Starting phenix.real_space_refine on Fri Aug 22 21:36:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xq6_38567/08_2025/8xq6_38567.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xq6_38567/08_2025/8xq6_38567.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xq6_38567/08_2025/8xq6_38567.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xq6_38567/08_2025/8xq6_38567.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xq6_38567/08_2025/8xq6_38567.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xq6_38567/08_2025/8xq6_38567.map" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 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: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 5269 2.51 5 N 1335 2.21 5 O 1416 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8063 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 8063 Classifications: {'peptide': 1020} Link IDs: {'PTRANS': 29, 'TRANS': 990} Chain breaks: 5 Time building chain proxies: 2.11, per 1000 atoms: 0.26 Number of scatterers: 8063 At special positions: 0 Unit cell: (82.08, 112.32, 123.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 1416 8.00 N 1335 7.00 C 5269 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 428.7 milliseconds Enol-peptide restraints added in 1.2 microseconds 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1924 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 4 sheets defined 76.4% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 75 through 95 removed outlier: 4.137A pdb=" N VAL A 79 " --> pdb=" O PRO A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 120 removed outlier: 4.018A pdb=" N VAL A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.613A pdb=" N HIS A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASP A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N VAL A 130 " --> pdb=" O HIS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 153 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 155 through 162 Processing helix chain 'A' and resid 162 through 188 Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 211 through 220 Processing helix chain 'A' and resid 223 through 253 Processing helix chain 'A' and resid 260 through 291 Proline residue: A 276 - end of helix Processing helix chain 'A' and resid 296 through 318 removed outlier: 4.076A pdb=" N GLU A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 337 removed outlier: 3.705A pdb=" N ALA A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 375 Processing helix chain 'A' and resid 381 through 412 removed outlier: 3.562A pdb=" N TRP A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) Proline residue: A 408 - end of helix Processing helix chain 'A' and resid 418 through 428 Processing helix chain 'A' and resid 432 through 447 removed outlier: 3.611A pdb=" N LEU A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 481 removed outlier: 4.414A pdb=" N SER A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 514 removed outlier: 3.974A pdb=" N SER A 514 " --> pdb=" O ASN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 520 removed outlier: 3.892A pdb=" N ALA A 519 " --> pdb=" O ARG A 516 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASP A 520 " --> pdb=" O PHE A 517 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 516 through 520' Processing helix chain 'A' and resid 522 through 530 removed outlier: 3.590A pdb=" N ALA A 526 " --> pdb=" O ASP A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 600 Processing helix chain 'A' and resid 604 through 621 removed outlier: 3.936A pdb=" N GLU A 621 " --> pdb=" O VAL A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 636 removed outlier: 4.270A pdb=" N LYS A 633 " --> pdb=" O ASP A 629 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N SER A 634 " --> pdb=" O ASP A 630 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TRP A 635 " --> pdb=" O LEU A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 652 removed outlier: 4.288A pdb=" N TRP A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 676 Processing helix chain 'A' and resid 679 through 705 Proline residue: A 694 - end of helix Processing helix chain 'A' and resid 727 through 754 Processing helix chain 'A' and resid 754 through 760 Processing helix chain 'A' and resid 761 through 784 Processing helix chain 'A' and resid 798 through 853 Proline residue: A 819 - end of helix Processing helix chain 'A' and resid 853 through 858 removed outlier: 4.023A pdb=" N MET A 857 " --> pdb=" O ILE A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 889 removed outlier: 3.524A pdb=" N HIS A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 919 Processing helix chain 'A' and resid 923 through 943 removed outlier: 3.589A pdb=" N ASN A 943 " --> pdb=" O LYS A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 958 Processing helix chain 'A' and resid 967 through 977 Processing helix chain 'A' and resid 1043 through 1050 Processing helix chain 'A' and resid 1070 through 1080 Processing helix chain 'A' and resid 1085 through 1107 Proline residue: A1101 - end of helix Processing helix chain 'A' and resid 1113 through 1123 removed outlier: 3.790A pdb=" N ARG A1123 " --> pdb=" O LEU A1119 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 979 through 982 removed outlier: 6.424A pdb=" N GLN A1064 " --> pdb=" O VAL A1002 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 987 through 989 removed outlier: 6.677A pdb=" N VAL A1057 " --> pdb=" O ILE A 988 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1125 through 1126 removed outlier: 6.426A pdb=" N ARG A1185 " --> pdb=" O ILE A1148 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1135 through 1137 removed outlier: 3.861A pdb=" N ASN A1154 " --> pdb=" O GLU A1159 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU A1159 " --> pdb=" O ASN A1154 " (cutoff:3.500A) 609 hydrogen bonds defined for protein. 1815 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.37 Time building geometry restraints manager: 0.87 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: 2390 1.34 - 1.46: 1226 1.46 - 1.57: 4523 1.57 - 1.69: 0 1.69 - 1.81: 79 Bond restraints: 8218 Sorted by residual: bond pdb=" C SER A 407 " pdb=" N PRO A 408 " ideal model delta sigma weight residual 1.335 1.383 -0.048 1.36e-02 5.41e+03 1.22e+01 bond pdb=" C ILE A 488 " pdb=" N PRO A 489 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.23e-02 6.61e+03 3.31e+00 bond pdb=" CA ILE A 742 " pdb=" CB ILE A 742 " ideal model delta sigma weight residual 1.540 1.563 -0.023 1.36e-02 5.41e+03 2.94e+00 bond pdb=" C ILE A 818 " pdb=" N PRO A 819 " ideal model delta sigma weight residual 1.336 1.356 -0.020 1.23e-02 6.61e+03 2.72e+00 bond pdb=" C LEU A 143 " pdb=" N PRO A 144 " ideal model delta sigma weight residual 1.335 1.357 -0.022 1.36e-02 5.41e+03 2.51e+00 ... (remaining 8213 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 10946 2.36 - 4.72: 160 4.72 - 7.08: 26 7.08 - 9.44: 11 9.44 - 11.81: 1 Bond angle restraints: 11144 Sorted by residual: angle pdb=" C GLY A 414 " pdb=" N TYR A 415 " pdb=" CA TYR A 415 " ideal model delta sigma weight residual 121.54 130.76 -9.22 1.91e+00 2.74e-01 2.33e+01 angle pdb=" C HIS A1156 " pdb=" N THR A1157 " pdb=" CA THR A1157 " ideal model delta sigma weight residual 122.46 128.56 -6.10 1.41e+00 5.03e-01 1.87e+01 angle pdb=" C HIS A 677 " pdb=" N MET A 678 " pdb=" CA MET A 678 " ideal model delta sigma weight residual 122.08 128.20 -6.12 1.47e+00 4.63e-01 1.73e+01 angle pdb=" C VAL A 741 " pdb=" N ILE A 742 " pdb=" CA ILE A 742 " ideal model delta sigma weight residual 121.97 128.97 -7.00 1.80e+00 3.09e-01 1.51e+01 angle pdb=" C LYS A 765 " pdb=" N PHE A 766 " pdb=" CA PHE A 766 " ideal model delta sigma weight residual 121.58 114.02 7.56 1.95e+00 2.63e-01 1.50e+01 ... (remaining 11139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.36: 4355 15.36 - 30.73: 438 30.73 - 46.09: 87 46.09 - 61.45: 27 61.45 - 76.81: 2 Dihedral angle restraints: 4909 sinusoidal: 1942 harmonic: 2967 Sorted by residual: dihedral pdb=" CA LEU A 963 " pdb=" C LEU A 963 " pdb=" N ALA A 964 " pdb=" CA ALA A 964 " ideal model delta harmonic sigma weight residual -180.00 -158.74 -21.26 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA PHE A 254 " pdb=" C PHE A 254 " pdb=" N PRO A 255 " pdb=" CA PRO A 255 " ideal model delta harmonic sigma weight residual 180.00 159.55 20.45 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA TYR A1083 " pdb=" C TYR A1083 " pdb=" N PRO A1084 " pdb=" CA PRO A1084 " ideal model delta harmonic sigma weight residual 180.00 160.39 19.61 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 4906 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1205 0.073 - 0.147: 121 0.147 - 0.220: 13 0.220 - 0.293: 1 0.293 - 0.366: 1 Chirality restraints: 1341 Sorted by residual: chirality pdb=" CB ILE A 742 " pdb=" CA ILE A 742 " pdb=" CG1 ILE A 742 " pdb=" CG2 ILE A 742 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" CA PHE A 766 " pdb=" N PHE A 766 " pdb=" C PHE A 766 " pdb=" CB PHE A 766 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CG LEU A 608 " pdb=" CB LEU A 608 " pdb=" CD1 LEU A 608 " pdb=" CD2 LEU A 608 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.66e-01 ... (remaining 1338 not shown) Planarity restraints: 1371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 415 " -0.013 2.00e-02 2.50e+03 2.56e-02 6.55e+00 pdb=" C TYR A 415 " 0.044 2.00e-02 2.50e+03 pdb=" O TYR A 415 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY A 416 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 467 " 0.012 2.00e-02 2.50e+03 2.42e-02 5.84e+00 pdb=" C LEU A 467 " -0.042 2.00e-02 2.50e+03 pdb=" O LEU A 467 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL A 468 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 168 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.17e+00 pdb=" C ILE A 168 " 0.035 2.00e-02 2.50e+03 pdb=" O ILE A 168 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU A 169 " -0.012 2.00e-02 2.50e+03 ... (remaining 1368 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2323 2.82 - 3.34: 7685 3.34 - 3.86: 13268 3.86 - 4.38: 14447 4.38 - 4.90: 26288 Nonbonded interactions: 64011 Sorted by model distance: nonbonded pdb=" O ILE A 469 " pdb=" OG1 THR A 473 " model vdw 2.301 3.040 nonbonded pdb=" OG1 THR A1179 " pdb=" OE1 GLU A1182 " model vdw 2.309 3.040 nonbonded pdb=" O SER A 404 " pdb=" OG SER A 407 " model vdw 2.310 3.040 nonbonded pdb=" O ILE A 230 " pdb=" OG SER A 234 " model vdw 2.312 3.040 nonbonded pdb=" N ASP A 983 " pdb=" OD1 ASP A 983 " model vdw 2.345 3.120 ... (remaining 64006 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.380 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 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 : 0.005 0.065 8218 Z= 0.228 Angle : 0.786 11.805 11144 Z= 0.437 Chirality : 0.049 0.366 1341 Planarity : 0.006 0.047 1371 Dihedral : 13.251 76.814 2985 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.56 % Allowed : 9.91 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.23), residues: 1008 helix: -0.66 (0.16), residues: 750 sheet: -0.04 (0.97), residues: 30 loop : -1.84 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 585 TYR 0.012 0.002 TYR A 984 PHE 0.031 0.002 PHE A 766 TRP 0.022 0.002 TRP A 635 HIS 0.003 0.001 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 8218) covalent geometry : angle 0.78633 (11144) hydrogen bonds : bond 0.10971 ( 609) hydrogen bonds : angle 5.93568 ( 1815) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 308 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 96 LYS cc_start: 0.7921 (mttp) cc_final: 0.7674 (ttpt) REVERT: A 112 ILE cc_start: 0.8228 (mm) cc_final: 0.7987 (mm) REVERT: A 180 LEU cc_start: 0.7993 (mt) cc_final: 0.7711 (mt) REVERT: A 200 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.8156 (ttp) REVERT: A 225 GLN cc_start: 0.8269 (mm-40) cc_final: 0.7951 (mm-40) REVERT: A 233 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7382 (tm-30) REVERT: A 236 LEU cc_start: 0.8274 (mt) cc_final: 0.8054 (mp) REVERT: A 251 MET cc_start: 0.7367 (ttm) cc_final: 0.7139 (ttm) REVERT: A 263 GLN cc_start: 0.8183 (mt0) cc_final: 0.7881 (mt0) REVERT: A 264 ASN cc_start: 0.7992 (m-40) cc_final: 0.7454 (m110) REVERT: A 267 TYR cc_start: 0.8335 (t80) cc_final: 0.7935 (t80) REVERT: A 320 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7612 (mm-30) REVERT: A 335 ASN cc_start: 0.8204 (t0) cc_final: 0.7959 (t0) REVERT: A 338 LYS cc_start: 0.8314 (mtmm) cc_final: 0.8012 (mtmm) REVERT: A 344 GLU cc_start: 0.7726 (pt0) cc_final: 0.7447 (tm-30) REVERT: A 355 MET cc_start: 0.8371 (ttp) cc_final: 0.7979 (ttp) REVERT: A 366 MET cc_start: 0.8477 (mmm) cc_final: 0.8222 (mmm) REVERT: A 383 MET cc_start: 0.7755 (mmt) cc_final: 0.6943 (mmt) REVERT: A 386 PHE cc_start: 0.8035 (t80) cc_final: 0.7676 (t80) REVERT: A 387 TYR cc_start: 0.8184 (m-10) cc_final: 0.7361 (m-10) REVERT: A 406 PHE cc_start: 0.7881 (m-80) cc_final: 0.7637 (m-80) REVERT: A 419 TRP cc_start: 0.8174 (p-90) cc_final: 0.7578 (p-90) REVERT: A 423 VAL cc_start: 0.8514 (t) cc_final: 0.8277 (t) REVERT: A 443 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7127 (tp30) REVERT: A 445 LEU cc_start: 0.8781 (mt) cc_final: 0.8440 (mt) REVERT: A 449 ASP cc_start: 0.8332 (t0) cc_final: 0.7963 (t0) REVERT: A 485 ASP cc_start: 0.7852 (p0) cc_final: 0.7525 (m-30) REVERT: A 500 ARG cc_start: 0.7172 (ptt180) cc_final: 0.4778 (ttp-110) REVERT: A 503 GLU cc_start: 0.8109 (tt0) cc_final: 0.7880 (tt0) REVERT: A 505 GLN cc_start: 0.8422 (mt0) cc_final: 0.8078 (mt0) REVERT: A 585 ARG cc_start: 0.7670 (mtm-85) cc_final: 0.7189 (mtm180) REVERT: A 587 LEU cc_start: 0.8777 (mt) cc_final: 0.8406 (mt) REVERT: A 588 LYS cc_start: 0.8492 (mmtt) cc_final: 0.8161 (mmtt) REVERT: A 591 LYS cc_start: 0.8329 (mttt) cc_final: 0.8018 (mtpp) REVERT: A 592 ILE cc_start: 0.8473 (mt) cc_final: 0.8154 (mm) REVERT: A 621 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7195 (tm-30) REVERT: A 628 VAL cc_start: 0.8507 (t) cc_final: 0.8161 (m) REVERT: A 632 LYS cc_start: 0.8585 (mttt) cc_final: 0.8313 (mttt) REVERT: A 641 TYR cc_start: 0.7893 (m-80) cc_final: 0.7362 (m-80) REVERT: A 670 LEU cc_start: 0.3115 (OUTLIER) cc_final: 0.1125 (mp) REVERT: A 681 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8129 (mt-10) REVERT: A 697 MET cc_start: 0.7056 (tpt) cc_final: 0.6757 (tpt) REVERT: A 743 TYR cc_start: 0.7601 (t80) cc_final: 0.7178 (t80) REVERT: A 769 PHE cc_start: 0.7924 (t80) cc_final: 0.7486 (t80) REVERT: A 777 ASP cc_start: 0.7721 (m-30) cc_final: 0.7146 (m-30) REVERT: A 808 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7745 (tp) REVERT: A 810 MET cc_start: 0.6063 (ptt) cc_final: 0.5577 (ptt) REVERT: A 821 LEU cc_start: 0.8487 (mt) cc_final: 0.8022 (mt) REVERT: A 824 VAL cc_start: 0.8801 (t) cc_final: 0.8565 (p) REVERT: A 828 LYS cc_start: 0.8330 (mttt) cc_final: 0.7874 (mttt) REVERT: A 837 TYR cc_start: 0.8370 (OUTLIER) cc_final: 0.7836 (m-80) REVERT: A 848 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7831 (mm-30) REVERT: A 857 MET cc_start: 0.7218 (mtt) cc_final: 0.6608 (mtt) REVERT: A 865 ARG cc_start: 0.8059 (ttm170) cc_final: 0.7783 (ttp-170) REVERT: A 872 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8043 (tp30) REVERT: A 938 MET cc_start: 0.8388 (mmm) cc_final: 0.8166 (mmm) REVERT: A 967 MET cc_start: 0.8030 (mtp) cc_final: 0.7332 (mtp) REVERT: A 968 LYS cc_start: 0.7915 (mmmm) cc_final: 0.7497 (mmmm) REVERT: A 971 ASP cc_start: 0.8136 (m-30) cc_final: 0.7739 (m-30) REVERT: A 981 HIS cc_start: 0.8723 (m-70) cc_final: 0.8521 (m90) REVERT: A 983 ASP cc_start: 0.8032 (p0) cc_final: 0.7531 (p0) REVERT: A 1009 TYR cc_start: 0.7952 (t80) cc_final: 0.7687 (t80) REVERT: A 1033 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7606 (mt-10) REVERT: A 1045 MET cc_start: 0.8611 (mmm) cc_final: 0.8259 (mmm) REVERT: A 1048 LEU cc_start: 0.8578 (mt) cc_final: 0.8368 (mt) REVERT: A 1053 ARG cc_start: 0.7542 (tpp80) cc_final: 0.7173 (mtt-85) REVERT: A 1063 VAL cc_start: 0.8014 (t) cc_final: 0.7798 (p) REVERT: A 1067 PHE cc_start: 0.8283 (t80) cc_final: 0.8017 (t80) REVERT: A 1104 MET cc_start: 0.8110 (mmm) cc_final: 0.7909 (mmm) REVERT: A 1110 GLN cc_start: 0.7950 (mm-40) cc_final: 0.7668 (mm-40) REVERT: A 1116 LYS cc_start: 0.8666 (tttp) cc_final: 0.8437 (tttm) REVERT: A 1134 PHE cc_start: 0.8239 (m-80) cc_final: 0.7528 (m-80) REVERT: A 1136 PHE cc_start: 0.8499 (t80) cc_final: 0.8185 (t80) REVERT: A 1139 ASP cc_start: 0.7147 (OUTLIER) cc_final: 0.6676 (m-30) REVERT: A 1144 ASP cc_start: 0.8097 (p0) cc_final: 0.7773 (p0) REVERT: A 1178 TYR cc_start: 0.6524 (t80) cc_final: 0.6072 (t80) outliers start: 40 outliers final: 11 residues processed: 331 average time/residue: 0.0994 time to fit residues: 43.7716 Evaluate side-chains 292 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 274 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 681 GLU Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1139 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A1064 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.128985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.110753 restraints weight = 12810.333| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.98 r_work: 0.3245 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8218 Z= 0.208 Angle : 0.612 8.336 11144 Z= 0.325 Chirality : 0.042 0.205 1341 Planarity : 0.004 0.042 1371 Dihedral : 6.681 53.529 1126 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.21 % Allowed : 18.91 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.26), residues: 1008 helix: 0.74 (0.19), residues: 744 sheet: 0.33 (0.96), residues: 31 loop : -1.67 (0.38), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 903 TYR 0.009 0.001 TYR A 672 PHE 0.027 0.002 PHE A 766 TRP 0.019 0.002 TRP A1112 HIS 0.004 0.001 HIS A 458 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 8218) covalent geometry : angle 0.61249 (11144) hydrogen bonds : bond 0.05407 ( 609) hydrogen bonds : angle 4.63925 ( 1815) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 263 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: A 112 ILE cc_start: 0.8388 (mm) cc_final: 0.8167 (mm) REVERT: A 176 VAL cc_start: 0.8689 (p) cc_final: 0.8474 (p) REVERT: A 180 LEU cc_start: 0.8083 (mt) cc_final: 0.7798 (mt) REVERT: A 183 VAL cc_start: 0.8037 (t) cc_final: 0.7680 (m) REVERT: A 199 MET cc_start: 0.8300 (mmm) cc_final: 0.8052 (tpp) REVERT: A 217 LEU cc_start: 0.8094 (mt) cc_final: 0.7881 (mt) REVERT: A 233 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7496 (tp30) REVERT: A 236 LEU cc_start: 0.8266 (mt) cc_final: 0.8010 (mp) REVERT: A 250 LYS cc_start: 0.7950 (mmmt) cc_final: 0.7565 (mmmt) REVERT: A 263 GLN cc_start: 0.8262 (mt0) cc_final: 0.7919 (mt0) REVERT: A 264 ASN cc_start: 0.8017 (m-40) cc_final: 0.7437 (m110) REVERT: A 267 TYR cc_start: 0.8344 (t80) cc_final: 0.7940 (t80) REVERT: A 284 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8236 (mmmm) REVERT: A 335 ASN cc_start: 0.8049 (t0) cc_final: 0.7686 (t0) REVERT: A 337 GLU cc_start: 0.7810 (tp30) cc_final: 0.7099 (tp30) REVERT: A 383 MET cc_start: 0.7779 (mmt) cc_final: 0.7028 (mmt) REVERT: A 387 TYR cc_start: 0.8194 (m-10) cc_final: 0.7369 (m-10) REVERT: A 406 PHE cc_start: 0.8042 (m-80) cc_final: 0.7795 (m-80) REVERT: A 411 SER cc_start: 0.8177 (t) cc_final: 0.7699 (p) REVERT: A 419 TRP cc_start: 0.8135 (p-90) cc_final: 0.7711 (p-90) REVERT: A 443 GLU cc_start: 0.7825 (tt0) cc_final: 0.7305 (tp30) REVERT: A 445 LEU cc_start: 0.8900 (mt) cc_final: 0.8656 (mt) REVERT: A 449 ASP cc_start: 0.8333 (t0) cc_final: 0.8078 (t0) REVERT: A 500 ARG cc_start: 0.7111 (ptt180) cc_final: 0.5472 (mmm-85) REVERT: A 503 GLU cc_start: 0.8004 (tt0) cc_final: 0.7803 (tt0) REVERT: A 579 MET cc_start: 0.8160 (mtt) cc_final: 0.7917 (ttt) REVERT: A 585 ARG cc_start: 0.7604 (mtm-85) cc_final: 0.7246 (mtm180) REVERT: A 587 LEU cc_start: 0.8807 (mt) cc_final: 0.8511 (mt) REVERT: A 588 LYS cc_start: 0.8528 (mmtt) cc_final: 0.8264 (mmtt) REVERT: A 591 LYS cc_start: 0.8418 (mttt) cc_final: 0.8172 (mtpp) REVERT: A 632 LYS cc_start: 0.8524 (mttt) cc_final: 0.8304 (mttt) REVERT: A 641 TYR cc_start: 0.7975 (m-80) cc_final: 0.7628 (m-80) REVERT: A 647 LYS cc_start: 0.8269 (mptt) cc_final: 0.7872 (mptt) REVERT: A 670 LEU cc_start: 0.3165 (OUTLIER) cc_final: 0.1554 (mp) REVERT: A 697 MET cc_start: 0.7009 (tpt) cc_final: 0.5943 (tpt) REVERT: A 729 GLU cc_start: 0.7741 (tp30) cc_final: 0.6743 (tp30) REVERT: A 733 ARG cc_start: 0.8101 (mmt180) cc_final: 0.7598 (mmt180) REVERT: A 743 TYR cc_start: 0.7522 (t80) cc_final: 0.7174 (t80) REVERT: A 758 TYR cc_start: 0.6011 (m-80) cc_final: 0.5578 (m-80) REVERT: A 808 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7782 (tp) REVERT: A 810 MET cc_start: 0.5967 (ptt) cc_final: 0.5515 (ptt) REVERT: A 821 LEU cc_start: 0.8402 (mt) cc_final: 0.8032 (mt) REVERT: A 824 VAL cc_start: 0.8704 (t) cc_final: 0.8497 (p) REVERT: A 828 LYS cc_start: 0.8309 (mttt) cc_final: 0.7938 (mttt) REVERT: A 837 TYR cc_start: 0.8399 (OUTLIER) cc_final: 0.8008 (m-80) REVERT: A 848 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7841 (mm-30) REVERT: A 857 MET cc_start: 0.7140 (mtt) cc_final: 0.6639 (mtt) REVERT: A 872 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7880 (tp30) REVERT: A 938 MET cc_start: 0.8372 (mmm) cc_final: 0.8170 (mmm) REVERT: A 967 MET cc_start: 0.7885 (mtp) cc_final: 0.7297 (mtp) REVERT: A 968 LYS cc_start: 0.7889 (mmmm) cc_final: 0.7528 (mmmm) REVERT: A 971 ASP cc_start: 0.8187 (m-30) cc_final: 0.7829 (m-30) REVERT: A 983 ASP cc_start: 0.7993 (p0) cc_final: 0.7382 (p0) REVERT: A 986 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7911 (mt-10) REVERT: A 1045 MET cc_start: 0.8641 (mmm) cc_final: 0.8256 (mmt) REVERT: A 1063 VAL cc_start: 0.8149 (t) cc_final: 0.7926 (p) REVERT: A 1089 ARG cc_start: 0.8079 (mtm180) cc_final: 0.7420 (mtm180) REVERT: A 1104 MET cc_start: 0.8111 (mmm) cc_final: 0.7468 (tpp) REVERT: A 1110 GLN cc_start: 0.7956 (mm-40) cc_final: 0.7677 (mm-40) REVERT: A 1116 LYS cc_start: 0.8678 (tttp) cc_final: 0.8384 (tptp) REVERT: A 1134 PHE cc_start: 0.8264 (m-80) cc_final: 0.7680 (m-80) REVERT: A 1135 GLN cc_start: 0.7963 (pt0) cc_final: 0.7630 (pt0) REVERT: A 1136 PHE cc_start: 0.8437 (t80) cc_final: 0.8198 (t80) REVERT: A 1139 ASP cc_start: 0.7303 (OUTLIER) cc_final: 0.6444 (m-30) REVERT: A 1178 TYR cc_start: 0.6489 (t80) cc_final: 0.6105 (t80) outliers start: 37 outliers final: 18 residues processed: 283 average time/residue: 0.0908 time to fit residues: 34.2724 Evaluate side-chains 271 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 248 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 GLN Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1139 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 99 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 26 optimal weight: 0.0060 chunk 69 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS ** A 597 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 = 0.3661 r_free = 0.3661 target = 0.130710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.112095 restraints weight = 12659.341| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.02 r_work: 0.3263 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8218 Z= 0.147 Angle : 0.560 7.799 11144 Z= 0.294 Chirality : 0.040 0.242 1341 Planarity : 0.004 0.037 1371 Dihedral : 5.534 53.407 1105 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.87 % Allowed : 19.93 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.27), residues: 1008 helix: 1.23 (0.19), residues: 746 sheet: 0.21 (0.91), residues: 31 loop : -1.55 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 491 TYR 0.007 0.001 TYR A 672 PHE 0.027 0.001 PHE A 766 TRP 0.029 0.001 TRP A1112 HIS 0.002 0.001 HIS A 458 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8218) covalent geometry : angle 0.56003 (11144) hydrogen bonds : bond 0.04856 ( 609) hydrogen bonds : angle 4.44204 ( 1815) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 251 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 152 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.8705 (t80) REVERT: A 155 ASP cc_start: 0.8287 (t0) cc_final: 0.8064 (t0) REVERT: A 199 MET cc_start: 0.8257 (mmm) cc_final: 0.7956 (tpp) REVERT: A 217 LEU cc_start: 0.7980 (mt) cc_final: 0.7757 (mt) REVERT: A 233 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7287 (tm-30) REVERT: A 236 LEU cc_start: 0.8218 (mt) cc_final: 0.7959 (mp) REVERT: A 250 LYS cc_start: 0.7863 (mmmt) cc_final: 0.7504 (mmmt) REVERT: A 263 GLN cc_start: 0.8197 (mt0) cc_final: 0.7846 (mt0) REVERT: A 264 ASN cc_start: 0.8006 (m-40) cc_final: 0.7398 (m-40) REVERT: A 267 TYR cc_start: 0.8327 (t80) cc_final: 0.7935 (t80) REVERT: A 335 ASN cc_start: 0.7919 (t0) cc_final: 0.7578 (t0) REVERT: A 337 GLU cc_start: 0.7791 (tp30) cc_final: 0.7069 (tp30) REVERT: A 346 GLU cc_start: 0.7765 (tp30) cc_final: 0.7512 (tp30) REVERT: A 383 MET cc_start: 0.7577 (mmt) cc_final: 0.6826 (mmt) REVERT: A 387 TYR cc_start: 0.8132 (m-10) cc_final: 0.7307 (m-10) REVERT: A 391 LEU cc_start: 0.8355 (tp) cc_final: 0.8117 (tt) REVERT: A 406 PHE cc_start: 0.8057 (m-80) cc_final: 0.7639 (m-80) REVERT: A 411 SER cc_start: 0.8201 (t) cc_final: 0.7706 (p) REVERT: A 412 ARG cc_start: 0.7611 (mtp180) cc_final: 0.7365 (mtp180) REVERT: A 419 TRP cc_start: 0.8038 (p-90) cc_final: 0.7679 (p-90) REVERT: A 443 GLU cc_start: 0.7723 (tt0) cc_final: 0.7158 (tp30) REVERT: A 444 ASN cc_start: 0.8286 (t0) cc_final: 0.7827 (t0) REVERT: A 445 LEU cc_start: 0.8847 (mt) cc_final: 0.8608 (mt) REVERT: A 449 ASP cc_start: 0.8190 (t0) cc_final: 0.7973 (t0) REVERT: A 500 ARG cc_start: 0.6926 (ptt180) cc_final: 0.5400 (mmm-85) REVERT: A 579 MET cc_start: 0.8099 (mtt) cc_final: 0.7867 (ttt) REVERT: A 587 LEU cc_start: 0.8751 (mt) cc_final: 0.8502 (mt) REVERT: A 591 LYS cc_start: 0.8539 (mttt) cc_final: 0.8215 (mtpp) REVERT: A 598 PHE cc_start: 0.9015 (t80) cc_final: 0.8800 (t80) REVERT: A 632 LYS cc_start: 0.8453 (mttt) cc_final: 0.8209 (mttt) REVERT: A 641 TYR cc_start: 0.7983 (m-80) cc_final: 0.7667 (m-80) REVERT: A 670 LEU cc_start: 0.2843 (OUTLIER) cc_final: 0.0802 (mp) REVERT: A 697 MET cc_start: 0.7089 (tpt) cc_final: 0.6748 (tpt) REVERT: A 705 MET cc_start: 0.6831 (mmt) cc_final: 0.6258 (mmt) REVERT: A 743 TYR cc_start: 0.7510 (t80) cc_final: 0.7154 (t80) REVERT: A 758 TYR cc_start: 0.5952 (m-80) cc_final: 0.5588 (m-80) REVERT: A 808 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7538 (tp) REVERT: A 810 MET cc_start: 0.5775 (ptt) cc_final: 0.5512 (ptt) REVERT: A 821 LEU cc_start: 0.8357 (mt) cc_final: 0.7967 (mt) REVERT: A 824 VAL cc_start: 0.8670 (t) cc_final: 0.8459 (p) REVERT: A 828 LYS cc_start: 0.8321 (mttt) cc_final: 0.7968 (mttt) REVERT: A 837 TYR cc_start: 0.8388 (OUTLIER) cc_final: 0.7981 (m-80) REVERT: A 848 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7671 (mt-10) REVERT: A 872 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7920 (tp30) REVERT: A 967 MET cc_start: 0.7929 (mtp) cc_final: 0.7274 (mtp) REVERT: A 968 LYS cc_start: 0.7806 (mmmm) cc_final: 0.7457 (mmmm) REVERT: A 971 ASP cc_start: 0.8191 (m-30) cc_final: 0.7791 (m-30) REVERT: A 1033 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7672 (mt-10) REVERT: A 1045 MET cc_start: 0.8607 (mmm) cc_final: 0.8255 (mmt) REVERT: A 1063 VAL cc_start: 0.8169 (t) cc_final: 0.7916 (p) REVERT: A 1104 MET cc_start: 0.8024 (mmm) cc_final: 0.7548 (tpp) REVERT: A 1105 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7680 (mm-30) REVERT: A 1110 GLN cc_start: 0.7947 (mm-40) cc_final: 0.7725 (mm-40) REVERT: A 1116 LYS cc_start: 0.8710 (tttp) cc_final: 0.8360 (tttm) REVERT: A 1134 PHE cc_start: 0.8244 (m-80) cc_final: 0.7617 (m-80) REVERT: A 1135 GLN cc_start: 0.7952 (pt0) cc_final: 0.7590 (pt0) REVERT: A 1136 PHE cc_start: 0.8421 (t80) cc_final: 0.8191 (t80) REVERT: A 1178 TYR cc_start: 0.6523 (t80) cc_final: 0.6108 (t80) outliers start: 34 outliers final: 17 residues processed: 272 average time/residue: 0.0952 time to fit residues: 34.7212 Evaluate side-chains 261 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 240 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 GLN Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1139 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 73 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 86 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 597 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 = 0.3654 r_free = 0.3654 target = 0.130307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.111547 restraints weight = 12948.753| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.10 r_work: 0.3255 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8218 Z= 0.161 Angle : 0.553 7.367 11144 Z= 0.293 Chirality : 0.041 0.178 1341 Planarity : 0.004 0.036 1371 Dihedral : 5.418 54.111 1103 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.99 % Allowed : 20.05 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.27), residues: 1008 helix: 1.45 (0.19), residues: 745 sheet: 0.37 (0.89), residues: 31 loop : -1.56 (0.38), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 491 TYR 0.009 0.001 TYR A 358 PHE 0.026 0.002 PHE A 766 TRP 0.024 0.002 TRP A1112 HIS 0.003 0.001 HIS A 458 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 8218) covalent geometry : angle 0.55258 (11144) hydrogen bonds : bond 0.04845 ( 609) hydrogen bonds : angle 4.35265 ( 1815) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 248 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 152 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.8709 (t80) REVERT: A 199 MET cc_start: 0.8176 (mmm) cc_final: 0.7343 (mpp) REVERT: A 217 LEU cc_start: 0.7965 (mt) cc_final: 0.7757 (mt) REVERT: A 233 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7237 (tm-30) REVERT: A 236 LEU cc_start: 0.8135 (mt) cc_final: 0.7901 (mp) REVERT: A 250 LYS cc_start: 0.7875 (mmmt) cc_final: 0.7519 (mmmt) REVERT: A 263 GLN cc_start: 0.8200 (mt0) cc_final: 0.7815 (mt0) REVERT: A 264 ASN cc_start: 0.8011 (m-40) cc_final: 0.7347 (m-40) REVERT: A 267 TYR cc_start: 0.8314 (t80) cc_final: 0.7892 (t80) REVERT: A 335 ASN cc_start: 0.7912 (t0) cc_final: 0.7583 (t0) REVERT: A 383 MET cc_start: 0.7570 (mmt) cc_final: 0.6826 (mmt) REVERT: A 387 TYR cc_start: 0.8123 (m-10) cc_final: 0.7326 (m-10) REVERT: A 391 LEU cc_start: 0.8332 (tp) cc_final: 0.8083 (tt) REVERT: A 411 SER cc_start: 0.8203 (t) cc_final: 0.7740 (p) REVERT: A 412 ARG cc_start: 0.7625 (mtp180) cc_final: 0.7390 (mtp180) REVERT: A 443 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7133 (tp30) REVERT: A 444 ASN cc_start: 0.8279 (t0) cc_final: 0.7837 (t0) REVERT: A 445 LEU cc_start: 0.8849 (mt) cc_final: 0.8644 (mt) REVERT: A 449 ASP cc_start: 0.8200 (t0) cc_final: 0.7990 (t0) REVERT: A 500 ARG cc_start: 0.6906 (ptt180) cc_final: 0.5423 (mmm-85) REVERT: A 579 MET cc_start: 0.8100 (mtt) cc_final: 0.7877 (ttt) REVERT: A 587 LEU cc_start: 0.8760 (mt) cc_final: 0.8501 (mt) REVERT: A 591 LYS cc_start: 0.8574 (mttt) cc_final: 0.8243 (mtpp) REVERT: A 598 PHE cc_start: 0.9018 (t80) cc_final: 0.8775 (t80) REVERT: A 632 LYS cc_start: 0.8518 (mttt) cc_final: 0.8228 (mttt) REVERT: A 641 TYR cc_start: 0.7989 (m-80) cc_final: 0.7271 (m-80) REVERT: A 670 LEU cc_start: 0.3325 (OUTLIER) cc_final: 0.1498 (mp) REVERT: A 697 MET cc_start: 0.7135 (tpt) cc_final: 0.6805 (tpt) REVERT: A 729 GLU cc_start: 0.7838 (tp30) cc_final: 0.7525 (tp30) REVERT: A 743 TYR cc_start: 0.7566 (t80) cc_final: 0.7234 (t80) REVERT: A 769 PHE cc_start: 0.7982 (t80) cc_final: 0.7579 (t80) REVERT: A 808 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7458 (tp) REVERT: A 810 MET cc_start: 0.5845 (ptt) cc_final: 0.5346 (ptt) REVERT: A 821 LEU cc_start: 0.8394 (mt) cc_final: 0.8009 (mt) REVERT: A 824 VAL cc_start: 0.8640 (t) cc_final: 0.8400 (p) REVERT: A 828 LYS cc_start: 0.8356 (mttt) cc_final: 0.7595 (mttt) REVERT: A 837 TYR cc_start: 0.8400 (OUTLIER) cc_final: 0.7944 (m-80) REVERT: A 848 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7712 (mt-10) REVERT: A 872 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7918 (tp30) REVERT: A 916 LEU cc_start: 0.8354 (mt) cc_final: 0.8097 (mp) REVERT: A 967 MET cc_start: 0.7989 (mtp) cc_final: 0.7388 (mtp) REVERT: A 968 LYS cc_start: 0.7782 (mmmm) cc_final: 0.7440 (mmmm) REVERT: A 971 ASP cc_start: 0.8178 (m-30) cc_final: 0.7832 (m-30) REVERT: A 986 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7842 (mt-10) REVERT: A 1033 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7722 (mt-10) REVERT: A 1034 ASP cc_start: 0.8294 (t0) cc_final: 0.7999 (t0) REVERT: A 1045 MET cc_start: 0.8592 (mmm) cc_final: 0.8263 (mmt) REVERT: A 1063 VAL cc_start: 0.8203 (t) cc_final: 0.7955 (p) REVERT: A 1104 MET cc_start: 0.7962 (mmm) cc_final: 0.7522 (tpp) REVERT: A 1110 GLN cc_start: 0.7938 (mm-40) cc_final: 0.7690 (mm-40) REVERT: A 1116 LYS cc_start: 0.8661 (tttp) cc_final: 0.8342 (tttm) REVERT: A 1134 PHE cc_start: 0.8213 (m-80) cc_final: 0.7597 (m-80) REVERT: A 1135 GLN cc_start: 0.7918 (pt0) cc_final: 0.7554 (pt0) REVERT: A 1136 PHE cc_start: 0.8413 (t80) cc_final: 0.8184 (t80) REVERT: A 1178 TYR cc_start: 0.6548 (t80) cc_final: 0.6162 (t80) outliers start: 35 outliers final: 21 residues processed: 266 average time/residue: 0.0935 time to fit residues: 33.7118 Evaluate side-chains 263 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 238 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 GLN Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1139 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 99 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 18 optimal weight: 0.0170 chunk 88 optimal weight: 0.3980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 597 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 = 0.3667 r_free = 0.3667 target = 0.131339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.112751 restraints weight = 12780.185| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.08 r_work: 0.3272 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8218 Z= 0.139 Angle : 0.538 7.241 11144 Z= 0.285 Chirality : 0.040 0.176 1341 Planarity : 0.003 0.035 1371 Dihedral : 5.339 54.206 1103 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.99 % Allowed : 20.96 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.27), residues: 1008 helix: 1.56 (0.19), residues: 746 sheet: 0.47 (0.87), residues: 31 loop : -1.59 (0.39), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 976 TYR 0.008 0.001 TYR A 358 PHE 0.027 0.001 PHE A 766 TRP 0.029 0.001 TRP A1112 HIS 0.002 0.000 HIS A 458 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 8218) covalent geometry : angle 0.53840 (11144) hydrogen bonds : bond 0.04607 ( 609) hydrogen bonds : angle 4.27555 ( 1815) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 245 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 ASP cc_start: 0.8327 (t0) cc_final: 0.8117 (t0) REVERT: A 199 MET cc_start: 0.8154 (mmm) cc_final: 0.7463 (mpp) REVERT: A 217 LEU cc_start: 0.7925 (mt) cc_final: 0.7706 (mt) REVERT: A 233 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7177 (tm-30) REVERT: A 236 LEU cc_start: 0.8147 (mt) cc_final: 0.7916 (mp) REVERT: A 250 LYS cc_start: 0.7835 (mmmt) cc_final: 0.7490 (mmmt) REVERT: A 263 GLN cc_start: 0.8194 (mt0) cc_final: 0.7815 (mt0) REVERT: A 264 ASN cc_start: 0.8009 (m-40) cc_final: 0.7350 (m-40) REVERT: A 267 TYR cc_start: 0.8317 (t80) cc_final: 0.7880 (t80) REVERT: A 289 PHE cc_start: 0.8171 (t80) cc_final: 0.7937 (t80) REVERT: A 335 ASN cc_start: 0.7861 (t0) cc_final: 0.7561 (t0) REVERT: A 383 MET cc_start: 0.7549 (mmt) cc_final: 0.6818 (mmt) REVERT: A 387 TYR cc_start: 0.8096 (m-10) cc_final: 0.7317 (m-10) REVERT: A 411 SER cc_start: 0.8185 (t) cc_final: 0.7726 (p) REVERT: A 419 TRP cc_start: 0.8027 (p-90) cc_final: 0.7808 (p-90) REVERT: A 444 ASN cc_start: 0.8277 (t0) cc_final: 0.7859 (t0) REVERT: A 500 ARG cc_start: 0.6844 (ptt180) cc_final: 0.5353 (mmm-85) REVERT: A 579 MET cc_start: 0.8069 (mtt) cc_final: 0.7833 (ttt) REVERT: A 587 LEU cc_start: 0.8739 (mt) cc_final: 0.8496 (mt) REVERT: A 591 LYS cc_start: 0.8568 (mttt) cc_final: 0.8229 (mtpp) REVERT: A 598 PHE cc_start: 0.8975 (t80) cc_final: 0.8721 (t80) REVERT: A 599 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7866 (tp30) REVERT: A 632 LYS cc_start: 0.8468 (mttt) cc_final: 0.8171 (mttt) REVERT: A 641 TYR cc_start: 0.7969 (m-80) cc_final: 0.7293 (m-80) REVERT: A 670 LEU cc_start: 0.3544 (OUTLIER) cc_final: 0.1307 (mt) REVERT: A 697 MET cc_start: 0.7131 (tpt) cc_final: 0.6771 (tpt) REVERT: A 705 MET cc_start: 0.6775 (mmt) cc_final: 0.6197 (mmt) REVERT: A 743 TYR cc_start: 0.7528 (t80) cc_final: 0.7216 (t80) REVERT: A 769 PHE cc_start: 0.7959 (t80) cc_final: 0.7552 (t80) REVERT: A 808 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7437 (tp) REVERT: A 810 MET cc_start: 0.5742 (ptt) cc_final: 0.5297 (ptt) REVERT: A 828 LYS cc_start: 0.8271 (mttt) cc_final: 0.7495 (mttt) REVERT: A 837 TYR cc_start: 0.8379 (OUTLIER) cc_final: 0.7949 (m-80) REVERT: A 848 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7738 (mt-10) REVERT: A 872 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7904 (tp30) REVERT: A 916 LEU cc_start: 0.8336 (mt) cc_final: 0.8084 (mp) REVERT: A 943 ASN cc_start: 0.7924 (m-40) cc_final: 0.7574 (p0) REVERT: A 967 MET cc_start: 0.7975 (mtp) cc_final: 0.7378 (mtp) REVERT: A 968 LYS cc_start: 0.7749 (mmmm) cc_final: 0.7414 (mmmm) REVERT: A 971 ASP cc_start: 0.8128 (m-30) cc_final: 0.7772 (m-30) REVERT: A 1045 MET cc_start: 0.8575 (mmm) cc_final: 0.8248 (mmt) REVERT: A 1063 VAL cc_start: 0.8193 (t) cc_final: 0.7922 (p) REVERT: A 1104 MET cc_start: 0.7965 (mmm) cc_final: 0.7479 (tpp) REVERT: A 1116 LYS cc_start: 0.8647 (tttp) cc_final: 0.8298 (tttm) REVERT: A 1134 PHE cc_start: 0.8195 (m-80) cc_final: 0.7578 (m-80) REVERT: A 1135 GLN cc_start: 0.7920 (pt0) cc_final: 0.7539 (pt0) REVERT: A 1136 PHE cc_start: 0.8395 (t80) cc_final: 0.8181 (t80) REVERT: A 1139 ASP cc_start: 0.7248 (OUTLIER) cc_final: 0.6129 (m-30) REVERT: A 1178 TYR cc_start: 0.6541 (t80) cc_final: 0.6161 (t80) outliers start: 35 outliers final: 21 residues processed: 263 average time/residue: 0.0823 time to fit residues: 29.3636 Evaluate side-chains 263 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 238 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 GLN Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 911 GLU Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain A residue 1142 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 65 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 99 optimal weight: 0.2980 chunk 25 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.130663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.112287 restraints weight = 12665.357| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.07 r_work: 0.3264 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8218 Z= 0.160 Angle : 0.548 7.117 11144 Z= 0.292 Chirality : 0.040 0.175 1341 Planarity : 0.003 0.034 1371 Dihedral : 5.302 54.568 1103 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.33 % Allowed : 20.39 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.27), residues: 1008 helix: 1.50 (0.19), residues: 746 sheet: 0.39 (0.88), residues: 31 loop : -1.59 (0.39), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 491 TYR 0.010 0.001 TYR A1088 PHE 0.026 0.002 PHE A 766 TRP 0.023 0.001 TRP A1112 HIS 0.003 0.001 HIS A 458 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 8218) covalent geometry : angle 0.54778 (11144) hydrogen bonds : bond 0.04756 ( 609) hydrogen bonds : angle 4.28499 ( 1815) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 245 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.8209 (ttm) cc_final: 0.7998 (ttm) REVERT: A 199 MET cc_start: 0.8143 (mmm) cc_final: 0.7375 (tpp) REVERT: A 217 LEU cc_start: 0.7927 (mt) cc_final: 0.7702 (mt) REVERT: A 233 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7135 (tm-30) REVERT: A 236 LEU cc_start: 0.8139 (mt) cc_final: 0.7922 (mp) REVERT: A 250 LYS cc_start: 0.7858 (mmmt) cc_final: 0.7518 (mmmt) REVERT: A 263 GLN cc_start: 0.8190 (mt0) cc_final: 0.7764 (mt0) REVERT: A 264 ASN cc_start: 0.7994 (m-40) cc_final: 0.7300 (m-40) REVERT: A 267 TYR cc_start: 0.8308 (t80) cc_final: 0.7882 (t80) REVERT: A 284 LYS cc_start: 0.8537 (mmmt) cc_final: 0.8270 (mmmm) REVERT: A 335 ASN cc_start: 0.7871 (t0) cc_final: 0.7576 (t0) REVERT: A 383 MET cc_start: 0.7524 (mmt) cc_final: 0.6805 (mmt) REVERT: A 387 TYR cc_start: 0.8085 (m-10) cc_final: 0.7316 (m-10) REVERT: A 449 ASP cc_start: 0.8295 (t0) cc_final: 0.7986 (t0) REVERT: A 500 ARG cc_start: 0.6873 (ptt180) cc_final: 0.5358 (mmm-85) REVERT: A 579 MET cc_start: 0.8053 (mtt) cc_final: 0.7816 (ttt) REVERT: A 587 LEU cc_start: 0.8760 (mt) cc_final: 0.8513 (mt) REVERT: A 591 LYS cc_start: 0.8578 (mttt) cc_final: 0.8234 (mtpp) REVERT: A 598 PHE cc_start: 0.8952 (t80) cc_final: 0.8725 (t80) REVERT: A 632 LYS cc_start: 0.8450 (mttt) cc_final: 0.8170 (mttt) REVERT: A 647 LYS cc_start: 0.8159 (mptt) cc_final: 0.7883 (mptt) REVERT: A 670 LEU cc_start: 0.3805 (OUTLIER) cc_final: 0.2081 (mp) REVERT: A 697 MET cc_start: 0.7121 (tpt) cc_final: 0.6787 (tpt) REVERT: A 705 MET cc_start: 0.6064 (mmt) cc_final: 0.5560 (mmt) REVERT: A 729 GLU cc_start: 0.7783 (tp30) cc_final: 0.7485 (tp30) REVERT: A 743 TYR cc_start: 0.7476 (t80) cc_final: 0.7173 (t80) REVERT: A 769 PHE cc_start: 0.7973 (t80) cc_final: 0.7583 (t80) REVERT: A 808 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7210 (tp) REVERT: A 810 MET cc_start: 0.5780 (ptt) cc_final: 0.5335 (ptt) REVERT: A 837 TYR cc_start: 0.8420 (OUTLIER) cc_final: 0.7966 (m-80) REVERT: A 848 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7708 (mt-10) REVERT: A 872 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7892 (mm-30) REVERT: A 916 LEU cc_start: 0.8356 (mt) cc_final: 0.8105 (mp) REVERT: A 943 ASN cc_start: 0.7994 (m-40) cc_final: 0.7546 (p0) REVERT: A 968 LYS cc_start: 0.7748 (mmmm) cc_final: 0.7474 (mmmm) REVERT: A 1045 MET cc_start: 0.8525 (mmm) cc_final: 0.8200 (mmt) REVERT: A 1051 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8564 (ttpp) REVERT: A 1063 VAL cc_start: 0.8207 (t) cc_final: 0.7932 (p) REVERT: A 1104 MET cc_start: 0.8087 (mmm) cc_final: 0.7667 (tpp) REVERT: A 1116 LYS cc_start: 0.8642 (tttp) cc_final: 0.8304 (tttm) REVERT: A 1134 PHE cc_start: 0.8191 (m-80) cc_final: 0.7611 (m-80) REVERT: A 1135 GLN cc_start: 0.7900 (pt0) cc_final: 0.7542 (pt0) REVERT: A 1136 PHE cc_start: 0.8400 (t80) cc_final: 0.8178 (t80) REVERT: A 1178 TYR cc_start: 0.6543 (t80) cc_final: 0.6215 (t80) outliers start: 38 outliers final: 29 residues processed: 265 average time/residue: 0.0838 time to fit residues: 29.9844 Evaluate side-chains 270 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 237 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 GLN Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 911 GLU Chi-restraints excluded: chain A residue 1051 LYS Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain A residue 1142 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 81 optimal weight: 0.0870 chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 597 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 = 0.3668 r_free = 0.3668 target = 0.131379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.112895 restraints weight = 12768.639| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.08 r_work: 0.3276 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8218 Z= 0.152 Angle : 0.551 7.251 11144 Z= 0.292 Chirality : 0.040 0.175 1341 Planarity : 0.003 0.034 1371 Dihedral : 5.332 54.827 1103 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.21 % Allowed : 20.84 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.27), residues: 1008 helix: 1.57 (0.19), residues: 747 sheet: 0.45 (0.89), residues: 31 loop : -1.61 (0.39), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 161 TYR 0.011 0.001 TYR A 641 PHE 0.027 0.002 PHE A 972 TRP 0.031 0.001 TRP A1112 HIS 0.003 0.001 HIS A 458 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 8218) covalent geometry : angle 0.55107 (11144) hydrogen bonds : bond 0.04643 ( 609) hydrogen bonds : angle 4.26127 ( 1815) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 252 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: A 199 MET cc_start: 0.8146 (mmm) cc_final: 0.7380 (tpp) REVERT: A 217 LEU cc_start: 0.7896 (mt) cc_final: 0.7679 (mt) REVERT: A 225 GLN cc_start: 0.8153 (mm-40) cc_final: 0.7910 (mm-40) REVERT: A 233 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7474 (tp30) REVERT: A 236 LEU cc_start: 0.8155 (mt) cc_final: 0.7913 (mp) REVERT: A 250 LYS cc_start: 0.7855 (mmmt) cc_final: 0.7519 (mmmt) REVERT: A 263 GLN cc_start: 0.8177 (mt0) cc_final: 0.7747 (mt0) REVERT: A 264 ASN cc_start: 0.7949 (m-40) cc_final: 0.7262 (m-40) REVERT: A 267 TYR cc_start: 0.8281 (t80) cc_final: 0.7815 (t80) REVERT: A 284 LYS cc_start: 0.8515 (mmmt) cc_final: 0.8296 (mmmm) REVERT: A 312 TYR cc_start: 0.8688 (t80) cc_final: 0.8391 (t80) REVERT: A 335 ASN cc_start: 0.7870 (t0) cc_final: 0.7568 (t0) REVERT: A 383 MET cc_start: 0.7483 (mmt) cc_final: 0.7054 (mmt) REVERT: A 449 ASP cc_start: 0.8295 (t0) cc_final: 0.7944 (t0) REVERT: A 500 ARG cc_start: 0.6820 (ptt180) cc_final: 0.5316 (mmm-85) REVERT: A 579 MET cc_start: 0.8003 (mtt) cc_final: 0.7759 (ttt) REVERT: A 586 MET cc_start: 0.8307 (ttm) cc_final: 0.8106 (ttp) REVERT: A 587 LEU cc_start: 0.8750 (mt) cc_final: 0.8515 (mt) REVERT: A 588 LYS cc_start: 0.8539 (mmtt) cc_final: 0.8201 (mmpt) REVERT: A 591 LYS cc_start: 0.8553 (mttt) cc_final: 0.8234 (mtpp) REVERT: A 598 PHE cc_start: 0.8956 (t80) cc_final: 0.8716 (t80) REVERT: A 621 GLU cc_start: 0.7319 (tm-30) cc_final: 0.7076 (tm-30) REVERT: A 632 LYS cc_start: 0.8432 (mttt) cc_final: 0.8153 (mttt) REVERT: A 647 LYS cc_start: 0.8169 (mptt) cc_final: 0.7841 (mptt) REVERT: A 670 LEU cc_start: 0.3607 (OUTLIER) cc_final: 0.1955 (mp) REVERT: A 697 MET cc_start: 0.7135 (tpt) cc_final: 0.6754 (tpt) REVERT: A 705 MET cc_start: 0.6121 (mmt) cc_final: 0.5624 (mmt) REVERT: A 743 TYR cc_start: 0.7482 (t80) cc_final: 0.7154 (t80) REVERT: A 769 PHE cc_start: 0.7971 (t80) cc_final: 0.7579 (t80) REVERT: A 808 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.7074 (tp) REVERT: A 810 MET cc_start: 0.5646 (ptt) cc_final: 0.5201 (ptt) REVERT: A 837 TYR cc_start: 0.8369 (OUTLIER) cc_final: 0.7935 (m-80) REVERT: A 848 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7768 (mt-10) REVERT: A 872 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7805 (tp30) REVERT: A 916 LEU cc_start: 0.8363 (mt) cc_final: 0.8110 (mp) REVERT: A 943 ASN cc_start: 0.7962 (m-40) cc_final: 0.7615 (p0) REVERT: A 968 LYS cc_start: 0.7710 (mmmm) cc_final: 0.7423 (mmmm) REVERT: A 1009 TYR cc_start: 0.7981 (t80) cc_final: 0.7763 (t80) REVERT: A 1033 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7656 (mt-10) REVERT: A 1045 MET cc_start: 0.8467 (mmm) cc_final: 0.8180 (mmt) REVERT: A 1051 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8539 (ttpp) REVERT: A 1063 VAL cc_start: 0.8197 (t) cc_final: 0.7932 (p) REVERT: A 1104 MET cc_start: 0.8073 (mmm) cc_final: 0.7772 (tpp) REVERT: A 1116 LYS cc_start: 0.8637 (tttp) cc_final: 0.8278 (tttm) REVERT: A 1134 PHE cc_start: 0.8227 (m-80) cc_final: 0.7631 (m-80) REVERT: A 1135 GLN cc_start: 0.7925 (pt0) cc_final: 0.7531 (pt0) REVERT: A 1136 PHE cc_start: 0.8350 (t80) cc_final: 0.8074 (t80) REVERT: A 1178 TYR cc_start: 0.6538 (t80) cc_final: 0.6195 (t80) outliers start: 37 outliers final: 28 residues processed: 270 average time/residue: 0.0906 time to fit residues: 33.2335 Evaluate side-chains 274 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 242 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 270 GLN Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 911 GLU Chi-restraints excluded: chain A residue 1051 LYS Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain A residue 1142 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 2 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1110 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 = 0.3657 r_free = 0.3657 target = 0.130484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.112412 restraints weight = 12711.907| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.00 r_work: 0.3274 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 8218 Z= 0.188 Angle : 0.589 7.345 11144 Z= 0.312 Chirality : 0.042 0.174 1341 Planarity : 0.004 0.034 1371 Dihedral : 5.415 57.997 1103 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.33 % Allowed : 21.41 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.27), residues: 1008 helix: 1.46 (0.19), residues: 747 sheet: 0.43 (0.91), residues: 31 loop : -1.66 (0.39), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 161 TYR 0.009 0.001 TYR A 641 PHE 0.028 0.002 PHE A 972 TRP 0.051 0.002 TRP A1112 HIS 0.003 0.001 HIS A 458 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 8218) covalent geometry : angle 0.58877 (11144) hydrogen bonds : bond 0.04906 ( 609) hydrogen bonds : angle 4.33899 ( 1815) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 246 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 199 MET cc_start: 0.8155 (mmm) cc_final: 0.7405 (tpp) REVERT: A 217 LEU cc_start: 0.7924 (mt) cc_final: 0.7705 (mt) REVERT: A 225 GLN cc_start: 0.8120 (mm-40) cc_final: 0.7876 (mm-40) REVERT: A 236 LEU cc_start: 0.8146 (mt) cc_final: 0.7915 (mp) REVERT: A 250 LYS cc_start: 0.7886 (mmmt) cc_final: 0.7551 (mmmt) REVERT: A 263 GLN cc_start: 0.8161 (mt0) cc_final: 0.7744 (mt0) REVERT: A 264 ASN cc_start: 0.8012 (m-40) cc_final: 0.7303 (m-40) REVERT: A 267 TYR cc_start: 0.8289 (t80) cc_final: 0.7848 (t80) REVERT: A 335 ASN cc_start: 0.7939 (t0) cc_final: 0.7575 (t0) REVERT: A 383 MET cc_start: 0.7547 (mmt) cc_final: 0.6859 (mmt) REVERT: A 385 TRP cc_start: 0.8077 (m100) cc_final: 0.7790 (m100) REVERT: A 387 TYR cc_start: 0.8085 (m-10) cc_final: 0.7329 (m-10) REVERT: A 449 ASP cc_start: 0.8308 (t0) cc_final: 0.7957 (t0) REVERT: A 500 ARG cc_start: 0.6888 (ptt180) cc_final: 0.5358 (mmm-85) REVERT: A 579 MET cc_start: 0.8011 (mtt) cc_final: 0.7775 (ttt) REVERT: A 587 LEU cc_start: 0.8764 (mt) cc_final: 0.8533 (mt) REVERT: A 588 LYS cc_start: 0.8551 (mmtt) cc_final: 0.8199 (mmpt) REVERT: A 591 LYS cc_start: 0.8539 (mttt) cc_final: 0.8219 (mtpp) REVERT: A 598 PHE cc_start: 0.8926 (t80) cc_final: 0.8691 (t80) REVERT: A 632 LYS cc_start: 0.8458 (mttt) cc_final: 0.8188 (mttt) REVERT: A 670 LEU cc_start: 0.3679 (OUTLIER) cc_final: 0.2363 (mp) REVERT: A 697 MET cc_start: 0.7122 (tpt) cc_final: 0.6739 (tpt) REVERT: A 705 MET cc_start: 0.6214 (mmt) cc_final: 0.5705 (mmt) REVERT: A 743 TYR cc_start: 0.7378 (t80) cc_final: 0.7098 (t80) REVERT: A 769 PHE cc_start: 0.7944 (t80) cc_final: 0.7566 (t80) REVERT: A 808 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7174 (tp) REVERT: A 810 MET cc_start: 0.5621 (ptt) cc_final: 0.5146 (ptt) REVERT: A 837 TYR cc_start: 0.8416 (OUTLIER) cc_final: 0.7943 (m-80) REVERT: A 848 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7789 (mt-10) REVERT: A 886 GLN cc_start: 0.8568 (tm-30) cc_final: 0.8322 (tm-30) REVERT: A 916 LEU cc_start: 0.8381 (mt) cc_final: 0.8136 (mp) REVERT: A 943 ASN cc_start: 0.8043 (m-40) cc_final: 0.7671 (p0) REVERT: A 968 LYS cc_start: 0.7760 (mmmm) cc_final: 0.7502 (mmmm) REVERT: A 986 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7604 (mt-10) REVERT: A 1009 TYR cc_start: 0.7959 (t80) cc_final: 0.7667 (t80) REVERT: A 1033 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7667 (mt-10) REVERT: A 1045 MET cc_start: 0.8486 (mmm) cc_final: 0.8164 (mmt) REVERT: A 1051 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8531 (ttpp) REVERT: A 1063 VAL cc_start: 0.8189 (t) cc_final: 0.7899 (p) REVERT: A 1064 GLN cc_start: 0.8524 (mt0) cc_final: 0.8221 (mt0) REVERT: A 1098 ILE cc_start: 0.8436 (tt) cc_final: 0.8052 (pt) REVERT: A 1104 MET cc_start: 0.8065 (mmm) cc_final: 0.7779 (tpp) REVERT: A 1105 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7590 (mm-30) REVERT: A 1116 LYS cc_start: 0.8585 (tttp) cc_final: 0.8203 (tttm) REVERT: A 1134 PHE cc_start: 0.8153 (m-80) cc_final: 0.7570 (m-80) REVERT: A 1135 GLN cc_start: 0.7875 (pt0) cc_final: 0.7492 (pt0) REVERT: A 1136 PHE cc_start: 0.8318 (t80) cc_final: 0.8085 (t80) REVERT: A 1178 TYR cc_start: 0.6567 (t80) cc_final: 0.6266 (t80) outliers start: 38 outliers final: 27 residues processed: 268 average time/residue: 0.0859 time to fit residues: 31.3792 Evaluate side-chains 269 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 238 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 GLN Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 1051 LYS Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1139 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 85 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.130946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.112866 restraints weight = 12721.167| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.02 r_work: 0.3277 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8218 Z= 0.172 Angle : 0.588 7.879 11144 Z= 0.311 Chirality : 0.041 0.176 1341 Planarity : 0.003 0.034 1371 Dihedral : 5.488 58.885 1103 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.87 % Allowed : 22.21 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.27), residues: 1008 helix: 1.47 (0.19), residues: 747 sheet: 0.38 (0.91), residues: 31 loop : -1.68 (0.39), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 976 TYR 0.009 0.001 TYR A 358 PHE 0.026 0.002 PHE A 766 TRP 0.018 0.001 TRP A1112 HIS 0.003 0.001 HIS A 458 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 8218) covalent geometry : angle 0.58801 (11144) hydrogen bonds : bond 0.04805 ( 609) hydrogen bonds : angle 4.33143 ( 1815) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 241 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7611 (tm-30) REVERT: A 199 MET cc_start: 0.8127 (mmm) cc_final: 0.7822 (mmm) REVERT: A 200 MET cc_start: 0.8405 (ttp) cc_final: 0.8198 (ttm) REVERT: A 217 LEU cc_start: 0.7894 (mt) cc_final: 0.7671 (mt) REVERT: A 225 GLN cc_start: 0.8111 (mm-40) cc_final: 0.7872 (mm-40) REVERT: A 233 GLU cc_start: 0.7961 (tp30) cc_final: 0.7675 (tp30) REVERT: A 236 LEU cc_start: 0.8133 (mt) cc_final: 0.7912 (mp) REVERT: A 250 LYS cc_start: 0.7883 (mmmt) cc_final: 0.7564 (mmmt) REVERT: A 263 GLN cc_start: 0.8133 (mt0) cc_final: 0.7732 (mt0) REVERT: A 264 ASN cc_start: 0.8001 (m-40) cc_final: 0.7299 (m110) REVERT: A 267 TYR cc_start: 0.8284 (t80) cc_final: 0.7850 (t80) REVERT: A 335 ASN cc_start: 0.7942 (t0) cc_final: 0.7557 (t0) REVERT: A 383 MET cc_start: 0.7469 (mmt) cc_final: 0.6807 (mmt) REVERT: A 385 TRP cc_start: 0.8073 (m100) cc_final: 0.7785 (m100) REVERT: A 449 ASP cc_start: 0.8269 (t0) cc_final: 0.7916 (t0) REVERT: A 500 ARG cc_start: 0.7049 (ptt180) cc_final: 0.5485 (mmm-85) REVERT: A 579 MET cc_start: 0.7981 (mtt) cc_final: 0.7755 (ttt) REVERT: A 587 LEU cc_start: 0.8716 (mt) cc_final: 0.8509 (mt) REVERT: A 588 LYS cc_start: 0.8503 (mmtt) cc_final: 0.8185 (mmpt) REVERT: A 591 LYS cc_start: 0.8519 (mttt) cc_final: 0.8205 (mtpp) REVERT: A 598 PHE cc_start: 0.8919 (t80) cc_final: 0.8680 (t80) REVERT: A 632 LYS cc_start: 0.8446 (mttt) cc_final: 0.8172 (mttt) REVERT: A 647 LYS cc_start: 0.8150 (mptt) cc_final: 0.7899 (mptt) REVERT: A 670 LEU cc_start: 0.3484 (OUTLIER) cc_final: 0.1456 (mp) REVERT: A 697 MET cc_start: 0.7131 (tpt) cc_final: 0.6733 (tpt) REVERT: A 705 MET cc_start: 0.6215 (mmt) cc_final: 0.5691 (mmt) REVERT: A 743 TYR cc_start: 0.7385 (t80) cc_final: 0.7086 (t80) REVERT: A 769 PHE cc_start: 0.7923 (t80) cc_final: 0.7576 (t80) REVERT: A 808 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7213 (tp) REVERT: A 810 MET cc_start: 0.5470 (ptt) cc_final: 0.5179 (ptt) REVERT: A 837 TYR cc_start: 0.8394 (OUTLIER) cc_final: 0.7931 (m-80) REVERT: A 848 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7803 (mt-10) REVERT: A 886 GLN cc_start: 0.8570 (tm-30) cc_final: 0.8333 (tm-30) REVERT: A 916 LEU cc_start: 0.8366 (mt) cc_final: 0.8118 (mp) REVERT: A 943 ASN cc_start: 0.7970 (m-40) cc_final: 0.7655 (p0) REVERT: A 968 LYS cc_start: 0.7744 (mmmm) cc_final: 0.7455 (mmmm) REVERT: A 986 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7685 (mt-10) REVERT: A 1009 TYR cc_start: 0.7928 (t80) cc_final: 0.7619 (t80) REVERT: A 1033 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7674 (mt-10) REVERT: A 1045 MET cc_start: 0.8408 (mmm) cc_final: 0.8160 (mmt) REVERT: A 1051 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8534 (ttpp) REVERT: A 1063 VAL cc_start: 0.8180 (t) cc_final: 0.7891 (p) REVERT: A 1098 ILE cc_start: 0.8392 (tt) cc_final: 0.8013 (pt) REVERT: A 1104 MET cc_start: 0.8063 (mmm) cc_final: 0.7784 (mmm) REVERT: A 1105 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7608 (mm-30) REVERT: A 1116 LYS cc_start: 0.8599 (tttp) cc_final: 0.8220 (tttm) REVERT: A 1134 PHE cc_start: 0.8138 (m-80) cc_final: 0.7607 (m-80) REVERT: A 1135 GLN cc_start: 0.7877 (pt0) cc_final: 0.7485 (pt0) REVERT: A 1136 PHE cc_start: 0.8310 (t80) cc_final: 0.8102 (t80) REVERT: A 1178 TYR cc_start: 0.6696 (t80) cc_final: 0.6355 (t80) outliers start: 34 outliers final: 28 residues processed: 258 average time/residue: 0.0828 time to fit residues: 28.7232 Evaluate side-chains 270 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 238 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 GLN Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 1051 LYS Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1139 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 52 optimal weight: 0.2980 chunk 85 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.130941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.112766 restraints weight = 12696.590| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.02 r_work: 0.3278 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8218 Z= 0.171 Angle : 0.604 8.386 11144 Z= 0.318 Chirality : 0.041 0.174 1341 Planarity : 0.003 0.034 1371 Dihedral : 5.527 55.970 1103 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.99 % Allowed : 21.98 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.27), residues: 1008 helix: 1.47 (0.19), residues: 747 sheet: 0.38 (0.91), residues: 31 loop : -1.67 (0.39), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 585 TYR 0.009 0.001 TYR A 358 PHE 0.026 0.002 PHE A 766 TRP 0.027 0.002 TRP A1112 HIS 0.003 0.001 HIS A 458 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 8218) covalent geometry : angle 0.60365 (11144) hydrogen bonds : bond 0.04821 ( 609) hydrogen bonds : angle 4.31842 ( 1815) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 247 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7586 (tm-30) REVERT: A 199 MET cc_start: 0.8121 (mmm) cc_final: 0.7253 (tmm) REVERT: A 217 LEU cc_start: 0.7890 (mt) cc_final: 0.7673 (mt) REVERT: A 225 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7875 (mm-40) REVERT: A 233 GLU cc_start: 0.7895 (tp30) cc_final: 0.7517 (tp30) REVERT: A 236 LEU cc_start: 0.8129 (mt) cc_final: 0.7922 (mp) REVERT: A 250 LYS cc_start: 0.7912 (mmmt) cc_final: 0.7604 (mmmt) REVERT: A 263 GLN cc_start: 0.8124 (mt0) cc_final: 0.7716 (mt0) REVERT: A 264 ASN cc_start: 0.7991 (m-40) cc_final: 0.7286 (m110) REVERT: A 267 TYR cc_start: 0.8287 (t80) cc_final: 0.7825 (t80) REVERT: A 284 LYS cc_start: 0.8483 (mmmt) cc_final: 0.8267 (mmmm) REVERT: A 312 TYR cc_start: 0.8692 (t80) cc_final: 0.8444 (t80) REVERT: A 335 ASN cc_start: 0.7939 (t0) cc_final: 0.7624 (t0) REVERT: A 383 MET cc_start: 0.7446 (mmt) cc_final: 0.6979 (mmt) REVERT: A 385 TRP cc_start: 0.8063 (m100) cc_final: 0.7783 (m100) REVERT: A 449 ASP cc_start: 0.8302 (t0) cc_final: 0.7912 (t0) REVERT: A 500 ARG cc_start: 0.7089 (ptt180) cc_final: 0.5546 (mmm-85) REVERT: A 579 MET cc_start: 0.7952 (mtt) cc_final: 0.7718 (ttt) REVERT: A 587 LEU cc_start: 0.8695 (mt) cc_final: 0.8476 (mt) REVERT: A 588 LYS cc_start: 0.8507 (mmtt) cc_final: 0.8168 (mmpt) REVERT: A 590 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7622 (mt-10) REVERT: A 591 LYS cc_start: 0.8530 (mttt) cc_final: 0.8202 (mtpp) REVERT: A 598 PHE cc_start: 0.8912 (t80) cc_final: 0.8681 (t80) REVERT: A 632 LYS cc_start: 0.8427 (mttt) cc_final: 0.8158 (mttt) REVERT: A 647 LYS cc_start: 0.8161 (mptt) cc_final: 0.7911 (mptt) REVERT: A 670 LEU cc_start: 0.3139 (OUTLIER) cc_final: 0.2382 (mp) REVERT: A 697 MET cc_start: 0.7143 (tpt) cc_final: 0.6720 (tpt) REVERT: A 705 MET cc_start: 0.6322 (mmt) cc_final: 0.5816 (mmt) REVERT: A 743 TYR cc_start: 0.7403 (t80) cc_final: 0.7104 (t80) REVERT: A 769 PHE cc_start: 0.7933 (t80) cc_final: 0.7567 (t80) REVERT: A 808 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7200 (tp) REVERT: A 810 MET cc_start: 0.5434 (ptt) cc_final: 0.5112 (ptt) REVERT: A 837 TYR cc_start: 0.8393 (OUTLIER) cc_final: 0.7868 (m-80) REVERT: A 848 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7786 (mt-10) REVERT: A 886 GLN cc_start: 0.8577 (tm-30) cc_final: 0.8339 (tm-30) REVERT: A 916 LEU cc_start: 0.8361 (mt) cc_final: 0.8110 (mp) REVERT: A 943 ASN cc_start: 0.8027 (m-40) cc_final: 0.7663 (p0) REVERT: A 968 LYS cc_start: 0.7744 (mmmm) cc_final: 0.7452 (mmmm) REVERT: A 986 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7653 (mt-10) REVERT: A 1009 TYR cc_start: 0.7943 (t80) cc_final: 0.7602 (t80) REVERT: A 1033 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7687 (mt-10) REVERT: A 1045 MET cc_start: 0.8417 (mmm) cc_final: 0.8178 (mmt) REVERT: A 1051 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8517 (ttpp) REVERT: A 1063 VAL cc_start: 0.8193 (t) cc_final: 0.7908 (p) REVERT: A 1064 GLN cc_start: 0.8538 (mt0) cc_final: 0.8273 (mt0) REVERT: A 1098 ILE cc_start: 0.8577 (tt) cc_final: 0.8123 (pt) REVERT: A 1104 MET cc_start: 0.8051 (mmm) cc_final: 0.7822 (mmm) REVERT: A 1105 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7508 (mm-30) REVERT: A 1116 LYS cc_start: 0.8577 (tttp) cc_final: 0.8189 (tttm) REVERT: A 1134 PHE cc_start: 0.8131 (m-80) cc_final: 0.7608 (m-80) REVERT: A 1135 GLN cc_start: 0.7863 (pt0) cc_final: 0.7480 (pt0) REVERT: A 1136 PHE cc_start: 0.8297 (t80) cc_final: 0.8082 (t80) REVERT: A 1178 TYR cc_start: 0.6753 (t80) cc_final: 0.6412 (t80) outliers start: 35 outliers final: 30 residues processed: 265 average time/residue: 0.0863 time to fit residues: 31.1769 Evaluate side-chains 278 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 244 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 GLN Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 1051 LYS Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain A residue 1142 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 23 optimal weight: 0.9990 chunk 54 optimal weight: 0.0030 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 14 optimal weight: 0.1980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.132188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.113894 restraints weight = 12646.576| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.02 r_work: 0.3295 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8218 Z= 0.143 Angle : 0.575 7.834 11144 Z= 0.304 Chirality : 0.040 0.175 1341 Planarity : 0.003 0.033 1371 Dihedral : 5.294 55.355 1103 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.99 % Allowed : 22.44 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.27), residues: 1008 helix: 1.54 (0.19), residues: 748 sheet: 0.50 (0.91), residues: 31 loop : -1.64 (0.39), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 976 TYR 0.010 0.001 TYR A 672 PHE 0.027 0.002 PHE A 766 TRP 0.025 0.001 TRP A1112 HIS 0.002 0.000 HIS A 458 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8218) covalent geometry : angle 0.57514 (11144) hydrogen bonds : bond 0.04607 ( 609) hydrogen bonds : angle 4.27533 ( 1815) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2059.00 seconds wall clock time: 35 minutes 58.80 seconds (2158.80 seconds total)