start: 0.8908 (mm-40) cc_final: 0.8545 (mm-40) REVERT: A 876 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8822 (mt) REVERT: A 885 MET cc_start: 0.6597 (ttm) cc_final: 0.6314 (tmm) REVERT: A 906 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7906 (mm-30) REVERT: A 908 GLU cc_start: 0.8673 (tp30) cc_final: 0.8185 (pt0) REVERT: A 929 ARG cc_start: 0.8297 (mmm-85) cc_final: 0.7451 (mmt90) REVERT: A 961 PHE cc_start: 0.8443 (t80) cc_final: 0.8174 (t80) REVERT: A 965 MET cc_start: 0.8032 (mmm) cc_final: 0.7649 (mmm) REVERT: A 976 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.7741 (t80) REVERT: A 1020 MET cc_start: 0.8283 (tpp) cc_final: 0.7976 (tpp) REVERT: A 1027 MET cc_start: 0.8818 (tmm) cc_final: 0.8166 (tmm) REVERT: A 1074 ASN cc_start: 0.8011 (p0) cc_final: 0.7567 (m110) REVERT: A 1125 TRP cc_start: 0.9002 (t-100) cc_final: 0.8671 (t-100) REVERT: A 1146 GLU cc_start: 0.8435 (pt0) cc_final: 0.8210 (pt0) REVERT: A 1150 TYR cc_start: 0.7895 (OUTLIER) cc_final: 0.7344 (t80) REVERT: A 1170 ASN cc_start: 0.7755 (t0) cc_final: 0.7349 (p0) REVERT: A 1277 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7124 (tp) outliers start: 46 outliers final: 31 residues processed: 206 average time/residue: 0.0847 time to fit residues: 25.4679 Evaluate side-chains 202 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 166 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 359 GLN Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 726 TRP Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 799 GLU Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 899 HIS Chi-restraints excluded: chain A residue 903 ASP Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 976 PHE Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1061 TYR Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain A residue 1142 CYS Chi-restraints excluded: chain A residue 1150 TYR Chi-restraints excluded: chain A residue 1277 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 69 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 7 optimal weight: 0.7980 chunk 105 optimal weight: 9.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.129607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.097753 restraints weight = 24422.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.101038 restraints weight = 13616.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.103198 restraints weight = 9090.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.104687 restraints weight = 6848.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.105644 restraints weight = 5621.719| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.8182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9009 Z= 0.141 Angle : 0.708 13.013 12172 Z= 0.350 Chirality : 0.042 0.198 1399 Planarity : 0.004 0.053 1549 Dihedral : 6.171 90.659 1235 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 4.78 % Allowed : 30.29 % Favored : 64.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.25), residues: 1132 helix: 1.29 (0.19), residues: 752 sheet: -2.58 (0.61), residues: 42 loop : -1.56 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 504 TYR 0.035 0.002 TYR A 378 PHE 0.019 0.001 PHE A1059 TRP 0.012 0.002 TRP A 148 HIS 0.003 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 9009) covalent geometry : angle 0.70817 (12172) hydrogen bonds : bond 0.04314 ( 588) hydrogen bonds : angle 4.64611 ( 1743) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 181 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.9275 (mmm) cc_final: 0.8706 (mmm) REVERT: A 192 TYR cc_start: 0.8851 (t80) cc_final: 0.8650 (t80) REVERT: A 295 ASP cc_start: 0.8596 (m-30) cc_final: 0.8150 (t70) REVERT: A 299 MET cc_start: 0.8323 (tpp) cc_final: 0.7900 (tpp) REVERT: A 316 LEU cc_start: 0.9484 (tp) cc_final: 0.9146 (tp) REVERT: A 327 TRP cc_start: 0.8454 (t60) cc_final: 0.7978 (t60) REVERT: A 334 MET cc_start: 0.7948 (mmm) cc_final: 0.7643 (mmm) REVERT: A 365 GLN cc_start: 0.8693 (mm110) cc_final: 0.8401 (pp30) REVERT: A 378 TYR cc_start: 0.9199 (m-80) cc_final: 0.8795 (m-80) REVERT: A 425 MET cc_start: 0.7628 (mmm) cc_final: 0.7217 (mmm) REVERT: A 453 GLN cc_start: 0.8612 (tp-100) cc_final: 0.8396 (tp-100) REVERT: A 454 ARG cc_start: 0.8860 (tpt-90) cc_final: 0.8610 (tpt-90) REVERT: A 455 PHE cc_start: 0.7937 (m-10) cc_final: 0.7471 (m-80) REVERT: A 480 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7899 (mm-30) REVERT: A 501 LYS cc_start: 0.7250 (tptp) cc_final: 0.6459 (tptt) REVERT: A 505 PRO cc_start: 0.6945 (Cg_exo) cc_final: 0.5670 (Cg_endo) REVERT: A 512 ILE cc_start: 0.6401 (OUTLIER) cc_final: 0.6037 (mm) REVERT: A 543 MET cc_start: 0.7614 (mpp) cc_final: 0.7185 (mpp) REVERT: A 745 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8652 (tp) REVERT: A 784 PHE cc_start: 0.9052 (t80) cc_final: 0.8408 (t80) REVERT: A 820 TRP cc_start: 0.8893 (t60) cc_final: 0.8607 (t60) REVERT: A 838 ASP cc_start: 0.8649 (m-30) cc_final: 0.8322 (m-30) REVERT: A 841 GLN cc_start: 0.8841 (mm-40) cc_final: 0.8539 (mm-40) REVERT: A 846 THR cc_start: 0.8500 (OUTLIER) cc_final: 0.7983 (t) REVERT: A 876 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8817 (mt) REVERT: A 885 MET cc_start: 0.6609 (ttm) cc_final: 0.6352 (tmm) REVERT: A 906 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7873 (mm-30) REVERT: A 908 GLU cc_start: 0.8712 (tp30) cc_final: 0.8230 (pt0) REVERT: A 916 GLU cc_start: 0.9177 (tp30) cc_final: 0.8807 (tp30) REVERT: A 961 PHE cc_start: 0.8434 (t80) cc_final: 0.8159 (t80) REVERT: A 965 MET cc_start: 0.7845 (mmm) cc_final: 0.7444 (mmm) REVERT: A 976 PHE cc_start: 0.8187 (OUTLIER) cc_final: 0.7765 (t80) REVERT: A 1020 MET cc_start: 0.8278 (tpp) cc_final: 0.7989 (tpp) REVERT: A 1027 MET cc_start: 0.8808 (tmm) cc_final: 0.8058 (tmm) REVERT: A 1074 ASN cc_start: 0.8080 (p0) cc_final: 0.7607 (m110) REVERT: A 1102 ARG cc_start: 0.7192 (tpt170) cc_final: 0.6868 (mmp-170) REVERT: A 1125 TRP cc_start: 0.9020 (t-100) cc_final: 0.8764 (t-100) REVERT: A 1150 TYR cc_start: 0.7835 (OUTLIER) cc_final: 0.7212 (t80) REVERT: A 1170 ASN cc_start: 0.7784 (t0) cc_final: 0.7351 (p0) REVERT: A 1277 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7318 (tp) outliers start: 45 outliers final: 33 residues processed: 208 average time/residue: 0.0878 time to fit residues: 26.3129 Evaluate side-chains 209 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 169 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 359 GLN Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 726 TRP Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 799 GLU Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 899 HIS Chi-restraints excluded: chain A residue 903 ASP Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 976 PHE Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1035 ILE Chi-restraints excluded: chain A residue 1061 TYR Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain A residue 1142 CYS Chi-restraints excluded: chain A residue 1150 TYR Chi-restraints excluded: chain A residue 1277 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 16 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 108 optimal weight: 8.9990 chunk 112 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 ASN ** A 722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.127376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.095671 restraints weight = 24762.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.098818 restraints weight = 13814.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.100894 restraints weight = 9294.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.102326 restraints weight = 7057.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.103208 restraints weight = 5823.121| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.8502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9009 Z= 0.175 Angle : 0.728 12.793 12172 Z= 0.365 Chirality : 0.043 0.211 1399 Planarity : 0.004 0.052 1549 Dihedral : 6.162 88.263 1235 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 4.68 % Allowed : 31.24 % Favored : 64.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.25), residues: 1132 helix: 1.20 (0.19), residues: 756 sheet: -2.44 (0.59), residues: 44 loop : -1.61 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 605 TYR 0.031 0.002 TYR A 378 PHE 0.035 0.002 PHE A 147 TRP 0.013 0.002 TRP A 872 HIS 0.003 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 9009) covalent geometry : angle 0.72832 (12172) hydrogen bonds : bond 0.04430 ( 588) hydrogen bonds : angle 4.69055 ( 1743) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 175 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.8722 (mmp) cc_final: 0.8248 (tpp) REVERT: A 147 PHE cc_start: 0.8915 (m-80) cc_final: 0.8709 (m-10) REVERT: A 168 MET cc_start: 0.9267 (mmm) cc_final: 0.8621 (mmm) REVERT: A 190 ASP cc_start: 0.8352 (m-30) cc_final: 0.7252 (m-30) REVERT: A 295 ASP cc_start: 0.8685 (m-30) cc_final: 0.8240 (t70) REVERT: A 299 MET cc_start: 0.8364 (tpp) cc_final: 0.7982 (tpp) REVERT: A 327 TRP cc_start: 0.8529 (t60) cc_final: 0.8081 (t60) REVERT: A 365 GLN cc_start: 0.8697 (mm110) cc_final: 0.8423 (pp30) REVERT: A 378 TYR cc_start: 0.9244 (m-80) cc_final: 0.8641 (m-80) REVERT: A 424 ASN cc_start: 0.9044 (t0) cc_final: 0.8564 (p0) REVERT: A 425 MET cc_start: 0.7678 (mmm) cc_final: 0.7147 (mmm) REVERT: A 454 ARG cc_start: 0.8966 (tpt-90) cc_final: 0.8673 (tpt-90) REVERT: A 480 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7934 (mm-30) REVERT: A 501 LYS cc_start: 0.7345 (tptp) cc_final: 0.6366 (tptt) REVERT: A 543 MET cc_start: 0.7554 (mpp) cc_final: 0.7192 (mpp) REVERT: A 594 THR cc_start: 0.8559 (OUTLIER) cc_final: 0.8247 (p) REVERT: A 745 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8560 (tp) REVERT: A 820 TRP cc_start: 0.8868 (t60) cc_final: 0.8568 (t60) REVERT: A 838 ASP cc_start: 0.8699 (m-30) cc_final: 0.8402 (m-30) REVERT: A 841 GLN cc_start: 0.8879 (mm-40) cc_final: 0.8562 (mm-40) REVERT: A 846 THR cc_start: 0.8540 (OUTLIER) cc_final: 0.8316 (t) REVERT: A 876 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8866 (mm) REVERT: A 885 MET cc_start: 0.6546 (ttm) cc_final: 0.6342 (tmm) REVERT: A 906 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7934 (mm-30) REVERT: A 908 GLU cc_start: 0.8709 (tp30) cc_final: 0.8216 (pt0) REVERT: A 916 GLU cc_start: 0.9137 (tp30) cc_final: 0.8813 (tp30) REVERT: A 961 PHE cc_start: 0.8494 (t80) cc_final: 0.8241 (t80) REVERT: A 965 MET cc_start: 0.7882 (mmm) cc_final: 0.7466 (mmm) REVERT: A 976 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7859 (t80) REVERT: A 1020 MET cc_start: 0.8302 (tpp) cc_final: 0.7994 (tpp) REVERT: A 1027 MET cc_start: 0.8801 (tmm) cc_final: 0.8053 (tmm) REVERT: A 1074 ASN cc_start: 0.8064 (p0) cc_final: 0.7577 (m110) REVERT: A 1125 TRP cc_start: 0.9037 (t-100) cc_final: 0.8820 (t-100) REVERT: A 1150 TYR cc_start: 0.7933 (OUTLIER) cc_final: 0.7277 (t80) REVERT: A 1170 ASN cc_start: 0.7902 (t0) cc_final: 0.7496 (p0) REVERT: A 1277 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7335 (tp) outliers start: 44 outliers final: 33 residues processed: 201 average time/residue: 0.0864 time to fit residues: 25.3401 Evaluate side-chains 211 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 171 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 359 GLN Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 726 TRP Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 799 GLU Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 899 HIS Chi-restraints excluded: chain A residue 903 ASP Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 976 PHE Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1061 TYR Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain A residue 1150 TYR Chi-restraints excluded: chain A residue 1277 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 22 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 44 optimal weight: 0.2980 chunk 2 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.129145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.097562 restraints weight = 24567.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.100781 restraints weight = 13585.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.102891 restraints weight = 9075.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.104374 restraints weight = 6850.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.105341 restraints weight = 5624.535| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.8618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9009 Z= 0.146 Angle : 0.736 12.750 12172 Z= 0.362 Chirality : 0.043 0.218 1399 Planarity : 0.004 0.051 1549 Dihedral : 6.189 90.719 1235 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.83 % Allowed : 32.20 % Favored : 63.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.25), residues: 1132 helix: 1.19 (0.19), residues: 755 sheet: -2.53 (0.61), residues: 42 loop : -1.52 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 592 TYR 0.032 0.001 TYR A 378 PHE 0.024 0.002 PHE A 147 TRP 0.014 0.002 TRP A 148 HIS 0.002 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 9009) covalent geometry : angle 0.73622 (12172) hydrogen bonds : bond 0.04370 ( 588) hydrogen bonds : angle 4.65025 ( 1743) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 179 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ASP cc_start: 0.8434 (m-30) cc_final: 0.8206 (m-30) REVERT: A 147 PHE cc_start: 0.8799 (m-80) cc_final: 0.8546 (m-10) REVERT: A 168 MET cc_start: 0.9297 (mmm) cc_final: 0.8660 (mmm) REVERT: A 295 ASP cc_start: 0.8624 (m-30) cc_final: 0.8199 (t70) REVERT: A 299 MET cc_start: 0.8329 (tpp) cc_final: 0.7972 (tpp) REVERT: A 327 TRP cc_start: 0.8500 (t60) cc_final: 0.8061 (t60) REVERT: A 365 GLN cc_start: 0.8692 (mm110) cc_final: 0.8398 (pp30) REVERT: A 378 TYR cc_start: 0.9217 (m-80) cc_final: 0.8614 (m-80) REVERT: A 424 ASN cc_start: 0.8992 (t0) cc_final: 0.8506 (p0) REVERT: A 425 MET cc_start: 0.7630 (mmm) cc_final: 0.7108 (mmm) REVERT: A 454 ARG cc_start: 0.9002 (tpt-90) cc_final: 0.8759 (tpt-90) REVERT: A 480 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7923 (mm-30) REVERT: A 501 LYS cc_start: 0.7170 (tptp) cc_final: 0.6312 (tptt) REVERT: A 505 PRO cc_start: 0.6977 (Cg_exo) cc_final: 0.6231 (Cg_endo) REVERT: A 543 MET cc_start: 0.7691 (mpp) cc_final: 0.7277 (mpp) REVERT: A 559 ARG cc_start: 0.8439 (mmm160) cc_final: 0.8234 (tpm170) REVERT: A 594 THR cc_start: 0.8463 (OUTLIER) cc_final: 0.8153 (p) REVERT: A 745 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8558 (tp) REVERT: A 820 TRP cc_start: 0.8823 (t60) cc_final: 0.8579 (t60) REVERT: A 838 ASP cc_start: 0.8651 (m-30) cc_final: 0.8326 (m-30) REVERT: A 841 GLN cc_start: 0.8842 (mm-40) cc_final: 0.8512 (mm-40) REVERT: A 876 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8873 (mt) REVERT: A 906 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7862 (mm-30) REVERT: A 908 GLU cc_start: 0.8688 (tp30) cc_final: 0.8151 (pt0) REVERT: A 916 GLU cc_start: 0.9132 (tp30) cc_final: 0.8142 (tp30) REVERT: A 920 ASN cc_start: 0.8562 (m-40) cc_final: 0.7506 (m110) REVERT: A 961 PHE cc_start: 0.8503 (t80) cc_final: 0.8162 (t80) REVERT: A 965 MET cc_start: 0.7860 (mmm) cc_final: 0.7376 (mmm) REVERT: A 976 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7838 (t80) REVERT: A 1020 MET cc_start: 0.8308 (tpp) cc_final: 0.7993 (tpp) REVERT: A 1027 MET cc_start: 0.8785 (tmm) cc_final: 0.8047 (tmm) REVERT: A 1074 ASN cc_start: 0.8067 (p0) cc_final: 0.7602 (m-40) REVERT: A 1102 ARG cc_start: 0.7278 (tpt170) cc_final: 0.6887 (mmp-170) REVERT: A 1170 ASN cc_start: 0.7868 (t0) cc_final: 0.7466 (p0) REVERT: A 1277 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7360 (tp) outliers start: 36 outliers final: 24 residues processed: 199 average time/residue: 0.0834 time to fit residues: 24.2500 Evaluate side-chains 199 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 359 GLN Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 726 TRP Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 899 HIS Chi-restraints excluded: chain A residue 903 ASP Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 976 PHE Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1035 ILE Chi-restraints excluded: chain A residue 1061 TYR Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain A residue 1277 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 33 optimal weight: 6.9990 chunk 86 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 111 optimal weight: 20.0000 chunk 3 optimal weight: 0.9990 chunk 98 optimal weight: 0.3980 chunk 90 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 ASN ** A 722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.130077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.098780 restraints weight = 24388.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.101987 restraints weight = 13527.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.104149 restraints weight = 9054.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.105588 restraints weight = 6826.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.106554 restraints weight = 5612.592| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.8824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9009 Z= 0.145 Angle : 0.742 12.486 12172 Z= 0.363 Chirality : 0.044 0.271 1399 Planarity : 0.004 0.051 1549 Dihedral : 5.509 59.758 1232 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.29 % Allowed : 32.94 % Favored : 63.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.25), residues: 1132 helix: 1.24 (0.19), residues: 754 sheet: -2.35 (0.64), residues: 42 loop : -1.54 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1102 TYR 0.029 0.001 TYR A 378 PHE 0.031 0.002 PHE A 788 TRP 0.041 0.002 TRP A1125 HIS 0.002 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9009) covalent geometry : angle 0.74208 (12172) hydrogen bonds : bond 0.04326 ( 588) hydrogen bonds : angle 4.67484 ( 1743) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1823.10 seconds wall clock time: 32 minutes 18.81 seconds (1938.81 seconds total)