Starting phenix.real_space_refine on Sat Jul 26 22:31:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nfm_49370/07_2025/9nfm_49370_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nfm_49370/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9nfm_49370/07_2025/9nfm_49370.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nfm_49370/07_2025/9nfm_49370.map" model { file = "/net/cci-nas-00/data/ceres_data/9nfm_49370/07_2025/9nfm_49370_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nfm_49370/07_2025/9nfm_49370_neut.cif" } resolution = 3.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.54, per 1000 atoms: 0.63 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: 2.49 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.97 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: 3.76 Time building geometry restraints manager: 2.91 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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.180 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.200 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (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 TRP 0.037 0.002 TRP A 820 HIS 0.006 0.001 HIS A 614 PHE 0.034 0.002 PHE A 147 TYR 0.021 0.002 TYR A 328 ARG 0.005 0.001 ARG A1031 Details of bonding type rmsd hydrogen bonds : bond 0.10545 ( 588) hydrogen bonds : angle 5.15682 ( 1743) covalent geometry : bond 0.00579 ( 9009) covalent geometry : angle 0.67602 (12172) *********************** 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 : 0.892 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: 0.7348 (tp40) REVERT: A 174 TRP cc_start: 0.8446 (t60) cc_final: 0.8126 (t60) REVERT: A 190 ASP cc_start: 0.8083 (m-30) cc_final: 0.7777 (m-30) REVERT: A 299 MET cc_start: 0.7488 (tpp) cc_final: 0.7179 (tpp) REVERT: A 333 ILE cc_start: 0.6791 (mt) cc_final: 0.6551 (mt) REVERT: A 501 LYS cc_start: 0.6002 (tptp) cc_final: 0.5772 (tptp) REVERT: A 794 PHE cc_start: 0.7022 (m-80) cc_final: 0.6769 (m-80) REVERT: A 838 ASP cc_start: 0.8032 (m-30) cc_final: 0.7739 (m-30) REVERT: A 961 PHE cc_start: 0.7254 (t80) cc_final: 0.6899 (t80) REVERT: A 999 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8828 (mm) REVERT: A 1020 MET cc_start: 0.7238 (tpp) cc_final: 0.6970 (tpp) REVERT: A 1027 MET cc_start: 0.8351 (tmm) cc_final: 0.7910 (tmm) REVERT: A 1077 VAL cc_start: 0.7519 (t) cc_final: 0.7250 (t) outliers start: 26 outliers final: 13 residues processed: 304 average time/residue: 0.2165 time to fit residues: 89.3232 Evaluate side-chains 205 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 191 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 58 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 103 optimal weight: 0.0770 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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 ** 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 = 0.4367 r_free = 0.4367 target = 0.152179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.120766 restraints weight = 23775.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.124602 restraints weight = 13481.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.127153 restraints weight = 8847.155| |-----------------------------------------------------------------------------| r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9009 Z= 0.161 Angle : 0.713 11.808 12172 Z= 0.362 Chirality : 0.045 0.266 1399 Planarity : 0.004 0.046 1549 Dihedral : 7.221 84.103 1250 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.78 % Allowed : 25.61 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.25), residues: 1132 helix: 1.49 (0.18), residues: 757 sheet: -3.14 (0.52), residues: 56 loop : -1.92 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A1125 HIS 0.004 0.001 HIS A 624 PHE 0.021 0.002 PHE A1059 TYR 0.024 0.002 TYR A 870 ARG 0.005 0.001 ARG A1127 Details of bonding type rmsd hydrogen bonds : bond 0.04793 ( 588) hydrogen bonds : angle 4.62825 ( 1743) covalent geometry : bond 0.00344 ( 9009) covalent geometry : angle 0.71285 (12172) *********************** 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 259 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 214 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 TRP cc_start: 0.8470 (t60) cc_final: 0.8102 (t60) REVERT: A 190 ASP cc_start: 0.8333 (m-30) cc_final: 0.7995 (m-30) REVERT: A 294 GLU cc_start: 0.8050 (tp30) cc_final: 0.7724 (mm-30) REVERT: A 299 MET cc_start: 0.8116 (tpp) cc_final: 0.7458 (tpp) REVERT: A 311 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8273 (mpp) REVERT: A 333 ILE cc_start: 0.7066 (mt) cc_final: 0.6725 (mt) REVERT: A 365 GLN cc_start: 0.8373 (mm-40) cc_final: 0.8129 (pp30) REVERT: A 425 MET cc_start: 0.7812 (mmm) cc_final: 0.7295 (mmm) REVERT: A 505 PRO cc_start: 0.6861 (Cg_exo) cc_final: 0.6649 (Cg_endo) REVERT: A 776 PHE cc_start: 0.7697 (OUTLIER) cc_final: 0.7380 (m-80) REVERT: A 794 PHE cc_start: 0.7742 (m-80) cc_final: 0.7454 (m-80) REVERT: A 801 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8854 (tp) REVERT: A 882 VAL cc_start: 0.9057 (t) cc_final: 0.8769 (m) REVERT: A 906 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8174 (mm-30) REVERT: A 908 GLU cc_start: 0.8757 (tp30) cc_final: 0.8267 (pt0) REVERT: A 1020 MET cc_start: 0.8291 (tpp) cc_final: 0.8027 (tpp) REVERT: A 1027 MET cc_start: 0.8955 (tmm) cc_final: 0.8384 (tmm) REVERT: A 1125 TRP cc_start: 0.8839 (t-100) cc_final: 0.8601 (t-100) REVERT: A 1245 ILE cc_start: 0.8839 (mm) cc_final: 0.8448 (tp) outliers start: 45 outliers final: 17 residues processed: 240 average time/residue: 0.1839 time to fit residues: 62.9986 Evaluate side-chains 206 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ASP 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 359 GLN 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 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 6 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 95 optimal weight: 20.0000 chunk 72 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 ASN ** A 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1037 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.136486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.103836 restraints weight = 24712.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.107236 restraints weight = 14030.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.109495 restraints weight = 9439.151| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.5195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 9009 Z= 0.256 Angle : 0.770 9.052 12172 Z= 0.404 Chirality : 0.046 0.214 1399 Planarity : 0.005 0.052 1549 Dihedral : 7.024 81.686 1241 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 6.70 % Allowed : 25.40 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.25), residues: 1132 helix: 1.06 (0.19), residues: 757 sheet: -3.24 (0.48), residues: 54 loop : -1.77 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 872 HIS 0.005 0.001 HIS A 624 PHE 0.027 0.003 PHE A 794 TYR 0.019 0.002 TYR A 328 ARG 0.007 0.001 ARG A 479 Details of bonding type rmsd hydrogen bonds : bond 0.05065 ( 588) hydrogen bonds : angle 4.82519 ( 1743) covalent geometry : bond 0.00548 ( 9009) covalent geometry : angle 0.76987 (12172) *********************** 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: 63 poor density : 197 time to evaluate : 0.946 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: A 150 LEU cc_start: 0.9575 (OUTLIER) cc_final: 0.9266 (mp) REVERT: A 190 ASP cc_start: 0.8568 (m-30) cc_final: 0.8201 (m-30) REVERT: A 295 ASP cc_start: 0.8255 (m-30) cc_final: 0.7988 (t70) REVERT: A 299 MET cc_start: 0.8167 (tpp) cc_final: 0.7498 (tpp) REVERT: A 365 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8456 (pp30) REVERT: A 480 GLU cc_start: 0.8562 (mm-30) cc_final: 0.7929 (mm-30) REVERT: A 764 ILE cc_start: 0.7388 (mt) cc_final: 0.7157 (mt) REVERT: A 775 MET cc_start: 0.6919 (ptp) cc_final: 0.6707 (ppp) REVERT: A 838 ASP cc_start: 0.8815 (m-30) cc_final: 0.8473 (m-30) REVERT: A 876 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8473 (mt) REVERT: A 882 VAL cc_start: 0.9245 (t) cc_final: 0.9013 (m) REVERT: A 906 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8199 (mm-30) REVERT: A 1020 MET cc_start: 0.8328 (tpp) cc_final: 0.8047 (tpp) REVERT: A 1027 MET cc_start: 0.8940 (tmm) cc_final: 0.8339 (tmm) REVERT: A 1125 TRP cc_start: 0.8978 (t-100) cc_final: 0.8250 (t-100) outliers start: 63 outliers final: 39 residues processed: 237 average time/residue: 0.2403 time to fit residues: 85.0378 Evaluate side-chains 216 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 175 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 94 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 233 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 359 GLN Chi-restraints excluded: chain A residue 446 SER 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 609 VAL 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 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 1061 TYR Chi-restraints excluded: chain A residue 1073 LEU Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain A residue 1134 SER Chi-restraints excluded: chain A residue 1142 CYS Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1214 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 25 optimal weight: 7.9990 chunk 47 optimal weight: 0.5980 chunk 109 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 90 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 111 optimal weight: 0.0060 chunk 87 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 920 ASN ** A 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1147 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.138576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.106129 restraints weight = 24053.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.109638 restraints weight = 13650.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.111980 restraints weight = 9138.092| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.5644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9009 Z= 0.141 Angle : 0.678 11.930 12172 Z= 0.335 Chirality : 0.042 0.193 1399 Planarity : 0.004 0.049 1549 Dihedral : 6.840 80.160 1241 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.14 % Allowed : 28.16 % Favored : 67.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.25), residues: 1132 helix: 1.24 (0.19), residues: 756 sheet: -3.16 (0.46), residues: 56 loop : -1.76 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1125 HIS 0.013 0.001 HIS A 73 PHE 0.026 0.002 PHE A 771 TYR 0.014 0.001 TYR A 955 ARG 0.004 0.001 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.04435 ( 588) hydrogen bonds : angle 4.58043 ( 1743) covalent geometry : bond 0.00298 ( 9009) covalent geometry : angle 0.67777 (12172) *********************** 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: 39 poor density : 206 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 PHE cc_start: 0.8852 (m-10) cc_final: 0.8568 (m-10) REVERT: A 190 ASP cc_start: 0.8300 (m-30) cc_final: 0.7951 (m-30) REVERT: A 299 MET cc_start: 0.8197 (tpp) cc_final: 0.7551 (tpp) REVERT: A 334 MET cc_start: 0.7792 (mmm) cc_final: 0.7582 (mmm) REVERT: A 365 GLN cc_start: 0.8655 (mm-40) cc_final: 0.8417 (pp30) REVERT: A 460 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7927 (tm-30) REVERT: A 480 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7954 (mm-30) REVERT: A 501 LYS cc_start: 0.6656 (tptp) cc_final: 0.6294 (tptt) REVERT: A 764 ILE cc_start: 0.7413 (mt) cc_final: 0.7176 (mt) REVERT: A 775 MET cc_start: 0.7015 (ptp) cc_final: 0.6640 (ppp) REVERT: A 813 MET cc_start: 0.7285 (mtt) cc_final: 0.7085 (mtm) REVERT: A 820 TRP cc_start: 0.8885 (t60) cc_final: 0.8406 (t60) REVERT: A 838 ASP cc_start: 0.8706 (m-30) cc_final: 0.8355 (m-30) REVERT: A 841 GLN cc_start: 0.8683 (mm-40) cc_final: 0.8283 (mm-40) REVERT: A 876 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8598 (mm) REVERT: A 885 MET cc_start: 0.6270 (ttm) cc_final: 0.6007 (tmm) REVERT: A 906 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8016 (mm-30) REVERT: A 908 GLU cc_start: 0.8869 (tp30) cc_final: 0.8150 (pt0) REVERT: A 1020 MET cc_start: 0.8307 (tpp) cc_final: 0.8041 (tpp) REVERT: A 1027 MET cc_start: 0.8940 (tmm) cc_final: 0.8330 (tmm) REVERT: A 1125 TRP cc_start: 0.9023 (t-100) cc_final: 0.8375 (t-100) REVERT: A 1129 GLN cc_start: 0.9114 (mm-40) cc_final: 0.8305 (tp40) outliers start: 39 outliers final: 28 residues processed: 225 average time/residue: 0.1775 time to fit residues: 56.9306 Evaluate side-chains 196 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 94 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 220 PHE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 359 GLN Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 451 LEU 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 776 PHE Chi-restraints excluded: chain A residue 799 GLU 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 1061 TYR Chi-restraints excluded: chain A residue 1073 LEU Chi-restraints excluded: chain A residue 1096 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 82 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 94 optimal weight: 0.0980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 631 GLN ** A 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1147 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.135928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.104039 restraints weight = 24181.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.107429 restraints weight = 13599.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.109632 restraints weight = 9091.032| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.6136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9009 Z= 0.142 Angle : 0.659 14.033 12172 Z= 0.328 Chirality : 0.042 0.200 1399 Planarity : 0.004 0.050 1549 Dihedral : 6.511 66.944 1241 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.99 % Allowed : 28.69 % Favored : 66.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.25), residues: 1132 helix: 1.33 (0.19), residues: 756 sheet: -3.26 (0.46), residues: 54 loop : -1.73 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 872 HIS 0.007 0.001 HIS A 73 PHE 0.024 0.002 PHE A 348 TYR 0.012 0.001 TYR A 322 ARG 0.003 0.000 ARG A 504 Details of bonding type rmsd hydrogen bonds : bond 0.04307 ( 588) hydrogen bonds : angle 4.60042 ( 1743) covalent geometry : bond 0.00311 ( 9009) covalent geometry : angle 0.65932 (12172) *********************** 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 232 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 185 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 PHE cc_start: 0.8868 (m-10) cc_final: 0.8642 (m-10) REVERT: A 190 ASP cc_start: 0.8245 (m-30) cc_final: 0.7903 (m-30) REVERT: A 192 TYR cc_start: 0.8658 (t80) cc_final: 0.8366 (t80) REVERT: A 196 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7826 (mm-30) REVERT: A 295 ASP cc_start: 0.8288 (m-30) cc_final: 0.7947 (t70) REVERT: A 299 MET cc_start: 0.8127 (tpp) cc_final: 0.7656 (tpp) REVERT: A 365 GLN cc_start: 0.8646 (mm-40) cc_final: 0.8398 (pp30) REVERT: A 425 MET cc_start: 0.7456 (mmm) cc_final: 0.6979 (mmm) REVERT: A 460 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7942 (tm-30) REVERT: A 480 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8014 (mm-30) REVERT: A 501 LYS cc_start: 0.6908 (tptp) cc_final: 0.6160 (tptp) REVERT: A 775 MET cc_start: 0.6976 (ptp) cc_final: 0.6708 (ppp) REVERT: A 801 LEU cc_start: 0.9458 (tp) cc_final: 0.9241 (tp) REVERT: A 838 ASP cc_start: 0.8658 (m-30) cc_final: 0.8309 (m-30) REVERT: A 841 GLN cc_start: 0.8707 (mm-40) cc_final: 0.8334 (mm-40) REVERT: A 882 VAL cc_start: 0.9189 (t) cc_final: 0.8981 (m) REVERT: A 885 MET cc_start: 0.6369 (ttm) cc_final: 0.6093 (tmm) REVERT: A 906 GLU cc_start: 0.8296 (mm-30) cc_final: 0.8073 (mm-30) REVERT: A 908 GLU cc_start: 0.8767 (tp30) cc_final: 0.8225 (pt0) REVERT: A 1020 MET cc_start: 0.8379 (tpp) cc_final: 0.8082 (tpp) REVERT: A 1027 MET cc_start: 0.8842 (tmm) cc_final: 0.8190 (tmm) REVERT: A 1125 TRP cc_start: 0.9053 (t-100) cc_final: 0.8400 (t-100) REVERT: A 1129 GLN cc_start: 0.9119 (mm-40) cc_final: 0.8347 (tp40) REVERT: A 1277 LEU cc_start: 0.7248 (OUTLIER) cc_final: 0.6901 (tp) outliers start: 47 outliers final: 31 residues processed: 213 average time/residue: 0.1696 time to fit residues: 53.1339 Evaluate side-chains 208 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 176 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 233 VAL 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 451 LEU Chi-restraints excluded: chain A residue 485 VAL 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 776 PHE Chi-restraints excluded: chain A residue 799 GLU 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 899 HIS Chi-restraints excluded: chain A residue 903 ASP Chi-restraints excluded: chain A residue 913 ILE 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 1073 LEU Chi-restraints excluded: chain A residue 1096 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 93 optimal weight: 0.3980 chunk 38 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 65 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 ASN ** A 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1147 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.135085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.103213 restraints weight = 24089.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.106520 restraints weight = 13666.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.108764 restraints weight = 9230.478| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.6509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9009 Z= 0.140 Angle : 0.676 13.748 12172 Z= 0.332 Chirality : 0.043 0.252 1399 Planarity : 0.004 0.050 1549 Dihedral : 5.954 59.195 1237 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 4.46 % Allowed : 29.22 % Favored : 66.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.25), residues: 1132 helix: 1.38 (0.19), residues: 756 sheet: -2.48 (0.58), residues: 44 loop : -1.78 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 872 HIS 0.006 0.001 HIS A 73 PHE 0.032 0.002 PHE A 348 TYR 0.009 0.001 TYR A 322 ARG 0.002 0.000 ARG A 479 Details of bonding type rmsd hydrogen bonds : bond 0.04269 ( 588) hydrogen bonds : angle 4.54801 ( 1743) covalent geometry : bond 0.00310 ( 9009) covalent geometry : angle 0.67631 (12172) *********************** 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 224 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 182 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 PHE cc_start: 0.8848 (m-10) cc_final: 0.8620 (m-10) REVERT: A 190 ASP cc_start: 0.8295 (m-30) cc_final: 0.7933 (m-30) REVERT: A 192 TYR cc_start: 0.8639 (t80) cc_final: 0.8333 (t80) REVERT: A 196 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7851 (mm-30) REVERT: A 295 ASP cc_start: 0.8324 (m-30) cc_final: 0.8009 (t70) REVERT: A 299 MET cc_start: 0.8223 (tpp) cc_final: 0.7741 (tpp) REVERT: A 365 GLN cc_start: 0.8660 (mm-40) cc_final: 0.8396 (pp30) REVERT: A 425 MET cc_start: 0.7613 (mmm) cc_final: 0.7112 (mmm) REVERT: A 460 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7924 (tm-30) REVERT: A 480 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7929 (mm-30) REVERT: A 801 LEU cc_start: 0.9392 (tp) cc_final: 0.9107 (tp) REVERT: A 820 TRP cc_start: 0.8798 (t60) cc_final: 0.8248 (t60) REVERT: A 838 ASP cc_start: 0.8698 (m-30) cc_final: 0.8332 (m-30) REVERT: A 841 GLN cc_start: 0.8702 (mm-40) cc_final: 0.8361 (mm-40) REVERT: A 882 VAL cc_start: 0.9207 (t) cc_final: 0.8995 (m) REVERT: A 885 MET cc_start: 0.6339 (ttm) cc_final: 0.6127 (tmm) REVERT: A 906 GLU cc_start: 0.8277 (mm-30) cc_final: 0.8027 (mm-30) REVERT: A 908 GLU cc_start: 0.8729 (tp30) cc_final: 0.8183 (pt0) REVERT: A 1020 MET cc_start: 0.8396 (tpp) cc_final: 0.8083 (tpp) REVERT: A 1027 MET cc_start: 0.8828 (tmm) cc_final: 0.8189 (tmm) REVERT: A 1074 ASN cc_start: 0.8012 (p0) cc_final: 0.7479 (m110) REVERT: A 1125 TRP cc_start: 0.9080 (t-100) cc_final: 0.8470 (t-100) REVERT: A 1129 GLN cc_start: 0.9107 (mm-40) cc_final: 0.8401 (tp40) REVERT: A 1277 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.7028 (tp) outliers start: 42 outliers final: 29 residues processed: 208 average time/residue: 0.1648 time to fit residues: 50.3499 Evaluate side-chains 204 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 220 PHE Chi-restraints excluded: chain A residue 233 VAL 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 359 GLN Chi-restraints excluded: chain A residue 451 LEU 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 860 LEU Chi-restraints excluded: chain A residue 868 PHE Chi-restraints excluded: chain A residue 874 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 1073 LEU Chi-restraints excluded: chain A residue 1096 THR 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 34 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 81 optimal weight: 0.0270 chunk 40 optimal weight: 7.9990 chunk 64 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 overall best weight: 0.9840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 938 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 = 0.4161 r_free = 0.4161 target = 0.134261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.101450 restraints weight = 24685.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.104764 restraints weight = 13983.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.106953 restraints weight = 9508.653| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.7045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9009 Z= 0.141 Angle : 0.666 12.940 12172 Z= 0.328 Chirality : 0.043 0.225 1399 Planarity : 0.004 0.050 1549 Dihedral : 5.800 58.587 1237 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.72 % Allowed : 30.29 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.25), residues: 1132 helix: 1.34 (0.19), residues: 757 sheet: -2.33 (0.60), residues: 44 loop : -1.67 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 872 HIS 0.005 0.001 HIS A 73 PHE 0.021 0.002 PHE A 734 TYR 0.010 0.001 TYR A 322 ARG 0.007 0.000 ARG A 454 Details of bonding type rmsd hydrogen bonds : bond 0.04315 ( 588) hydrogen bonds : angle 4.52485 ( 1743) covalent geometry : bond 0.00304 ( 9009) covalent geometry : angle 0.66619 (12172) *********************** 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 219 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 184 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ASP cc_start: 0.8375 (m-30) cc_final: 0.8014 (m-30) REVERT: A 295 ASP cc_start: 0.8389 (m-30) cc_final: 0.8010 (t70) REVERT: A 299 MET cc_start: 0.8246 (tpp) cc_final: 0.7795 (tpp) REVERT: A 316 LEU cc_start: 0.9366 (tp) cc_final: 0.9125 (tp) REVERT: A 334 MET cc_start: 0.7842 (mmm) cc_final: 0.7627 (mmm) REVERT: A 365 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8395 (pp30) REVERT: A 425 MET cc_start: 0.7754 (mmm) cc_final: 0.7203 (mmm) REVERT: A 454 ARG cc_start: 0.8694 (tpt-90) cc_final: 0.8479 (tpt-90) REVERT: A 460 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7971 (tm-30) REVERT: A 480 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7913 (mm-30) REVERT: A 501 LYS cc_start: 0.7110 (tptp) cc_final: 0.6273 (tptt) REVERT: A 799 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7693 (tp30) REVERT: A 820 TRP cc_start: 0.8811 (t60) cc_final: 0.8334 (t60) REVERT: A 838 ASP cc_start: 0.8713 (m-30) cc_final: 0.8340 (m-30) REVERT: A 841 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8426 (mm-40) REVERT: A 882 VAL cc_start: 0.9224 (t) cc_final: 0.9016 (m) REVERT: A 885 MET cc_start: 0.6502 (ttm) cc_final: 0.6297 (tmm) REVERT: A 906 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7981 (mm-30) REVERT: A 908 GLU cc_start: 0.8697 (tp30) cc_final: 0.8137 (pt0) REVERT: A 1020 MET cc_start: 0.8390 (tpp) cc_final: 0.8082 (tpp) REVERT: A 1027 MET cc_start: 0.8793 (tmm) cc_final: 0.8072 (tmm) REVERT: A 1074 ASN cc_start: 0.8165 (p0) cc_final: 0.7686 (m110) REVERT: A 1125 TRP cc_start: 0.9135 (t-100) cc_final: 0.8588 (t-100) REVERT: A 1129 GLN cc_start: 0.9096 (mm-40) cc_final: 0.8410 (tp40) REVERT: A 1277 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7118 (tp) outliers start: 35 outliers final: 24 residues processed: 204 average time/residue: 0.1772 time to fit residues: 52.4811 Evaluate side-chains 196 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 320 LEU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 359 GLN Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 603 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 776 PHE Chi-restraints excluded: chain A residue 799 GLU Chi-restraints excluded: chain A residue 860 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 1061 TYR Chi-restraints excluded: chain A residue 1073 LEU Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain A residue 1142 CYS 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 57 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 28 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 11 optimal weight: 0.1980 chunk 80 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 GLN ** A 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 938 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 = 0.4159 r_free = 0.4159 target = 0.134003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.101688 restraints weight = 24763.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.105091 restraints weight = 13862.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.107357 restraints weight = 9279.350| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.7319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9009 Z= 0.134 Angle : 0.686 12.691 12172 Z= 0.335 Chirality : 0.042 0.238 1399 Planarity : 0.004 0.050 1549 Dihedral : 5.615 57.836 1235 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.19 % Allowed : 31.14 % Favored : 65.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.25), residues: 1132 helix: 1.33 (0.19), residues: 757 sheet: -2.20 (0.62), residues: 44 loop : -1.64 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 872 HIS 0.005 0.001 HIS A 73 PHE 0.029 0.002 PHE A 147 TYR 0.020 0.001 TYR A1182 ARG 0.003 0.000 ARG A1102 Details of bonding type rmsd hydrogen bonds : bond 0.04234 ( 588) hydrogen bonds : angle 4.53874 ( 1743) covalent geometry : bond 0.00285 ( 9009) covalent geometry : angle 0.68616 (12172) *********************** 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 208 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 178 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 MET cc_start: 0.8411 (tpp) cc_final: 0.7835 (tpp) REVERT: A 190 ASP cc_start: 0.8381 (m-30) cc_final: 0.8019 (m-30) REVERT: A 192 TYR cc_start: 0.8573 (t80) cc_final: 0.8260 (t80) REVERT: A 196 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7874 (mm-30) REVERT: A 295 ASP cc_start: 0.8430 (m-30) cc_final: 0.8042 (t70) REVERT: A 299 MET cc_start: 0.8201 (tpp) cc_final: 0.7758 (tpp) REVERT: A 316 LEU cc_start: 0.9440 (tp) cc_final: 0.9102 (tp) REVERT: A 334 MET cc_start: 0.7882 (mmm) cc_final: 0.7581 (mmm) REVERT: A 365 GLN cc_start: 0.8644 (mm-40) cc_final: 0.8352 (pp30) REVERT: A 425 MET cc_start: 0.7798 (mmm) cc_final: 0.7247 (mmm) REVERT: A 454 ARG cc_start: 0.8744 (tpt-90) cc_final: 0.8522 (tpt-90) REVERT: A 460 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7976 (tm-30) REVERT: A 480 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7956 (mm-30) REVERT: A 501 LYS cc_start: 0.7128 (tptp) cc_final: 0.6277 (tptt) REVERT: A 745 LEU cc_start: 0.9048 (mm) cc_final: 0.8534 (tp) REVERT: A 784 PHE cc_start: 0.8961 (t80) cc_final: 0.8746 (t80) REVERT: A 799 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7739 (tp30) REVERT: A 820 TRP cc_start: 0.8787 (t60) cc_final: 0.8391 (t60) REVERT: A 838 ASP cc_start: 0.8696 (m-30) cc_final: 0.8320 (m-30) REVERT: A 841 GLN cc_start: 0.8776 (mm-40) cc_final: 0.8458 (mm-40) REVERT: A 906 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7979 (mm-30) REVERT: A 908 GLU cc_start: 0.8720 (tp30) cc_final: 0.8175 (pt0) REVERT: A 916 GLU cc_start: 0.9229 (tp30) cc_final: 0.8816 (tp30) REVERT: A 965 MET cc_start: 0.8097 (mmm) cc_final: 0.7846 (mmm) REVERT: A 1020 MET cc_start: 0.8396 (tpp) cc_final: 0.8078 (tpp) REVERT: A 1027 MET cc_start: 0.8833 (tmm) cc_final: 0.8130 (tmm) REVERT: A 1074 ASN cc_start: 0.8101 (p0) cc_final: 0.7657 (m110) REVERT: A 1125 TRP cc_start: 0.9132 (t-100) cc_final: 0.8614 (t-100) REVERT: A 1129 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8414 (tp40) REVERT: A 1277 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7139 (tp) outliers start: 30 outliers final: 22 residues processed: 199 average time/residue: 0.1777 time to fit residues: 51.0020 Evaluate side-chains 193 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 320 LEU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 359 GLN Chi-restraints excluded: chain A residue 565 LEU 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 776 PHE Chi-restraints excluded: chain A residue 799 GLU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 874 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 1073 LEU Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain A residue 1142 CYS 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 64 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 HIS A 560 ASN ** A 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.128710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.094994 restraints weight = 25000.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.098154 restraints weight = 14173.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.100251 restraints weight = 9692.513| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.7996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9009 Z= 0.195 Angle : 0.747 12.935 12172 Z= 0.373 Chirality : 0.044 0.200 1399 Planarity : 0.004 0.051 1549 Dihedral : 5.682 54.614 1235 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.83 % Allowed : 30.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.25), residues: 1132 helix: 1.06 (0.19), residues: 758 sheet: -2.17 (0.60), residues: 44 loop : -1.59 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 872 HIS 0.006 0.001 HIS A 73 PHE 0.032 0.002 PHE A 147 TYR 0.018 0.002 TYR A 322 ARG 0.003 0.001 ARG A1209 Details of bonding type rmsd hydrogen bonds : bond 0.04697 ( 588) hydrogen bonds : angle 4.74123 ( 1743) covalent geometry : bond 0.00430 ( 9009) covalent geometry : angle 0.74732 (12172) *********************** 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 218 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 182 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 ASP cc_start: 0.8521 (m-30) cc_final: 0.8124 (m-30) REVERT: A 196 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7946 (mm-30) REVERT: A 295 ASP cc_start: 0.8656 (m-30) cc_final: 0.8166 (t70) REVERT: A 299 MET cc_start: 0.8305 (tpp) cc_final: 0.7845 (tpp) REVERT: A 365 GLN cc_start: 0.8688 (mm-40) cc_final: 0.8449 (pp30) REVERT: A 423 ASN cc_start: 0.9064 (p0) cc_final: 0.8703 (p0) REVERT: A 424 ASN cc_start: 0.9158 (t0) cc_final: 0.8618 (p0) REVERT: A 425 MET cc_start: 0.7856 (mmm) cc_final: 0.7338 (mmm) REVERT: A 480 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8038 (mm-30) REVERT: A 501 LYS cc_start: 0.7555 (tptp) cc_final: 0.6742 (tptt) REVERT: A 505 PRO cc_start: 0.6935 (Cg_endo) cc_final: 0.6606 (Cg_exo) REVERT: A 548 LYS cc_start: 0.8879 (mmtt) cc_final: 0.8578 (mttt) REVERT: A 745 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8599 (tp) REVERT: A 799 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7770 (tp30) REVERT: A 820 TRP cc_start: 0.8886 (t60) cc_final: 0.8380 (t60) REVERT: A 838 ASP cc_start: 0.8807 (m-30) cc_final: 0.8497 (m-30) REVERT: A 841 GLN cc_start: 0.8884 (mm-40) cc_final: 0.8536 (mm-40) REVERT: A 906 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7972 (mm-30) REVERT: A 908 GLU cc_start: 0.8705 (tp30) cc_final: 0.8170 (pt0) REVERT: A 916 GLU cc_start: 0.9221 (tp30) cc_final: 0.8767 (tp30) REVERT: A 1027 MET cc_start: 0.8829 (tmm) cc_final: 0.8113 (tmm) REVERT: A 1074 ASN cc_start: 0.8195 (p0) cc_final: 0.7699 (m110) REVERT: A 1125 TRP cc_start: 0.9192 (t-100) cc_final: 0.8737 (t-100) REVERT: A 1129 GLN cc_start: 0.9112 (mm-40) cc_final: 0.8497 (tp40) REVERT: A 1170 ASN cc_start: 0.7875 (t0) cc_final: 0.7502 (p0) REVERT: A 1277 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7235 (tp) outliers start: 36 outliers final: 23 residues processed: 206 average time/residue: 0.1760 time to fit residues: 53.0479 Evaluate side-chains 196 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 339 THR Chi-restraints excluded: chain A residue 359 GLN Chi-restraints excluded: chain A residue 560 ASN 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 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 966 ILE 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 1073 LEU Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain A residue 1142 CYS 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 91 optimal weight: 20.0000 chunk 59 optimal weight: 0.9990 chunk 35 optimal weight: 0.2980 chunk 21 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 103 optimal weight: 0.3980 chunk 74 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 GLN ** A 722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 938 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 = 0.4118 r_free = 0.4118 target = 0.130998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.097940 restraints weight = 24705.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.101193 restraints weight = 13994.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.103271 restraints weight = 9526.981| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.8200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9009 Z= 0.151 Angle : 0.757 12.723 12172 Z= 0.369 Chirality : 0.044 0.222 1399 Planarity : 0.004 0.048 1549 Dihedral : 5.307 52.855 1231 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.55 % Allowed : 32.73 % Favored : 64.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.25), residues: 1132 helix: 1.17 (0.19), residues: 757 sheet: -2.31 (0.61), residues: 43 loop : -1.60 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 174 HIS 0.005 0.001 HIS A 73 PHE 0.026 0.002 PHE A 734 TYR 0.017 0.001 TYR A 992 ARG 0.006 0.001 ARG A 559 Details of bonding type rmsd hydrogen bonds : bond 0.04490 ( 588) hydrogen bonds : angle 4.60752 ( 1743) covalent geometry : bond 0.00332 ( 9009) covalent geometry : angle 0.75704 (12172) ********************** 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 198 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 ASP cc_start: 0.8445 (m-30) cc_final: 0.8056 (m-30) REVERT: A 196 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7952 (mm-30) REVERT: A 200 ASP cc_start: 0.8631 (m-30) cc_final: 0.8274 (m-30) REVERT: A 295 ASP cc_start: 0.8565 (m-30) cc_final: 0.8111 (t70) REVERT: A 299 MET cc_start: 0.8322 (tpp) cc_final: 0.7894 (tpp) REVERT: A 425 MET cc_start: 0.7838 (mmm) cc_final: 0.7227 (mmm) REVERT: A 480 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8036 (mm-30) REVERT: A 501 LYS cc_start: 0.7453 (tptp) cc_final: 0.6701 (tptt) REVERT: A 505 PRO cc_start: 0.6669 (Cg_endo) cc_final: 0.6442 (Cg_exo) REVERT: A 548 LYS cc_start: 0.8862 (mmtt) cc_final: 0.8554 (mptt) REVERT: A 799 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7830 (tp30) REVERT: A 820 TRP cc_start: 0.8853 (t60) cc_final: 0.8470 (t60) REVERT: A 838 ASP cc_start: 0.8749 (m-30) cc_final: 0.8408 (m-30) REVERT: A 841 GLN cc_start: 0.8855 (mm-40) cc_final: 0.8515 (mm-40) REVERT: A 906 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7957 (mm-30) REVERT: A 908 GLU cc_start: 0.8715 (tp30) cc_final: 0.8142 (pt0) REVERT: A 916 GLU cc_start: 0.9225 (tp30) cc_final: 0.8893 (tp30) REVERT: A 965 MET cc_start: 0.8023 (mmm) cc_final: 0.7783 (mmm) REVERT: A 1027 MET cc_start: 0.8831 (tmm) cc_final: 0.8103 (tmm) REVERT: A 1074 ASN cc_start: 0.8188 (p0) cc_final: 0.7746 (m110) REVERT: A 1125 TRP cc_start: 0.9170 (t-100) cc_final: 0.8762 (t-100) REVERT: A 1129 GLN cc_start: 0.9108 (mm-40) cc_final: 0.8471 (tp40) REVERT: A 1170 ASN cc_start: 0.7836 (t0) cc_final: 0.7402 (p0) REVERT: A 1277 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7334 (tp) outliers start: 24 outliers final: 20 residues processed: 189 average time/residue: 0.1714 time to fit residues: 47.4592 Evaluate side-chains 190 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 359 GLN Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 485 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 799 GLU Chi-restraints excluded: chain A residue 860 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 1073 LEU Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain A residue 1142 CYS 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 103 optimal weight: 10.0000 chunk 81 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 4 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.130500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.097538 restraints weight = 24878.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.100770 restraints weight = 14044.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.102893 restraints weight = 9537.458| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.8417 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= 0.155 Angle : 0.745 12.204 12172 Z= 0.364 Chirality : 0.043 0.201 1399 Planarity : 0.004 0.047 1549 Dihedral : 5.265 52.426 1231 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.87 % Allowed : 32.84 % Favored : 64.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.25), residues: 1132 helix: 1.19 (0.19), residues: 757 sheet: -2.33 (0.62), residues: 43 loop : -1.61 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 148 HIS 0.005 0.001 HIS A 73 PHE 0.024 0.002 PHE A 147 TYR 0.012 0.001 TYR A 322 ARG 0.003 0.000 ARG A 815 Details of bonding type rmsd hydrogen bonds : bond 0.04393 ( 588) hydrogen bonds : angle 4.60382 ( 1743) covalent geometry : bond 0.00348 ( 9009) covalent geometry : angle 0.74497 (12172) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3321.87 seconds wall clock time: 58 minutes 26.51 seconds (3506.51 seconds total)