Starting phenix.real_space_refine on Tue Feb 11 14:25:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q76_18205/02_2025/8q76_18205.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q76_18205/02_2025/8q76_18205.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q76_18205/02_2025/8q76_18205.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q76_18205/02_2025/8q76_18205.map" model { file = "/net/cci-nas-00/data/ceres_data/8q76_18205/02_2025/8q76_18205.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q76_18205/02_2025/8q76_18205.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.047 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: 7 Type Number sf(0) Gaussians Mg 1 5.21 5 S 34 5.16 5 Be 1 3.05 5 C 3760 2.51 5 N 975 2.21 5 O 1095 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5869 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 774, 5868 Classifications: {'peptide': 774} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 738} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.40, per 1000 atoms: 0.75 Number of scatterers: 5869 At special positions: 0 Unit cell: (81.536, 83.2, 136.448, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 34 16.00 Mg 1 11.99 F 3 9.00 O 1095 8.00 N 975 7.00 C 3760 6.00 Be 1 4.00 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: 1.72 Conformation dependent library (CDL) restraints added in 882.8 milliseconds 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1430 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 7 sheets defined 51.9% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 197 through 210 removed outlier: 3.738A pdb=" N ILE A 201 " --> pdb=" O SER A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 246 removed outlier: 4.356A pdb=" N LEU A 240 " --> pdb=" O GLY A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 296 removed outlier: 4.252A pdb=" N ALA A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 305 through 309 removed outlier: 3.795A pdb=" N TYR A 309 " --> pdb=" O TRP A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 332 Proline residue: A 328 - end of helix Processing helix chain 'A' and resid 334 through 344 Processing helix chain 'A' and resid 354 through 377 removed outlier: 5.943A pdb=" N THR A 360 " --> pdb=" O VAL A 356 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ASN A 361 " --> pdb=" O ALA A 357 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 362 " --> pdb=" O LEU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 407 removed outlier: 4.146A pdb=" N SER A 389 " --> pdb=" O PHE A 385 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 removed outlier: 3.703A pdb=" N THR A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA A 421 " --> pdb=" O LEU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 512 through 515 Processing helix chain 'A' and resid 516 through 530 Processing helix chain 'A' and resid 537 through 545 Processing helix chain 'A' and resid 546 through 567 Processing helix chain 'A' and resid 571 through 575 Processing helix chain 'A' and resid 580 through 596 removed outlier: 3.672A pdb=" N VAL A 592 " --> pdb=" O PHE A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 620 removed outlier: 5.654A pdb=" N VAL A 611 " --> pdb=" O THR A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 632 removed outlier: 3.858A pdb=" N LEU A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 676 Processing helix chain 'A' and resid 680 through 697 Processing helix chain 'A' and resid 731 through 738 removed outlier: 3.637A pdb=" N PHE A 738 " --> pdb=" O LEU A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 748 Processing helix chain 'A' and resid 782 through 793 Processing helix chain 'A' and resid 804 through 816 Processing helix chain 'A' and resid 825 through 839 Processing helix chain 'A' and resid 849 through 851 No H-bonds generated for 'chain 'A' and resid 849 through 851' Processing helix chain 'A' and resid 852 through 859 Processing helix chain 'A' and resid 869 through 876 Processing helix chain 'A' and resid 885 through 900 removed outlier: 3.870A pdb=" N ILE A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 922 removed outlier: 4.266A pdb=" N TYR A 912 " --> pdb=" O TRP A 908 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ASN A 913 " --> pdb=" O ALA A 909 " (cutoff:3.500A) Proline residue: A 918 - end of helix Processing helix chain 'A' and resid 934 through 939 removed outlier: 4.002A pdb=" N GLY A 938 " --> pdb=" O PRO A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 948 Processing sheet with id=AA1, first strand: chain 'A' and resid 216 through 220 removed outlier: 3.625A pdb=" N ASP A 220 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR A 225 " --> pdb=" O ASP A 220 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN A 255 " --> pdb=" O GLU A 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 424 through 426 Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 453 removed outlier: 7.460A pdb=" N ILE A 506 " --> pdb=" O ILE A 468 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 472 through 474 Processing sheet with id=AA5, first strand: chain 'A' and resid 621 through 623 removed outlier: 6.165A pdb=" N GLY A 862 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU A 880 " --> pdb=" O GLY A 862 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALA A 864 " --> pdb=" O LEU A 880 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL A 861 " --> pdb=" O VAL A 843 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET A 845 " --> pdb=" O VAL A 861 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA A 637 " --> pdb=" O ALA A 844 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N VAL A 846 " --> pdb=" O ALA A 637 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE A 639 " --> pdb=" O VAL A 846 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE A 638 " --> pdb=" O ILE A 798 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N VAL A 800 " --> pdb=" O ILE A 638 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N PHE A 640 " --> pdb=" O VAL A 800 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N SER A 797 " --> pdb=" O THR A 819 " (cutoff:3.500A) removed outlier: 8.886A pdb=" N PHE A 821 " --> pdb=" O SER A 797 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N MET A 799 " --> pdb=" O PHE A 821 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 652 through 654 Processing sheet with id=AA7, first strand: chain 'A' and resid 707 through 708 291 hydrogen bonds defined for protein. 834 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: 1.88 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1098 1.33 - 1.45: 1356 1.45 - 1.57: 3471 1.57 - 1.69: 1 1.69 - 1.81: 54 Bond restraints: 5980 Sorted by residual: bond pdb=" OD1 BFD A 641 " pdb="BE BFD A 641 " ideal model delta sigma weight residual 1.737 1.533 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" CA ALA A 637 " pdb=" C ALA A 637 " ideal model delta sigma weight residual 1.522 1.458 0.063 1.21e-02 6.83e+03 2.74e+01 bond pdb=" N ILE A 638 " pdb=" CA ILE A 638 " ideal model delta sigma weight residual 1.457 1.400 0.057 1.14e-02 7.69e+03 2.50e+01 bond pdb=" N ALA A 637 " pdb=" CA ALA A 637 " ideal model delta sigma weight residual 1.454 1.411 0.044 1.27e-02 6.20e+03 1.19e+01 bond pdb=" CA ILE A 638 " pdb=" C ILE A 638 " ideal model delta sigma weight residual 1.522 1.483 0.039 1.20e-02 6.94e+03 1.07e+01 ... (remaining 5975 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.93: 8075 3.93 - 7.87: 42 7.87 - 11.80: 5 11.80 - 15.73: 0 15.73 - 19.67: 2 Bond angle restraints: 8124 Sorted by residual: angle pdb=" O BFD A 641 " pdb=" C BFD A 641 " pdb=" N LYS A 642 " ideal model delta sigma weight residual 123.00 103.33 19.67 1.60e+00 3.91e-01 1.51e+02 angle pdb=" CA BFD A 641 " pdb=" C BFD A 641 " pdb=" N LYS A 642 " ideal model delta sigma weight residual 116.20 134.22 -18.02 2.00e+00 2.50e-01 8.12e+01 angle pdb=" C PHE A 640 " pdb=" N BFD A 641 " pdb=" CA BFD A 641 " ideal model delta sigma weight residual 121.70 111.61 10.09 1.80e+00 3.09e-01 3.15e+01 angle pdb=" N GLY A 748 " pdb=" CA GLY A 748 " pdb=" C GLY A 748 " ideal model delta sigma weight residual 113.18 123.41 -10.23 2.37e+00 1.78e-01 1.86e+01 angle pdb=" C LYS A 636 " pdb=" N ALA A 637 " pdb=" CA ALA A 637 " ideal model delta sigma weight residual 122.62 117.18 5.44 1.56e+00 4.11e-01 1.21e+01 ... (remaining 8119 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.92: 3209 15.92 - 31.85: 294 31.85 - 47.77: 72 47.77 - 63.70: 14 63.70 - 79.62: 12 Dihedral angle restraints: 3601 sinusoidal: 1380 harmonic: 2221 Sorted by residual: dihedral pdb=" CA SER A 301 " pdb=" C SER A 301 " pdb=" N PRO A 302 " pdb=" CA PRO A 302 " ideal model delta harmonic sigma weight residual -180.00 -146.83 -33.17 0 5.00e+00 4.00e-02 4.40e+01 dihedral pdb=" CA GLU A 752 " pdb=" C GLU A 752 " pdb=" N THR A 753 " pdb=" CA THR A 753 " ideal model delta harmonic sigma weight residual 180.00 146.90 33.10 0 5.00e+00 4.00e-02 4.38e+01 dihedral pdb=" CA LEU A 910 " pdb=" C LEU A 910 " pdb=" N GLY A 911 " pdb=" CA GLY A 911 " ideal model delta harmonic sigma weight residual 180.00 150.21 29.79 0 5.00e+00 4.00e-02 3.55e+01 ... (remaining 3598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 778 0.059 - 0.118: 171 0.118 - 0.177: 12 0.177 - 0.236: 1 0.236 - 0.295: 1 Chirality restraints: 963 Sorted by residual: chirality pdb=" CA BFD A 641 " pdb=" N BFD A 641 " pdb=" C BFD A 641 " pdb=" CB BFD A 641 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA VAL A 311 " pdb=" N VAL A 311 " pdb=" C VAL A 311 " pdb=" CB VAL A 311 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.90e-01 chirality pdb=" CA PRO A 302 " pdb=" N PRO A 302 " pdb=" C PRO A 302 " pdb=" CB PRO A 302 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.80e-01 ... (remaining 960 not shown) Planarity restraints: 1027 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 640 " 0.019 2.00e-02 2.50e+03 4.03e-02 1.62e+01 pdb=" C PHE A 640 " -0.070 2.00e-02 2.50e+03 pdb=" O PHE A 640 " 0.027 2.00e-02 2.50e+03 pdb=" N BFD A 641 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 236 " -0.041 5.00e-02 4.00e+02 6.27e-02 6.30e+00 pdb=" N PRO A 237 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 237 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 237 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 297 " -0.041 5.00e-02 4.00e+02 6.25e-02 6.26e+00 pdb=" N PRO A 298 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 298 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 298 " -0.035 5.00e-02 4.00e+02 ... (remaining 1024 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.54: 63 2.54 - 3.13: 5041 3.13 - 3.72: 9719 3.72 - 4.31: 12835 4.31 - 4.90: 20738 Nonbonded interactions: 48396 Sorted by model distance: nonbonded pdb=" OD2 BFD A 641 " pdb="MG MG A1001 " model vdw 1.945 2.170 nonbonded pdb=" OD2 ASP A 848 " pdb="MG MG A1001 " model vdw 2.048 2.170 nonbonded pdb=" NH1 ARG A 269 " pdb=" O GLY A 408 " model vdw 2.192 3.120 nonbonded pdb=" NZ LYS A 488 " pdb=" O LYS A 493 " model vdw 2.220 3.120 nonbonded pdb=" O ALA A 267 " pdb=" ND1 HIS A 271 " model vdw 2.275 3.120 ... (remaining 48391 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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 18.450 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 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 0.204 5980 Z= 0.343 Angle : 0.849 19.668 8124 Z= 0.452 Chirality : 0.048 0.295 963 Planarity : 0.007 0.063 1027 Dihedral : 14.275 79.622 2171 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.52 % Allowed : 12.22 % Favored : 87.26 % Rotamer: Outliers : 0.16 % Allowed : 0.16 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.31), residues: 769 helix: 1.22 (0.28), residues: 369 sheet: -2.19 (0.56), residues: 81 loop : -3.10 (0.31), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 935 HIS 0.006 0.001 HIS A 270 PHE 0.013 0.001 PHE A 337 TYR 0.012 0.001 TYR A 338 ARG 0.004 0.001 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 PHE cc_start: 0.9086 (m-10) cc_final: 0.8883 (m-10) REVERT: A 387 GLU cc_start: 0.8275 (mp0) cc_final: 0.8031 (mp0) REVERT: A 403 GLU cc_start: 0.8946 (tp30) cc_final: 0.8649 (tp30) REVERT: A 526 GLU cc_start: 0.8796 (pm20) cc_final: 0.8555 (pm20) REVERT: A 630 GLU cc_start: 0.8610 (mp0) cc_final: 0.8247 (mp0) REVERT: A 647 THR cc_start: 0.7809 (p) cc_final: 0.7269 (p) REVERT: A 659 PHE cc_start: 0.9502 (p90) cc_final: 0.9236 (p90) REVERT: A 881 MET cc_start: 0.9033 (tpp) cc_final: 0.8789 (mmm) REVERT: A 887 ASP cc_start: 0.8728 (m-30) cc_final: 0.8449 (m-30) REVERT: A 915 LEU cc_start: 0.9216 (mt) cc_final: 0.9009 (tp) outliers start: 1 outliers final: 0 residues processed: 111 average time/residue: 0.1781 time to fit residues: 27.0328 Evaluate side-chains 64 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 0.8980 chunk 58 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.126480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.084540 restraints weight = 16993.017| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 4.76 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 5980 Z= 0.238 Angle : 0.754 10.637 8124 Z= 0.382 Chirality : 0.048 0.216 963 Planarity : 0.006 0.050 1027 Dihedral : 5.638 28.422 818 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.39 % Allowed : 12.35 % Favored : 87.26 % Rotamer: Outliers : 2.03 % Allowed : 10.64 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.31), residues: 769 helix: 1.20 (0.28), residues: 374 sheet: -1.71 (0.66), residues: 54 loop : -2.87 (0.31), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 935 HIS 0.002 0.001 HIS A 473 PHE 0.015 0.001 PHE A 337 TYR 0.013 0.001 TYR A 689 ARG 0.004 0.000 ARG A 896 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 361 ASN cc_start: 0.8546 (t0) cc_final: 0.8242 (m-40) REVERT: A 403 GLU cc_start: 0.8938 (tp30) cc_final: 0.8666 (tp30) REVERT: A 659 PHE cc_start: 0.9492 (p90) cc_final: 0.9180 (p90) REVERT: A 887 ASP cc_start: 0.8701 (m-30) cc_final: 0.8389 (m-30) REVERT: A 924 LEU cc_start: 0.9398 (mt) cc_final: 0.9036 (tt) outliers start: 13 outliers final: 7 residues processed: 83 average time/residue: 0.1733 time to fit residues: 19.5859 Evaluate side-chains 72 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 907 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 35 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 27 optimal weight: 0.0970 chunk 52 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.125944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.083844 restraints weight = 17081.641| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 5.06 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 5980 Z= 0.210 Angle : 0.723 10.461 8124 Z= 0.365 Chirality : 0.047 0.220 963 Planarity : 0.005 0.052 1027 Dihedral : 5.535 28.460 818 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.39 % Allowed : 12.22 % Favored : 87.39 % Rotamer: Outliers : 2.66 % Allowed : 12.68 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.31), residues: 769 helix: 1.30 (0.28), residues: 375 sheet: -1.48 (0.65), residues: 66 loop : -2.88 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 935 HIS 0.003 0.001 HIS A 473 PHE 0.012 0.001 PHE A 337 TYR 0.007 0.001 TYR A 570 ARG 0.002 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 361 ASN cc_start: 0.8592 (t0) cc_final: 0.8261 (m-40) REVERT: A 403 GLU cc_start: 0.8938 (tp30) cc_final: 0.8685 (tp30) REVERT: A 659 PHE cc_start: 0.9510 (p90) cc_final: 0.9200 (p90) REVERT: A 887 ASP cc_start: 0.8740 (m-30) cc_final: 0.8370 (m-30) REVERT: A 924 LEU cc_start: 0.9440 (mt) cc_final: 0.9087 (tt) outliers start: 17 outliers final: 11 residues processed: 78 average time/residue: 0.1647 time to fit residues: 17.6102 Evaluate side-chains 72 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 907 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 23 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 chunk 6 optimal weight: 20.0000 chunk 13 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4099 r_free = 0.4099 target = 0.125667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.084484 restraints weight = 17658.536| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 4.88 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 5980 Z= 0.220 Angle : 0.731 11.307 8124 Z= 0.367 Chirality : 0.047 0.216 963 Planarity : 0.005 0.050 1027 Dihedral : 5.460 28.627 818 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.39 % Allowed : 11.96 % Favored : 87.65 % Rotamer: Outliers : 2.19 % Allowed : 14.87 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.32), residues: 769 helix: 1.40 (0.28), residues: 375 sheet: -1.58 (0.66), residues: 59 loop : -2.76 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 935 HIS 0.014 0.001 HIS A 270 PHE 0.012 0.001 PHE A 337 TYR 0.007 0.001 TYR A 570 ARG 0.005 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 MET cc_start: 0.8733 (ttm) cc_final: 0.8139 (mtp) REVERT: A 375 LEU cc_start: 0.9630 (tp) cc_final: 0.9418 (tp) REVERT: A 387 GLU cc_start: 0.8161 (mp0) cc_final: 0.7821 (mp0) REVERT: A 403 GLU cc_start: 0.8966 (tp30) cc_final: 0.8685 (tp30) REVERT: A 630 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8171 (mp0) REVERT: A 659 PHE cc_start: 0.9458 (p90) cc_final: 0.9146 (p90) REVERT: A 750 MET cc_start: 0.9088 (tpt) cc_final: 0.8787 (tpt) REVERT: A 887 ASP cc_start: 0.8739 (m-30) cc_final: 0.8359 (m-30) REVERT: A 924 LEU cc_start: 0.9429 (mt) cc_final: 0.9078 (tt) outliers start: 14 outliers final: 13 residues processed: 75 average time/residue: 0.1676 time to fit residues: 17.0903 Evaluate side-chains 76 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 907 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 76 optimal weight: 0.0470 chunk 38 optimal weight: 0.0470 chunk 28 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 37 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 5 optimal weight: 30.0000 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.126388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.084581 restraints weight = 17330.848| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 4.91 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5980 Z= 0.190 Angle : 0.715 12.092 8124 Z= 0.356 Chirality : 0.046 0.213 963 Planarity : 0.005 0.049 1027 Dihedral : 5.385 28.041 818 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.39 % Allowed : 11.57 % Favored : 88.04 % Rotamer: Outliers : 2.82 % Allowed : 16.12 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.32), residues: 769 helix: 1.53 (0.28), residues: 375 sheet: -1.35 (0.70), residues: 49 loop : -2.71 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 935 HIS 0.003 0.001 HIS A 189 PHE 0.011 0.001 PHE A 337 TYR 0.010 0.001 TYR A 689 ARG 0.002 0.000 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 630 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8157 (mp0) REVERT: A 659 PHE cc_start: 0.9524 (p90) cc_final: 0.9125 (p90) REVERT: A 750 MET cc_start: 0.9160 (tpt) cc_final: 0.8887 (tpt) REVERT: A 881 MET cc_start: 0.9155 (mmm) cc_final: 0.8666 (mmm) REVERT: A 887 ASP cc_start: 0.8751 (m-30) cc_final: 0.8351 (m-30) REVERT: A 924 LEU cc_start: 0.9412 (mt) cc_final: 0.9068 (tt) outliers start: 18 outliers final: 11 residues processed: 86 average time/residue: 0.1626 time to fit residues: 19.0433 Evaluate side-chains 76 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 907 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 67 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 56 optimal weight: 20.0000 chunk 57 optimal weight: 0.2980 chunk 0 optimal weight: 20.0000 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 680 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.125452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.083077 restraints weight = 17165.286| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 5.37 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5980 Z= 0.197 Angle : 0.732 12.410 8124 Z= 0.366 Chirality : 0.047 0.203 963 Planarity : 0.005 0.047 1027 Dihedral : 5.333 28.736 818 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.26 % Allowed : 11.44 % Favored : 88.30 % Rotamer: Outliers : 2.35 % Allowed : 18.78 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.32), residues: 769 helix: 1.64 (0.28), residues: 374 sheet: -1.61 (0.58), residues: 81 loop : -2.83 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 935 HIS 0.004 0.001 HIS A 189 PHE 0.018 0.001 PHE A 562 TYR 0.011 0.001 TYR A 689 ARG 0.002 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 MET cc_start: 0.8587 (ttm) cc_final: 0.8306 (mtp) REVERT: A 630 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8174 (mp0) REVERT: A 659 PHE cc_start: 0.9564 (p90) cc_final: 0.9134 (p90) REVERT: A 750 MET cc_start: 0.9148 (OUTLIER) cc_final: 0.8887 (tpt) REVERT: A 881 MET cc_start: 0.9109 (mmm) cc_final: 0.8672 (mmm) REVERT: A 887 ASP cc_start: 0.8676 (m-30) cc_final: 0.8295 (m-30) REVERT: A 924 LEU cc_start: 0.9401 (mt) cc_final: 0.9065 (tt) outliers start: 15 outliers final: 11 residues processed: 77 average time/residue: 0.1806 time to fit residues: 18.8924 Evaluate side-chains 81 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 907 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 25 optimal weight: 9.9990 chunk 46 optimal weight: 0.8980 chunk 56 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 37 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN A 680 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.121159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.078110 restraints weight = 17423.473| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 4.75 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 5980 Z= 0.417 Angle : 0.826 10.635 8124 Z= 0.424 Chirality : 0.050 0.195 963 Planarity : 0.005 0.044 1027 Dihedral : 5.670 30.615 818 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.87 % Favored : 87.00 % Rotamer: Outliers : 3.44 % Allowed : 17.53 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.31), residues: 769 helix: 1.26 (0.27), residues: 376 sheet: -1.68 (0.62), residues: 66 loop : -2.85 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 935 HIS 0.004 0.001 HIS A 270 PHE 0.018 0.002 PHE A 925 TYR 0.011 0.001 TYR A 789 ARG 0.003 0.001 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 MET cc_start: 0.8718 (ttm) cc_final: 0.8473 (mtp) REVERT: A 319 MET cc_start: 0.8819 (mtm) cc_final: 0.8562 (mtm) REVERT: A 387 GLU cc_start: 0.8293 (mp0) cc_final: 0.8066 (mp0) REVERT: A 630 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8191 (mp0) REVERT: A 659 PHE cc_start: 0.9626 (p90) cc_final: 0.9151 (p90) REVERT: A 750 MET cc_start: 0.9178 (OUTLIER) cc_final: 0.8864 (tpt) REVERT: A 834 LYS cc_start: 0.9577 (mmtm) cc_final: 0.9307 (mmmm) REVERT: A 881 MET cc_start: 0.9136 (mmm) cc_final: 0.8589 (mmm) REVERT: A 887 ASP cc_start: 0.8819 (m-30) cc_final: 0.8401 (m-30) REVERT: A 924 LEU cc_start: 0.9483 (mt) cc_final: 0.9146 (pt) outliers start: 22 outliers final: 16 residues processed: 78 average time/residue: 0.1750 time to fit residues: 18.5017 Evaluate side-chains 78 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 914 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 59 optimal weight: 0.0970 chunk 66 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 7 optimal weight: 40.0000 chunk 28 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 680 HIS 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 = 0.124324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.082373 restraints weight = 17116.500| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 4.74 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5980 Z= 0.202 Angle : 0.784 13.893 8124 Z= 0.386 Chirality : 0.048 0.197 963 Planarity : 0.005 0.046 1027 Dihedral : 5.574 30.363 818 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.44 % Favored : 88.43 % Rotamer: Outliers : 2.35 % Allowed : 19.41 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.31), residues: 769 helix: 1.55 (0.28), residues: 372 sheet: -1.30 (0.63), residues: 64 loop : -2.82 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 935 HIS 0.004 0.001 HIS A 189 PHE 0.011 0.001 PHE A 337 TYR 0.016 0.001 TYR A 689 ARG 0.002 0.000 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 630 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8160 (mp0) REVERT: A 659 PHE cc_start: 0.9594 (p90) cc_final: 0.9179 (p90) REVERT: A 750 MET cc_start: 0.9229 (OUTLIER) cc_final: 0.8952 (tpt) REVERT: A 881 MET cc_start: 0.9118 (mmm) cc_final: 0.8582 (mmm) REVERT: A 887 ASP cc_start: 0.8745 (m-30) cc_final: 0.8323 (m-30) REVERT: A 924 LEU cc_start: 0.9391 (mt) cc_final: 0.9062 (pt) outliers start: 15 outliers final: 12 residues processed: 80 average time/residue: 0.1468 time to fit residues: 16.3976 Evaluate side-chains 77 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 899 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 69 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 25 optimal weight: 8.9990 chunk 73 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 0.0770 chunk 42 optimal weight: 0.6980 chunk 63 optimal weight: 0.2980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 680 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.125096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.082957 restraints weight = 17205.434| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 4.80 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5980 Z= 0.196 Angle : 0.781 13.969 8124 Z= 0.386 Chirality : 0.048 0.190 963 Planarity : 0.005 0.048 1027 Dihedral : 5.466 28.521 818 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.57 % Favored : 88.30 % Rotamer: Outliers : 1.88 % Allowed : 19.72 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.32), residues: 769 helix: 1.57 (0.28), residues: 374 sheet: -1.10 (0.61), residues: 74 loop : -2.88 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 561 HIS 0.003 0.001 HIS A 189 PHE 0.026 0.001 PHE A 562 TYR 0.016 0.001 TYR A 689 ARG 0.002 0.000 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 MET cc_start: 0.8564 (mtm) cc_final: 0.8291 (mtm) REVERT: A 630 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8195 (mp0) REVERT: A 735 MET cc_start: 0.8988 (pmm) cc_final: 0.8677 (pmm) REVERT: A 750 MET cc_start: 0.9239 (OUTLIER) cc_final: 0.8957 (tpt) REVERT: A 887 ASP cc_start: 0.8699 (m-30) cc_final: 0.8310 (m-30) REVERT: A 924 LEU cc_start: 0.9410 (mt) cc_final: 0.9072 (pt) outliers start: 12 outliers final: 10 residues processed: 76 average time/residue: 0.1546 time to fit residues: 16.6322 Evaluate side-chains 78 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 899 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 63 optimal weight: 0.2980 chunk 13 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 7 optimal weight: 40.0000 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 59 optimal weight: 0.0050 chunk 55 optimal weight: 2.9990 chunk 32 optimal weight: 0.2980 chunk 35 optimal weight: 1.9990 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 680 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.125331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.083485 restraints weight = 17209.389| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 5.00 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5980 Z= 0.192 Angle : 0.804 14.439 8124 Z= 0.391 Chirality : 0.048 0.194 963 Planarity : 0.005 0.047 1027 Dihedral : 5.365 28.393 818 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.18 % Favored : 88.69 % Rotamer: Outliers : 1.72 % Allowed : 20.34 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.32), residues: 769 helix: 1.65 (0.28), residues: 374 sheet: -1.04 (0.61), residues: 74 loop : -2.89 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 935 HIS 0.004 0.001 HIS A 189 PHE 0.011 0.001 PHE A 337 TYR 0.016 0.001 TYR A 689 ARG 0.003 0.000 ARG A 882 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.8500 (ttp) cc_final: 0.8221 (mmm) REVERT: A 586 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9055 (mm) REVERT: A 630 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8216 (mp0) REVERT: A 735 MET cc_start: 0.9112 (pmm) cc_final: 0.8852 (pmm) REVERT: A 750 MET cc_start: 0.9238 (OUTLIER) cc_final: 0.9005 (tpt) REVERT: A 887 ASP cc_start: 0.8646 (m-30) cc_final: 0.8285 (m-30) outliers start: 11 outliers final: 9 residues processed: 75 average time/residue: 0.1683 time to fit residues: 18.2557 Evaluate side-chains 77 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 899 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 chunk 14 optimal weight: 0.2980 chunk 51 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 39 optimal weight: 0.2980 chunk 25 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 ASN 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 = 0.124477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.082005 restraints weight = 17342.463| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 5.07 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 5980 Z= 0.229 Angle : 0.814 16.971 8124 Z= 0.395 Chirality : 0.048 0.196 963 Planarity : 0.005 0.047 1027 Dihedral : 5.361 27.779 818 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.31 % Favored : 88.56 % Rotamer: Outliers : 1.88 % Allowed : 20.66 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.32), residues: 769 helix: 1.63 (0.28), residues: 375 sheet: -0.99 (0.61), residues: 74 loop : -2.84 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 935 HIS 0.004 0.001 HIS A 189 PHE 0.012 0.001 PHE A 337 TYR 0.012 0.001 TYR A 689 ARG 0.002 0.000 ARG A 694 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2928.43 seconds wall clock time: 53 minutes 17.37 seconds (3197.37 seconds total)