Starting phenix.real_space_refine on Wed Sep 17 14:45:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fgm_50413/09_2025/9fgm_50413.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fgm_50413/09_2025/9fgm_50413.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fgm_50413/09_2025/9fgm_50413.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fgm_50413/09_2025/9fgm_50413.map" model { file = "/net/cci-nas-00/data/ceres_data/9fgm_50413/09_2025/9fgm_50413.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fgm_50413/09_2025/9fgm_50413.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 39 5.16 5 C 5682 2.51 5 N 1563 2.21 5 O 1748 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9032 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1135, 9032 Classifications: {'peptide': 1135} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1079} Time building chain proxies: 2.34, per 1000 atoms: 0.26 Number of scatterers: 9032 At special positions: 0 Unit cell: (136.779, 133.548, 151.857, 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 39 16.00 O 1748 8.00 N 1563 7.00 C 5682 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 559 " - pdb=" SG CYS A 566 " distance=2.03 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: 0.91 Conformation dependent library (CDL) restraints added in 361.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2166 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 4 sheets defined 67.9% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 232 through 237 removed outlier: 3.538A pdb=" N ASN A 236 " --> pdb=" O LYS A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 251 Processing helix chain 'A' and resid 265 through 269 Processing helix chain 'A' and resid 283 through 308 Processing helix chain 'A' and resid 319 through 323 removed outlier: 3.714A pdb=" N VAL A 323 " --> pdb=" O LEU A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 336 Processing helix chain 'A' and resid 356 through 376 removed outlier: 3.523A pdb=" N GLU A 360 " --> pdb=" O ASN A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 398 removed outlier: 3.520A pdb=" N VAL A 389 " --> pdb=" O ASP A 385 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 421 removed outlier: 4.037A pdb=" N GLY A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 443 removed outlier: 4.046A pdb=" N GLY A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR A 441 " --> pdb=" O THR A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 462 removed outlier: 3.862A pdb=" N LEU A 451 " --> pdb=" O ALA A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 505 Processing helix chain 'A' and resid 523 through 529 Processing helix chain 'A' and resid 530 through 537 Processing helix chain 'A' and resid 538 through 541 removed outlier: 4.276A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 538 through 541' Processing helix chain 'A' and resid 546 through 551 removed outlier: 3.862A pdb=" N TYR A 550 " --> pdb=" O ALA A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 562 through 586 removed outlier: 3.933A pdb=" N CYS A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A 582 " --> pdb=" O GLN A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 614 removed outlier: 3.967A pdb=" N ASN A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 642 removed outlier: 3.629A pdb=" N PHE A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 651 removed outlier: 3.618A pdb=" N LEU A 651 " --> pdb=" O VAL A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 666 removed outlier: 3.684A pdb=" N ASP A 660 " --> pdb=" O ILE A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 690 Processing helix chain 'A' and resid 697 through 711 removed outlier: 3.543A pdb=" N ASN A 711 " --> pdb=" O PHE A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 723 Processing helix chain 'A' and resid 731 through 753 removed outlier: 3.512A pdb=" N VAL A 735 " --> pdb=" O ASN A 731 " (cutoff:3.500A) Proline residue: A 743 - end of helix removed outlier: 4.517A pdb=" N SER A 753 " --> pdb=" O LEU A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 786 removed outlier: 3.685A pdb=" N LYS A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 806 Processing helix chain 'A' and resid 807 through 812 Processing helix chain 'A' and resid 821 through 828 removed outlier: 3.921A pdb=" N LEU A 825 " --> pdb=" O ASN A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 901 Processing helix chain 'A' and resid 909 through 935 removed outlier: 3.782A pdb=" N PHE A 913 " --> pdb=" O ALA A 909 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR A 935 " --> pdb=" O ASP A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 953 Processing helix chain 'A' and resid 959 through 969 Processing helix chain 'A' and resid 978 through 1003 removed outlier: 4.334A pdb=" N ILE A 990 " --> pdb=" O ASN A 986 " (cutoff:3.500A) Proline residue: A 991 - end of helix Processing helix chain 'A' and resid 1004 through 1015 Processing helix chain 'A' and resid 1017 through 1024 removed outlier: 3.523A pdb=" N TRP A1021 " --> pdb=" O THR A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1052 Processing helix chain 'A' and resid 1052 through 1067 Processing helix chain 'A' and resid 1068 through 1079 Processing helix chain 'A' and resid 1081 through 1088 removed outlier: 3.601A pdb=" N VAL A1088 " --> pdb=" O GLU A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1115 Proline residue: A1112 - end of helix removed outlier: 3.625A pdb=" N ARG A1115 " --> pdb=" O GLU A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1124 through 1149 removed outlier: 3.616A pdb=" N ILE A1149 " --> pdb=" O ASP A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1153 through 1182 Processing helix chain 'A' and resid 1191 through 1224 Proline residue: A1209 - end of helix Processing helix chain 'A' and resid 1231 through 1261 removed outlier: 3.748A pdb=" N ALA A1261 " --> pdb=" O ILE A1257 " (cutoff:3.500A) Processing helix chain 'A' and resid 1269 through 1300 Processing helix chain 'A' and resid 1303 through 1328 Proline residue: A1312 - end of helix Processing helix chain 'A' and resid 1331 through 1356 Processing sheet with id=AA1, first strand: chain 'A' and resid 492 through 493 Processing sheet with id=AA2, first strand: chain 'A' and resid 623 through 625 Processing sheet with id=AA3, first strand: chain 'A' and resid 760 through 765 removed outlier: 6.878A pdb=" N ILE A 834 " --> pdb=" O PHE A 890 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LEU A 892 " --> pdb=" O ILE A 834 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLU A 836 " --> pdb=" O LEU A 892 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ALA A 894 " --> pdb=" O GLU A 836 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N LEU A 838 " --> pdb=" O ALA A 894 " (cutoff:3.500A) removed outlier: 9.293A pdb=" N LYS A 896 " --> pdb=" O LEU A 838 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY A 879 " --> pdb=" O ARG A 887 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE A 889 " --> pdb=" O LEU A 877 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LEU A 877 " --> pdb=" O ILE A 889 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N THR A 891 " --> pdb=" O VAL A 875 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL A 875 " --> pdb=" O THR A 891 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N VAL A 893 " --> pdb=" O THR A 873 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N THR A 873 " --> pdb=" O VAL A 893 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL A 895 " --> pdb=" O VAL A 871 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL A 871 " --> pdb=" O VAL A 895 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 816 through 818 555 hydrogen bonds defined for protein. 1617 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: 1.41 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3036 1.35 - 1.47: 1841 1.47 - 1.59: 4247 1.59 - 1.71: 0 1.71 - 1.83: 69 Bond restraints: 9193 Sorted by residual: bond pdb=" N MET A1269 " pdb=" CA MET A1269 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.00e-02 1.00e+04 9.87e+00 bond pdb=" N ASN A 598 " pdb=" CA ASN A 598 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.31e-02 5.83e+03 7.18e+00 bond pdb=" N ASP A 517 " pdb=" CA ASP A 517 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.25e+00 bond pdb=" N MET A 599 " pdb=" CA MET A 599 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.23e-02 6.61e+03 5.25e+00 bond pdb=" C GLN A 596 " pdb=" N PRO A 597 " ideal model delta sigma weight residual 1.332 1.360 -0.028 1.34e-02 5.57e+03 4.31e+00 ... (remaining 9188 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 12245 2.35 - 4.70: 131 4.70 - 7.04: 19 7.04 - 9.39: 4 9.39 - 11.74: 1 Bond angle restraints: 12400 Sorted by residual: angle pdb=" CB MET A 644 " pdb=" CG MET A 644 " pdb=" SD MET A 644 " ideal model delta sigma weight residual 112.70 124.44 -11.74 3.00e+00 1.11e-01 1.53e+01 angle pdb=" N PRO A 597 " pdb=" CA PRO A 597 " pdb=" C PRO A 597 " ideal model delta sigma weight residual 111.21 116.96 -5.75 1.59e+00 3.96e-01 1.31e+01 angle pdb=" CA MET A1048 " pdb=" CB MET A1048 " pdb=" CG MET A1048 " ideal model delta sigma weight residual 114.10 121.09 -6.99 2.00e+00 2.50e-01 1.22e+01 angle pdb=" N MET A1269 " pdb=" CA MET A1269 " pdb=" C MET A1269 " ideal model delta sigma weight residual 112.54 107.39 5.15 1.51e+00 4.39e-01 1.16e+01 angle pdb=" C LYS A1014 " pdb=" N PHE A1015 " pdb=" CA PHE A1015 " ideal model delta sigma weight residual 120.51 125.29 -4.78 1.45e+00 4.76e-01 1.08e+01 ... (remaining 12395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 5165 17.79 - 35.58: 465 35.58 - 53.37: 82 53.37 - 71.16: 17 71.16 - 88.95: 9 Dihedral angle restraints: 5738 sinusoidal: 2407 harmonic: 3331 Sorted by residual: dihedral pdb=" CB CYS A 559 " pdb=" SG CYS A 559 " pdb=" SG CYS A 566 " pdb=" CB CYS A 566 " ideal model delta sinusoidal sigma weight residual -86.00 -164.96 78.96 1 1.00e+01 1.00e-02 7.76e+01 dihedral pdb=" CA ASP A 974 " pdb=" C ASP A 974 " pdb=" N ASN A 975 " pdb=" CA ASN A 975 " ideal model delta harmonic sigma weight residual 180.00 160.08 19.92 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA ASP A1004 " pdb=" C ASP A1004 " pdb=" N MET A1005 " pdb=" CA MET A1005 " ideal model delta harmonic sigma weight residual -180.00 -160.29 -19.71 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 5735 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1106 0.045 - 0.089: 213 0.089 - 0.134: 56 0.134 - 0.178: 1 0.178 - 0.223: 3 Chirality restraints: 1379 Sorted by residual: chirality pdb=" CA PHE A 551 " pdb=" N PHE A 551 " pdb=" C PHE A 551 " pdb=" CB PHE A 551 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB VAL A1139 " pdb=" CA VAL A1139 " pdb=" CG1 VAL A1139 " pdb=" CG2 VAL A1139 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.74e-01 chirality pdb=" CA PRO A 597 " pdb=" N PRO A 597 " pdb=" C PRO A 597 " pdb=" CB PRO A 597 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.38e-01 ... (remaining 1376 not shown) Planarity restraints: 1626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 553 " -0.036 5.00e-02 4.00e+02 5.49e-02 4.82e+00 pdb=" N PRO A 554 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 554 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 554 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A1352 " -0.011 2.00e-02 2.50e+03 2.12e-02 4.50e+00 pdb=" C GLN A1352 " 0.037 2.00e-02 2.50e+03 pdb=" O GLN A1352 " -0.014 2.00e-02 2.50e+03 pdb=" N GLU A1353 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 908 " 0.010 2.00e-02 2.50e+03 1.30e-02 3.38e+00 pdb=" CG TYR A 908 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR A 908 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A 908 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A 908 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 908 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 908 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 908 " 0.000 2.00e-02 2.50e+03 ... (remaining 1623 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1773 2.77 - 3.30: 9140 3.30 - 3.84: 14642 3.84 - 4.37: 16358 4.37 - 4.90: 27591 Nonbonded interactions: 69504 Sorted by model distance: nonbonded pdb=" OD2 ASP A 867 " pdb=" NZ LYS A 896 " model vdw 2.241 3.120 nonbonded pdb=" OG SER A 808 " pdb=" O LEU A 870 " model vdw 2.245 3.040 nonbonded pdb=" OG SER A 228 " pdb=" OD1 ASP A 230 " model vdw 2.249 3.040 nonbonded pdb=" NZ LYS A 747 " pdb=" OD2 ASP A 751 " model vdw 2.272 3.120 nonbonded pdb=" OD1 ASP A 685 " pdb=" ND2 ASN A 689 " model vdw 2.278 3.120 ... (remaining 69499 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.270 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 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 : 0.003 0.074 9194 Z= 0.158 Angle : 0.639 11.739 12402 Z= 0.364 Chirality : 0.038 0.223 1379 Planarity : 0.004 0.055 1626 Dihedral : 14.238 88.950 3569 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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: 1.72 (0.25), residues: 1133 helix: 1.97 (0.20), residues: 689 sheet: -0.19 (0.70), residues: 44 loop : -0.11 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 690 TYR 0.032 0.001 TYR A 908 PHE 0.023 0.001 PHE A 551 TRP 0.005 0.001 TRP A 403 HIS 0.004 0.001 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9193) covalent geometry : angle 0.63851 (12400) SS BOND : bond 0.00392 ( 1) SS BOND : angle 1.52198 ( 2) hydrogen bonds : bond 0.13070 ( 555) hydrogen bonds : angle 4.85246 ( 1617) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 944 LEU cc_start: 0.9505 (tp) cc_final: 0.8948 (mt) REVERT: A 984 PHE cc_start: 0.8425 (t80) cc_final: 0.8090 (t80) REVERT: A 1007 MET cc_start: 0.9074 (tpt) cc_final: 0.8269 (ttt) REVERT: A 1098 GLN cc_start: 0.9517 (mt0) cc_final: 0.9285 (mt0) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1356 time to fit residues: 21.7996 Evaluate side-chains 74 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 20.0000 chunk 106 optimal weight: 8.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 HIS A 711 ASN ** A1283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.124029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.085126 restraints weight = 28408.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.086678 restraints weight = 19798.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.087422 restraints weight = 16075.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.087749 restraints weight = 13389.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.087877 restraints weight = 13344.032| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 9194 Z= 0.256 Angle : 0.727 11.590 12402 Z= 0.376 Chirality : 0.044 0.160 1379 Planarity : 0.005 0.071 1626 Dihedral : 4.835 20.941 1214 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.41 % Allowed : 9.56 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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: 1.31 (0.25), residues: 1133 helix: 1.60 (0.19), residues: 700 sheet: -1.03 (0.66), residues: 44 loop : -0.16 (0.33), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1256 TYR 0.025 0.002 TYR A 550 PHE 0.034 0.002 PHE A1318 TRP 0.005 0.001 TRP A 714 HIS 0.005 0.001 HIS A 286 Details of bonding type rmsd covalent geometry : bond 0.00587 ( 9193) covalent geometry : angle 0.72702 (12400) SS BOND : bond 0.00143 ( 1) SS BOND : angle 1.99427 ( 2) hydrogen bonds : bond 0.05817 ( 555) hydrogen bonds : angle 4.63881 ( 1617) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 MET cc_start: 0.7635 (ttm) cc_final: 0.7398 (ttp) REVERT: A 690 ARG cc_start: 0.8214 (ttt180) cc_final: 0.7879 (ttt180) REVERT: A 715 TYR cc_start: 0.8053 (OUTLIER) cc_final: 0.7500 (t80) REVERT: A 914 MET cc_start: 0.9099 (mmp) cc_final: 0.8831 (mmp) REVERT: A 984 PHE cc_start: 0.8233 (t80) cc_final: 0.7970 (t80) REVERT: A 993 LEU cc_start: 0.9344 (mp) cc_final: 0.9127 (mp) REVERT: A 996 CYS cc_start: 0.9312 (m) cc_final: 0.8913 (p) REVERT: A 1021 TRP cc_start: 0.7802 (m100) cc_final: 0.7420 (m100) REVERT: A 1234 ASP cc_start: 0.8852 (t0) cc_final: 0.7636 (t0) REVERT: A 1238 MET cc_start: 0.5481 (mtt) cc_final: 0.4893 (ptt) outliers start: 24 outliers final: 13 residues processed: 104 average time/residue: 0.1003 time to fit residues: 14.8121 Evaluate side-chains 84 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 715 TYR Chi-restraints excluded: chain A residue 737 PHE Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1102 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 54 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 8 optimal weight: 0.4980 chunk 75 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 82 optimal weight: 8.9990 chunk 2 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 HIS A 587 GLN A 746 ASN ** A1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1104 GLN ** A1283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.115971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.078652 restraints weight = 27572.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.079573 restraints weight = 23637.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.080039 restraints weight = 17438.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.080059 restraints weight = 17742.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.080349 restraints weight = 15730.967| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9194 Z= 0.132 Angle : 0.617 12.793 12402 Z= 0.312 Chirality : 0.040 0.184 1379 Planarity : 0.005 0.059 1626 Dihedral : 4.552 19.464 1214 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.51 % Allowed : 11.27 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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: 1.65 (0.25), residues: 1133 helix: 1.83 (0.19), residues: 698 sheet: -0.93 (0.69), residues: 44 loop : 0.09 (0.34), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1256 TYR 0.014 0.001 TYR A 256 PHE 0.019 0.001 PHE A 551 TRP 0.015 0.001 TRP A1021 HIS 0.006 0.001 HIS A 966 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9193) covalent geometry : angle 0.61683 (12400) SS BOND : bond 0.00225 ( 1) SS BOND : angle 1.44774 ( 2) hydrogen bonds : bond 0.04663 ( 555) hydrogen bonds : angle 4.38926 ( 1617) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 690 ARG cc_start: 0.8342 (ttt180) cc_final: 0.8022 (ttt180) REVERT: A 715 TYR cc_start: 0.8013 (OUTLIER) cc_final: 0.7457 (t80) REVERT: A 914 MET cc_start: 0.9112 (mmp) cc_final: 0.8869 (mmp) REVERT: A 993 LEU cc_start: 0.9221 (mp) cc_final: 0.8973 (mp) REVERT: A 996 CYS cc_start: 0.9210 (m) cc_final: 0.8590 (p) REVERT: A 1234 ASP cc_start: 0.8927 (t0) cc_final: 0.7600 (t0) REVERT: A 1238 MET cc_start: 0.5597 (mtt) cc_final: 0.4352 (ptt) REVERT: A 1269 MET cc_start: 0.4929 (tpt) cc_final: 0.4175 (mmm) REVERT: A 1282 TYR cc_start: 0.8673 (t80) cc_final: 0.7840 (m-80) outliers start: 15 outliers final: 7 residues processed: 87 average time/residue: 0.1039 time to fit residues: 12.8371 Evaluate side-chains 78 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 715 TYR Chi-restraints excluded: chain A residue 737 PHE Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1154 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 94 optimal weight: 3.9990 chunk 61 optimal weight: 0.0570 chunk 99 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 ASN ** A 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1283 ASN ** 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 = 0.4074 r_free = 0.4074 target = 0.118375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.081402 restraints weight = 29825.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.081642 restraints weight = 25859.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.081462 restraints weight = 22785.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.081519 restraints weight = 22643.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.081525 restraints weight = 22212.018| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9194 Z= 0.129 Angle : 0.603 11.668 12402 Z= 0.301 Chirality : 0.040 0.162 1379 Planarity : 0.004 0.046 1626 Dihedral : 4.443 19.518 1214 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.01 % Allowed : 11.57 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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: 1.72 (0.25), residues: 1133 helix: 1.91 (0.19), residues: 704 sheet: -0.62 (0.71), residues: 42 loop : -0.00 (0.34), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1256 TYR 0.017 0.001 TYR A 550 PHE 0.021 0.002 PHE A 984 TRP 0.010 0.001 TRP A1021 HIS 0.003 0.001 HIS A 966 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 9193) covalent geometry : angle 0.60248 (12400) SS BOND : bond 0.00240 ( 1) SS BOND : angle 1.29738 ( 2) hydrogen bonds : bond 0.04371 ( 555) hydrogen bonds : angle 4.29234 ( 1617) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 MET cc_start: 0.8180 (mtm) cc_final: 0.7867 (ttm) REVERT: A 690 ARG cc_start: 0.8477 (ttt180) cc_final: 0.8178 (ttt180) REVERT: A 914 MET cc_start: 0.9086 (mmp) cc_final: 0.8871 (mmp) REVERT: A 984 PHE cc_start: 0.8018 (t80) cc_final: 0.7735 (t80) REVERT: A 1008 MET cc_start: 0.8266 (mmt) cc_final: 0.7791 (mmt) REVERT: A 1234 ASP cc_start: 0.9029 (t0) cc_final: 0.7820 (t0) REVERT: A 1238 MET cc_start: 0.5665 (mtt) cc_final: 0.4220 (ptt) REVERT: A 1282 TYR cc_start: 0.8658 (t80) cc_final: 0.7976 (m-80) outliers start: 10 outliers final: 7 residues processed: 82 average time/residue: 0.1082 time to fit residues: 12.5701 Evaluate side-chains 74 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 737 PHE Chi-restraints excluded: chain A residue 1154 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 74 optimal weight: 30.0000 chunk 34 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1041 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 = 0.4003 r_free = 0.4003 target = 0.113699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.078335 restraints weight = 28305.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.078061 restraints weight = 21519.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.077844 restraints weight = 18393.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.077909 restraints weight = 20857.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.077892 restraints weight = 19232.327| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9194 Z= 0.202 Angle : 0.647 10.768 12402 Z= 0.330 Chirality : 0.042 0.187 1379 Planarity : 0.005 0.045 1626 Dihedral : 4.558 18.095 1214 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.41 % Allowed : 11.37 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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: 1.57 (0.25), residues: 1133 helix: 1.81 (0.19), residues: 705 sheet: -0.47 (0.73), residues: 40 loop : -0.14 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1256 TYR 0.015 0.001 TYR A 256 PHE 0.024 0.002 PHE A1015 TRP 0.028 0.002 TRP A1021 HIS 0.005 0.001 HIS A 286 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 9193) covalent geometry : angle 0.64645 (12400) SS BOND : bond 0.00238 ( 1) SS BOND : angle 1.51844 ( 2) hydrogen bonds : bond 0.05074 ( 555) hydrogen bonds : angle 4.43178 ( 1617) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 67 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 690 ARG cc_start: 0.8356 (ttt180) cc_final: 0.8085 (ttt180) REVERT: A 715 TYR cc_start: 0.8011 (OUTLIER) cc_final: 0.7489 (t80) REVERT: A 914 MET cc_start: 0.9145 (mmp) cc_final: 0.8943 (mmp) REVERT: A 1008 MET cc_start: 0.8095 (mmt) cc_final: 0.7724 (mmt) REVERT: A 1031 ARG cc_start: 0.9004 (ptp-110) cc_final: 0.8548 (ptp-170) REVERT: A 1269 MET cc_start: 0.5523 (mmm) cc_final: 0.4890 (mmm) outliers start: 24 outliers final: 15 residues processed: 84 average time/residue: 0.0987 time to fit residues: 12.0631 Evaluate side-chains 80 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 715 TYR Chi-restraints excluded: chain A residue 737 PHE Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 852 HIS Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 1154 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 2 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 96 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.117689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.080103 restraints weight = 29444.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.080427 restraints weight = 27089.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.080454 restraints weight = 24879.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.080439 restraints weight = 24236.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.080514 restraints weight = 22769.099| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9194 Z= 0.128 Angle : 0.608 11.968 12402 Z= 0.302 Chirality : 0.039 0.167 1379 Planarity : 0.004 0.045 1626 Dihedral : 4.417 20.838 1214 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.31 % Allowed : 12.78 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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: 1.70 (0.25), residues: 1133 helix: 1.92 (0.20), residues: 705 sheet: -0.92 (0.73), residues: 44 loop : -0.04 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1256 TYR 0.024 0.001 TYR A 256 PHE 0.041 0.002 PHE A1015 TRP 0.010 0.001 TRP A1021 HIS 0.003 0.001 HIS A 454 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9193) covalent geometry : angle 0.60597 (12400) SS BOND : bond 0.00077 ( 1) SS BOND : angle 3.77558 ( 2) hydrogen bonds : bond 0.04368 ( 555) hydrogen bonds : angle 4.28588 ( 1617) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 690 ARG cc_start: 0.8599 (ttt180) cc_final: 0.8343 (ttt180) REVERT: A 715 TYR cc_start: 0.7901 (OUTLIER) cc_final: 0.7522 (t80) REVERT: A 914 MET cc_start: 0.9173 (mmp) cc_final: 0.8959 (mmp) REVERT: A 1008 MET cc_start: 0.8287 (mmt) cc_final: 0.7791 (mmt) REVERT: A 1036 MET cc_start: 0.7868 (ptt) cc_final: 0.6897 (ppp) REVERT: A 1168 GLN cc_start: 0.8726 (tm-30) cc_final: 0.8464 (tm-30) REVERT: A 1238 MET cc_start: 0.5884 (mtt) cc_final: 0.4814 (ptt) REVERT: A 1269 MET cc_start: 0.5998 (mmm) cc_final: 0.5428 (mmm) outliers start: 13 outliers final: 10 residues processed: 80 average time/residue: 0.1004 time to fit residues: 11.6597 Evaluate side-chains 79 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 715 TYR Chi-restraints excluded: chain A residue 737 PHE Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 852 HIS Chi-restraints excluded: chain A residue 1079 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 49 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 73 optimal weight: 9.9990 chunk 68 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 103 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.117664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 111)---------------| | r_work = 0.3299 r_free = 0.3299 target = 0.079828 restraints weight = 29610.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.080284 restraints weight = 27675.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.080562 restraints weight = 22864.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.080506 restraints weight = 22243.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.080560 restraints weight = 21903.570| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9194 Z= 0.132 Angle : 0.616 12.122 12402 Z= 0.305 Chirality : 0.040 0.170 1379 Planarity : 0.004 0.045 1626 Dihedral : 4.379 28.714 1214 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.51 % Allowed : 12.88 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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: 1.66 (0.25), residues: 1133 helix: 1.87 (0.19), residues: 706 sheet: -0.73 (0.71), residues: 49 loop : -0.03 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1115 TYR 0.022 0.001 TYR A 256 PHE 0.030 0.002 PHE A1318 TRP 0.012 0.001 TRP A1021 HIS 0.003 0.001 HIS A 454 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 9193) covalent geometry : angle 0.61463 (12400) SS BOND : bond 0.00036 ( 1) SS BOND : angle 2.70355 ( 2) hydrogen bonds : bond 0.04333 ( 555) hydrogen bonds : angle 4.31277 ( 1617) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 690 ARG cc_start: 0.8558 (ttt180) cc_final: 0.8298 (ttt180) REVERT: A 715 TYR cc_start: 0.7885 (OUTLIER) cc_final: 0.7565 (t80) REVERT: A 1234 ASP cc_start: 0.8482 (t70) cc_final: 0.7136 (t0) REVERT: A 1238 MET cc_start: 0.6058 (mtt) cc_final: 0.4891 (ptt) REVERT: A 1269 MET cc_start: 0.6054 (mmm) cc_final: 0.5521 (mmm) outliers start: 15 outliers final: 9 residues processed: 82 average time/residue: 0.0978 time to fit residues: 11.6139 Evaluate side-chains 74 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 715 TYR Chi-restraints excluded: chain A residue 737 PHE Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 852 HIS Chi-restraints excluded: chain A residue 861 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 83 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 30 optimal weight: 0.0970 chunk 26 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.115394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.079506 restraints weight = 28260.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.079566 restraints weight = 23259.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.079800 restraints weight = 18003.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.079686 restraints weight = 20686.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.080081 restraints weight = 16900.881| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9194 Z= 0.131 Angle : 0.655 13.104 12402 Z= 0.325 Chirality : 0.041 0.268 1379 Planarity : 0.004 0.050 1626 Dihedral : 4.399 31.269 1214 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.51 % Allowed : 12.98 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.60 (0.25), residues: 1133 helix: 1.80 (0.20), residues: 706 sheet: -0.66 (0.71), residues: 49 loop : -0.01 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 887 TYR 0.020 0.001 TYR A 256 PHE 0.034 0.002 PHE A1015 TRP 0.010 0.001 TRP A1021 HIS 0.003 0.001 HIS A 454 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9193) covalent geometry : angle 0.65449 (12400) SS BOND : bond 0.00197 ( 1) SS BOND : angle 2.01472 ( 2) hydrogen bonds : bond 0.04258 ( 555) hydrogen bonds : angle 4.32554 ( 1617) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 690 ARG cc_start: 0.8349 (ttt180) cc_final: 0.8086 (ttt180) REVERT: A 715 TYR cc_start: 0.7796 (OUTLIER) cc_final: 0.7455 (t80) REVERT: A 1005 MET cc_start: 0.6953 (mtt) cc_final: 0.6403 (ttm) REVERT: A 1031 ARG cc_start: 0.9142 (ptp-110) cc_final: 0.8701 (ptp-170) REVERT: A 1036 MET cc_start: 0.7645 (ptt) cc_final: 0.6708 (ppp) REVERT: A 1234 ASP cc_start: 0.8323 (t70) cc_final: 0.6853 (t0) REVERT: A 1238 MET cc_start: 0.5854 (mtt) cc_final: 0.4871 (ptt) REVERT: A 1269 MET cc_start: 0.5809 (mmm) cc_final: 0.5255 (mmm) outliers start: 15 outliers final: 12 residues processed: 81 average time/residue: 0.0955 time to fit residues: 11.3432 Evaluate side-chains 81 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 715 TYR Chi-restraints excluded: chain A residue 737 PHE Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 852 HIS Chi-restraints excluded: chain A residue 861 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 25 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 92 optimal weight: 0.0370 chunk 83 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- 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 = 0.4039 r_free = 0.4039 target = 0.115782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.077513 restraints weight = 28311.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.079654 restraints weight = 21473.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.079826 restraints weight = 16625.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.080387 restraints weight = 14197.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.080602 restraints weight = 13788.262| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9194 Z= 0.133 Angle : 0.671 13.278 12402 Z= 0.335 Chirality : 0.040 0.278 1379 Planarity : 0.004 0.054 1626 Dihedral : 4.368 32.517 1214 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.61 % Allowed : 13.78 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.59 (0.26), residues: 1133 helix: 1.76 (0.20), residues: 708 sheet: -0.59 (0.72), residues: 49 loop : 0.03 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 887 TYR 0.018 0.001 TYR A 256 PHE 0.034 0.001 PHE A1318 TRP 0.011 0.001 TRP A1021 HIS 0.003 0.001 HIS A 454 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9193) covalent geometry : angle 0.67083 (12400) SS BOND : bond 0.00257 ( 1) SS BOND : angle 1.67283 ( 2) hydrogen bonds : bond 0.04279 ( 555) hydrogen bonds : angle 4.38667 ( 1617) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 600 ASP cc_start: 0.7478 (OUTLIER) cc_final: 0.6731 (m-30) REVERT: A 690 ARG cc_start: 0.8371 (ttt180) cc_final: 0.8118 (ttt180) REVERT: A 715 TYR cc_start: 0.7736 (OUTLIER) cc_final: 0.7457 (t80) REVERT: A 1005 MET cc_start: 0.7131 (mtt) cc_final: 0.5869 (ttm) REVERT: A 1008 MET cc_start: 0.8788 (mmp) cc_final: 0.8569 (mmt) REVERT: A 1031 ARG cc_start: 0.9297 (ptp-110) cc_final: 0.8806 (ptp-170) REVERT: A 1036 MET cc_start: 0.7891 (ptt) cc_final: 0.6971 (ppp) REVERT: A 1234 ASP cc_start: 0.8365 (t70) cc_final: 0.7128 (t0) REVERT: A 1238 MET cc_start: 0.5975 (mtt) cc_final: 0.4919 (ptt) outliers start: 16 outliers final: 13 residues processed: 77 average time/residue: 0.0970 time to fit residues: 10.8828 Evaluate side-chains 79 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 715 TYR Chi-restraints excluded: chain A residue 737 PHE Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 852 HIS Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 1251 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 4 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 0.3980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 936 ASN ** 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 = 0.4005 r_free = 0.4005 target = 0.113717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.076850 restraints weight = 28280.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.077029 restraints weight = 25419.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.076796 restraints weight = 22654.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.076942 restraints weight = 22023.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.077311 restraints weight = 18519.665| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 9194 Z= 0.198 Angle : 0.749 18.841 12402 Z= 0.372 Chirality : 0.043 0.269 1379 Planarity : 0.005 0.051 1626 Dihedral : 4.515 31.387 1214 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.51 % Allowed : 13.98 % Favored : 84.51 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.38 (0.25), residues: 1133 helix: 1.62 (0.20), residues: 706 sheet: -0.74 (0.70), residues: 49 loop : -0.10 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 422 TYR 0.024 0.001 TYR A 256 PHE 0.044 0.002 PHE A1318 TRP 0.011 0.001 TRP A1021 HIS 0.005 0.001 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 9193) covalent geometry : angle 0.74819 (12400) SS BOND : bond 0.00287 ( 1) SS BOND : angle 2.15741 ( 2) hydrogen bonds : bond 0.04914 ( 555) hydrogen bonds : angle 4.55110 ( 1617) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 600 ASP cc_start: 0.7704 (OUTLIER) cc_final: 0.6882 (m-30) REVERT: A 690 ARG cc_start: 0.8438 (ttt180) cc_final: 0.8175 (ttt180) REVERT: A 715 TYR cc_start: 0.7791 (OUTLIER) cc_final: 0.7533 (t80) REVERT: A 1005 MET cc_start: 0.7080 (mtt) cc_final: 0.6171 (ttm) REVERT: A 1008 MET cc_start: 0.8656 (mmp) cc_final: 0.8431 (mmt) REVERT: A 1031 ARG cc_start: 0.9100 (ptp-110) cc_final: 0.8632 (ptp-170) REVERT: A 1036 MET cc_start: 0.7692 (ptt) cc_final: 0.6740 (ppp) REVERT: A 1226 MET cc_start: 0.4552 (mmt) cc_final: 0.4170 (mmt) REVERT: A 1234 ASP cc_start: 0.8276 (t70) cc_final: 0.6948 (t0) REVERT: A 1238 MET cc_start: 0.5905 (mtt) cc_final: 0.4851 (ptt) outliers start: 15 outliers final: 12 residues processed: 76 average time/residue: 0.0998 time to fit residues: 10.6304 Evaluate side-chains 78 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 715 TYR Chi-restraints excluded: chain A residue 737 PHE Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 852 HIS Chi-restraints excluded: chain A residue 861 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 90 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 16 optimal weight: 0.3980 chunk 12 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 1 optimal weight: 0.4980 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 = 0.4016 r_free = 0.4016 target = 0.114292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.075684 restraints weight = 28145.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.077178 restraints weight = 22457.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.077367 restraints weight = 19767.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.077851 restraints weight = 16259.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.078102 restraints weight = 16635.004| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9194 Z= 0.164 Angle : 0.732 17.549 12402 Z= 0.357 Chirality : 0.042 0.275 1379 Planarity : 0.004 0.052 1626 Dihedral : 4.465 30.209 1214 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.61 % Allowed : 14.08 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.38 (0.25), residues: 1133 helix: 1.61 (0.20), residues: 701 sheet: -0.74 (0.70), residues: 49 loop : -0.05 (0.33), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1115 TYR 0.022 0.001 TYR A 256 PHE 0.043 0.002 PHE A1318 TRP 0.012 0.001 TRP A1021 HIS 0.004 0.001 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 9193) covalent geometry : angle 0.73127 (12400) SS BOND : bond 0.00217 ( 1) SS BOND : angle 2.03850 ( 2) hydrogen bonds : bond 0.04648 ( 555) hydrogen bonds : angle 4.51203 ( 1617) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2007.89 seconds wall clock time: 35 minutes 25.20 seconds (2125.20 seconds total)