Starting phenix.real_space_refine on Mon Dec 30 07:09:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b9j_15933/12_2024/8b9j_15933.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b9j_15933/12_2024/8b9j_15933.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8b9j_15933/12_2024/8b9j_15933.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b9j_15933/12_2024/8b9j_15933.map" model { file = "/net/cci-nas-00/data/ceres_data/8b9j_15933/12_2024/8b9j_15933.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b9j_15933/12_2024/8b9j_15933.cif" } resolution = 3.45 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= 0.001 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6846 atoms to isotropic. 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: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 2 5.49 5 Mg 1 5.21 5 S 46 5.16 5 C 4362 2.51 5 N 1186 2.21 5 O 1277 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6879 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6846 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 864, 6843 Classifications: {'peptide': 864} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 821} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 864, 6843 Classifications: {'peptide': 864} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 821} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 6967 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.74, per 1000 atoms: 1.13 Number of scatterers: 6879 At special positions: 0 Unit cell: (73.158, 95.352, 101.928, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 46 16.00 P 2 15.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1277 8.00 N 1186 7.00 C 4362 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 1.6 seconds 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1650 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 4 sheets defined 52.3% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 268 through 283 Processing helix chain 'A' and resid 352 through 371 removed outlier: 3.510A pdb=" N LEU A 356 " --> pdb=" O SER A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 382 Processing helix chain 'A' and resid 384 through 400 removed outlier: 3.970A pdb=" N ALA A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET A 389 " --> pdb=" O PRO A 385 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N SER A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N GLU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 428 Processing helix chain 'A' and resid 430 through 433 Processing helix chain 'A' and resid 442 through 457 Processing helix chain 'A' and resid 487 through 494 Processing helix chain 'A' and resid 508 through 512 removed outlier: 4.042A pdb=" N GLU A 511 " --> pdb=" O GLU A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 530 Processing helix chain 'A' and resid 544 through 551 Processing helix chain 'A' and resid 570 through 579 Processing helix chain 'A' and resid 583 through 600 removed outlier: 4.835A pdb=" N GLU A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N GLU A 597 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN A 598 " --> pdb=" O GLU A 594 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU A 600 " --> pdb=" O GLU A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 630 Processing helix chain 'A' and resid 636 through 651 Processing helix chain 'A' and resid 662 through 676 Processing helix chain 'A' and resid 695 through 704 removed outlier: 3.807A pdb=" N GLN A 699 " --> pdb=" O PRO A 695 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS A 701 " --> pdb=" O ASP A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 721 removed outlier: 3.877A pdb=" N GLU A 721 " --> pdb=" O ASN A 718 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 718 through 721' Processing helix chain 'A' and resid 758 through 768 Processing helix chain 'A' and resid 782 through 789 Processing helix chain 'A' and resid 795 through 800 removed outlier: 3.974A pdb=" N THR A 800 " --> pdb=" O MET A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 812 Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 829 through 842 Processing helix chain 'A' and resid 865 through 879 Processing helix chain 'A' and resid 880 through 892 Processing helix chain 'A' and resid 909 through 914 removed outlier: 3.715A pdb=" N LEU A 914 " --> pdb=" O HIS A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 919 removed outlier: 3.637A pdb=" N CYS A 919 " --> pdb=" O GLY A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 938 Processing helix chain 'A' and resid 939 through 950 Processing helix chain 'A' and resid 953 through 973 Processing helix chain 'A' and resid 977 through 982 removed outlier: 3.709A pdb=" N CYS A 980 " --> pdb=" O PRO A 977 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE A 982 " --> pdb=" O GLU A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1008 Processing helix chain 'A' and resid 1024 through 1026 No H-bonds generated for 'chain 'A' and resid 1024 through 1026' Processing helix chain 'A' and resid 1070 through 1077 Processing helix chain 'A' and resid 1101 through 1125 Proline residue: A1113 - end of helix Processing helix chain 'A' and resid 1126 through 1129 removed outlier: 4.006A pdb=" N ILE A1129 " --> pdb=" O PRO A1126 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1126 through 1129' Processing helix chain 'A' and resid 1133 through 1147 Processing helix chain 'A' and resid 1148 through 1153 removed outlier: 4.416A pdb=" N GLY A1152 " --> pdb=" O LYS A1149 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 263 through 264 removed outlier: 3.722A pdb=" N TYR A 263 " --> pdb=" O ASN A1097 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP A1099 " --> pdb=" O TYR A 263 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 472 through 474 removed outlier: 6.744A pdb=" N GLY A 466 " --> pdb=" O PHE A 484 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N THR A 486 " --> pdb=" O GLY A 466 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N SER A 468 " --> pdb=" O THR A 486 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE A 436 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N CYS A 485 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N VAL A 438 " --> pdb=" O CYS A 485 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ASN A 435 " --> pdb=" O HIS A 503 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ILE A 505 " --> pdb=" O ASN A 435 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TYR A 437 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE A 504 " --> pdb=" O ILE A 536 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N MET A 538 " --> pdb=" O ILE A 504 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL A 506 " --> pdb=" O MET A 538 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N LEU A 557 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE A 404 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL A 559 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ARG A 406 " --> pdb=" O VAL A 559 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 566 through 569 removed outlier: 6.057A pdb=" N GLN A 567 " --> pdb=" O CYS A 777 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N THR A 779 " --> pdb=" O GLN A 567 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N PHE A 569 " --> pdb=" O THR A 779 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU A 657 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE A 656 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N SER A 716 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N VAL A 658 " --> pdb=" O SER A 716 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 737 through 740 removed outlier: 8.295A pdb=" N CYS A1063 " --> pdb=" O ALA A1028 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LEU A1030 " --> pdb=" O CYS A1063 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LYS A1020 " --> pdb=" O LYS A1016 " (cutoff:3.500A) 321 hydrogen bonds defined for protein. 927 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: 2.36 Time building geometry restraints manager: 2.31 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: 1693 1.33 - 1.45: 1230 1.45 - 1.57: 4007 1.57 - 1.69: 4 1.69 - 1.82: 74 Bond restraints: 7008 Sorted by residual: bond pdb=" F3 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.685 1.784 -0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" F1 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.684 1.783 -0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" F2 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.685 1.783 -0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" F4 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.686 1.783 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" N VAL A 772 " pdb=" CA VAL A 772 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.08e+01 ... (remaining 7003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.24: 9492 14.24 - 28.49: 4 28.49 - 42.73: 0 42.73 - 56.97: 0 56.97 - 71.21: 2 Bond angle restraints: 9498 Sorted by residual: angle pdb=" F1 ALF A1202 " pdb="AL ALF A1202 " pdb=" F2 ALF A1202 " ideal model delta sigma weight residual 108.68 179.89 -71.21 3.00e+00 1.11e-01 5.63e+02 angle pdb=" F3 ALF A1202 " pdb="AL ALF A1202 " pdb=" F4 ALF A1202 " ideal model delta sigma weight residual 109.63 179.36 -69.73 3.00e+00 1.11e-01 5.40e+02 angle pdb=" CA PRO A 653 " pdb=" N PRO A 653 " pdb=" CD PRO A 653 " ideal model delta sigma weight residual 112.00 99.57 12.43 1.40e+00 5.10e-01 7.88e+01 angle pdb=" C GLN A 567 " pdb=" N GLN A 568 " pdb=" CA GLN A 568 " ideal model delta sigma weight residual 123.05 110.76 12.29 1.40e+00 5.10e-01 7.70e+01 angle pdb=" F2 ALF A1202 " pdb="AL ALF A1202 " pdb=" F4 ALF A1202 " ideal model delta sigma weight residual 110.21 90.00 20.21 3.00e+00 1.11e-01 4.54e+01 ... (remaining 9493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 3638 17.69 - 35.38: 493 35.38 - 53.07: 134 53.07 - 70.76: 26 70.76 - 88.45: 6 Dihedral angle restraints: 4297 sinusoidal: 1766 harmonic: 2531 Sorted by residual: dihedral pdb=" CD ARG A 773 " pdb=" NE ARG A 773 " pdb=" CZ ARG A 773 " pdb=" NH1 ARG A 773 " ideal model delta sinusoidal sigma weight residual 0.00 60.89 -60.89 1 1.00e+01 1.00e-02 4.93e+01 dihedral pdb=" CA GLU A 842 " pdb=" C GLU A 842 " pdb=" N MET A 843 " pdb=" CA MET A 843 " ideal model delta harmonic sigma weight residual 180.00 -154.16 -25.84 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CD ARG A 562 " pdb=" NE ARG A 562 " pdb=" CZ ARG A 562 " pdb=" NH1 ARG A 562 " ideal model delta sinusoidal sigma weight residual 0.00 33.69 -33.69 1 1.00e+01 1.00e-02 1.61e+01 ... (remaining 4294 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 891 0.056 - 0.112: 169 0.112 - 0.168: 25 0.168 - 0.223: 3 0.223 - 0.279: 4 Chirality restraints: 1092 Sorted by residual: chirality pdb=" CA ARG A 773 " pdb=" N ARG A 773 " pdb=" C ARG A 773 " pdb=" CB ARG A 773 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA GLN A 567 " pdb=" N GLN A 567 " pdb=" C GLN A 567 " pdb=" CB GLN A 567 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA PHE A 564 " pdb=" N PHE A 564 " pdb=" C PHE A 564 " pdb=" CB PHE A 564 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 1089 not shown) Planarity restraints: 1219 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 773 " -0.962 9.50e-02 1.11e+02 4.31e-01 1.13e+02 pdb=" NE ARG A 773 " 0.057 2.00e-02 2.50e+03 pdb=" CZ ARG A 773 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 773 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 773 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 562 " 0.598 9.50e-02 1.11e+02 2.68e-01 4.39e+01 pdb=" NE ARG A 562 " -0.036 2.00e-02 2.50e+03 pdb=" CZ ARG A 562 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A 562 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 562 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 652 " 0.071 5.00e-02 4.00e+02 9.97e-02 1.59e+01 pdb=" N PRO A 653 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO A 653 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 653 " 0.056 5.00e-02 4.00e+02 ... (remaining 1216 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 65 2.60 - 3.17: 5955 3.17 - 3.75: 10797 3.75 - 4.32: 14237 4.32 - 4.90: 23895 Nonbonded interactions: 54949 Sorted by model distance: nonbonded pdb=" O ILE A 724 " pdb="MG MG A1203 " model vdw 2.019 2.170 nonbonded pdb=" OG1 THR A 676 " pdb=" O PHE A 679 " model vdw 2.153 3.040 nonbonded pdb=" O3B ADP A1201 " pdb=" F3 ALF A1202 " model vdw 2.193 2.990 nonbonded pdb=" NZ LYS A 413 " pdb=" F4 ALF A1202 " model vdw 2.196 3.070 nonbonded pdb=" OG SER A 448 " pdb=" N6 ADP A1201 " model vdw 2.225 3.120 ... (remaining 54944 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=0.50 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 24.250 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 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 0.135 7008 Z= 0.329 Angle : 1.365 71.213 9498 Z= 0.578 Chirality : 0.048 0.279 1092 Planarity : 0.016 0.431 1219 Dihedral : 17.470 88.445 2647 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.70 % Allowed : 7.24 % Favored : 92.06 % Rotamer: Outliers : 1.18 % Allowed : 24.74 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.29), residues: 857 helix: 0.70 (0.26), residues: 400 sheet: -1.05 (0.50), residues: 106 loop : -1.18 (0.36), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 949 HIS 0.003 0.001 HIS A 941 PHE 0.031 0.002 PHE A 672 TYR 0.009 0.001 TYR A 550 ARG 0.013 0.001 ARG A 938 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 679 PHE cc_start: 0.6036 (m-80) cc_final: 0.5590 (m-10) outliers start: 8 outliers final: 4 residues processed: 74 average time/residue: 0.2090 time to fit residues: 21.0054 Evaluate side-chains 48 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 902 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 0.0040 chunk 65 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 GLN ** A 910 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 ASN A1037 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 7008 Z= 0.211 Angle : 0.711 7.967 9498 Z= 0.353 Chirality : 0.044 0.147 1092 Planarity : 0.005 0.057 1219 Dihedral : 5.956 52.309 955 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.06 % Favored : 91.59 % Rotamer: Outliers : 2.09 % Allowed : 24.35 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.07 (0.30), residues: 857 helix: 1.32 (0.26), residues: 396 sheet: -0.87 (0.54), residues: 100 loop : -1.10 (0.35), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 949 HIS 0.005 0.001 HIS A 984 PHE 0.017 0.001 PHE A 518 TYR 0.014 0.001 TYR A1009 ARG 0.008 0.001 ARG A 590 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.915 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 59 average time/residue: 0.1409 time to fit residues: 12.9009 Evaluate side-chains 46 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 762 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7008 Z= 0.200 Angle : 0.664 10.652 9498 Z= 0.327 Chirality : 0.043 0.157 1092 Planarity : 0.005 0.045 1219 Dihedral : 4.983 41.325 946 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.24 % Favored : 92.41 % Rotamer: Outliers : 1.83 % Allowed : 23.04 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.34 (0.30), residues: 857 helix: 1.46 (0.26), residues: 403 sheet: -0.71 (0.52), residues: 106 loop : -0.92 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 663 HIS 0.004 0.001 HIS A 984 PHE 0.013 0.001 PHE A 518 TYR 0.027 0.001 TYR A1009 ARG 0.005 0.000 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.788 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 52 average time/residue: 0.1360 time to fit residues: 11.2813 Evaluate side-chains 46 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 919 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7008 Z= 0.184 Angle : 0.641 10.713 9498 Z= 0.315 Chirality : 0.043 0.267 1092 Planarity : 0.004 0.045 1219 Dihedral : 4.905 41.222 946 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.24 % Favored : 92.41 % Rotamer: Outliers : 2.36 % Allowed : 22.25 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.30), residues: 857 helix: 1.59 (0.26), residues: 403 sheet: -0.41 (0.54), residues: 98 loop : -0.94 (0.36), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 949 HIS 0.004 0.001 HIS A 984 PHE 0.008 0.001 PHE A 518 TYR 0.008 0.001 TYR A 619 ARG 0.003 0.000 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.777 Fit side-chains revert: symmetry clash REVERT: A 965 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.7245 (mp10) outliers start: 16 outliers final: 7 residues processed: 55 average time/residue: 0.1675 time to fit residues: 13.8053 Evaluate side-chains 46 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 965 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7008 Z= 0.295 Angle : 0.690 10.193 9498 Z= 0.336 Chirality : 0.045 0.231 1092 Planarity : 0.004 0.044 1219 Dihedral : 5.051 40.426 946 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.24 % Favored : 92.41 % Rotamer: Outliers : 2.62 % Allowed : 21.99 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.30), residues: 857 helix: 1.57 (0.26), residues: 404 sheet: -0.51 (0.56), residues: 96 loop : -1.05 (0.36), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 932 HIS 0.004 0.001 HIS A 984 PHE 0.014 0.001 PHE A 518 TYR 0.010 0.001 TYR A 619 ARG 0.005 0.000 ARG A 844 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 35 time to evaluate : 0.861 Fit side-chains revert: symmetry clash REVERT: A 965 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.7323 (mt0) outliers start: 18 outliers final: 8 residues processed: 50 average time/residue: 0.1529 time to fit residues: 12.0459 Evaluate side-chains 43 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 1006 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 83 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 38 optimal weight: 0.0770 chunk 6 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 80 optimal weight: 0.1980 overall best weight: 1.1540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7008 Z= 0.198 Angle : 0.649 10.180 9498 Z= 0.315 Chirality : 0.043 0.218 1092 Planarity : 0.004 0.044 1219 Dihedral : 4.940 39.138 946 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.89 % Favored : 92.76 % Rotamer: Outliers : 1.70 % Allowed : 22.91 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.30), residues: 857 helix: 1.65 (0.26), residues: 404 sheet: -0.46 (0.55), residues: 98 loop : -1.02 (0.36), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 663 HIS 0.004 0.001 HIS A 984 PHE 0.011 0.001 PHE A 518 TYR 0.012 0.001 TYR A1009 ARG 0.003 0.000 ARG A 844 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.797 Fit side-chains revert: symmetry clash REVERT: A 965 GLN cc_start: 0.7542 (OUTLIER) cc_final: 0.7270 (mt0) outliers start: 11 outliers final: 10 residues processed: 44 average time/residue: 0.1511 time to fit residues: 10.4967 Evaluate side-chains 45 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 1006 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 3.9990 chunk 47 optimal weight: 0.4980 chunk 60 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 38 optimal weight: 0.0070 chunk 33 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 overall best weight: 1.2602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7008 Z= 0.206 Angle : 0.655 9.981 9498 Z= 0.315 Chirality : 0.043 0.209 1092 Planarity : 0.004 0.043 1219 Dihedral : 4.905 39.799 946 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.13 % Favored : 92.52 % Rotamer: Outliers : 1.70 % Allowed : 22.91 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.51 (0.30), residues: 857 helix: 1.69 (0.26), residues: 404 sheet: -0.42 (0.55), residues: 98 loop : -1.02 (0.36), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 932 HIS 0.005 0.001 HIS A 984 PHE 0.013 0.001 PHE A 518 TYR 0.011 0.001 TYR A1009 ARG 0.003 0.000 ARG A 768 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.800 Fit side-chains revert: symmetry clash REVERT: A 965 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.7352 (mt0) outliers start: 11 outliers final: 8 residues processed: 46 average time/residue: 0.1468 time to fit residues: 10.6837 Evaluate side-chains 44 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 1006 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 75 optimal weight: 0.0470 chunk 79 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 overall best weight: 2.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7008 Z= 0.300 Angle : 0.705 9.820 9498 Z= 0.340 Chirality : 0.045 0.191 1092 Planarity : 0.004 0.042 1219 Dihedral : 5.080 39.170 946 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.24 % Favored : 92.41 % Rotamer: Outliers : 2.23 % Allowed : 23.04 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.30), residues: 857 helix: 1.50 (0.26), residues: 404 sheet: -0.57 (0.56), residues: 96 loop : -1.04 (0.36), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 932 HIS 0.006 0.001 HIS A 984 PHE 0.014 0.001 PHE A 518 TYR 0.013 0.001 TYR A 619 ARG 0.003 0.000 ARG A 773 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 33 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: A 965 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7408 (mt0) outliers start: 15 outliers final: 10 residues processed: 46 average time/residue: 0.1537 time to fit residues: 11.2946 Evaluate side-chains 43 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 919 CYS Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 1006 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 69 optimal weight: 0.0040 chunk 73 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 overall best weight: 2.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7008 Z= 0.275 Angle : 0.689 9.710 9498 Z= 0.331 Chirality : 0.044 0.192 1092 Planarity : 0.004 0.042 1219 Dihedral : 5.060 39.114 946 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.13 % Favored : 92.52 % Rotamer: Outliers : 1.83 % Allowed : 22.91 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.31 (0.30), residues: 857 helix: 1.43 (0.26), residues: 405 sheet: -0.69 (0.57), residues: 95 loop : -0.95 (0.36), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 932 HIS 0.005 0.001 HIS A 984 PHE 0.021 0.001 PHE A 946 TYR 0.012 0.001 TYR A 619 ARG 0.003 0.000 ARG A 773 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 33 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: A 965 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.7406 (mt0) outliers start: 12 outliers final: 10 residues processed: 44 average time/residue: 0.1474 time to fit residues: 10.1989 Evaluate side-chains 44 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 1006 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 52 optimal weight: 0.0980 chunk 41 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7008 Z= 0.211 Angle : 0.671 9.794 9498 Z= 0.321 Chirality : 0.043 0.192 1092 Planarity : 0.004 0.045 1219 Dihedral : 4.966 39.239 946 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.13 % Favored : 92.52 % Rotamer: Outliers : 1.57 % Allowed : 23.04 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.39 (0.30), residues: 857 helix: 1.52 (0.26), residues: 404 sheet: -0.59 (0.57), residues: 95 loop : -0.95 (0.36), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 932 HIS 0.005 0.001 HIS A 984 PHE 0.015 0.001 PHE A 518 TYR 0.013 0.001 TYR A1009 ARG 0.003 0.000 ARG A 768 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.658 Fit side-chains revert: symmetry clash REVERT: A 965 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.7391 (mt0) outliers start: 10 outliers final: 8 residues processed: 42 average time/residue: 0.1519 time to fit residues: 10.0129 Evaluate side-chains 42 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 1006 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 28 optimal weight: 0.0670 chunk 70 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 3 optimal weight: 0.0020 chunk 49 optimal weight: 0.5980 overall best weight: 0.5126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 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 = 0.3610 r_free = 0.3610 target = 0.077323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.055600 restraints weight = 44793.741| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 6.72 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3092 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7008 Z= 0.163 Angle : 0.644 9.751 9498 Z= 0.309 Chirality : 0.043 0.199 1092 Planarity : 0.004 0.044 1219 Dihedral : 4.811 39.737 946 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.36 % Favored : 92.29 % Rotamer: Outliers : 1.70 % Allowed : 23.04 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.64 (0.30), residues: 857 helix: 1.75 (0.26), residues: 399 sheet: -0.36 (0.57), residues: 95 loop : -0.85 (0.36), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 932 HIS 0.005 0.001 HIS A 984 PHE 0.012 0.001 PHE A 946 TYR 0.014 0.001 TYR A1009 ARG 0.004 0.000 ARG A 768 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1545.99 seconds wall clock time: 29 minutes 3.60 seconds (1743.60 seconds total)