Starting phenix.real_space_refine on Wed May 14 22:23:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b9l_15935/05_2025/8b9l_15935.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b9l_15935/05_2025/8b9l_15935.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/8b9l_15935/05_2025/8b9l_15935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b9l_15935/05_2025/8b9l_15935.map" model { file = "/net/cci-nas-00/data/ceres_data/8b9l_15935/05_2025/8b9l_15935.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b9l_15935/05_2025/8b9l_15935.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= 0.000 sd= 0.010 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 6819 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: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 4335 2.51 5 N 1179 2.21 5 O 1266 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6826 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6826 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 862, 6823 Classifications: {'peptide': 862} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 818} Chain breaks: 2 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: 862, 6823 Classifications: {'peptide': 862} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 818} Chain breaks: 2 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: 6948 Time building chain proxies: 7.01, per 1000 atoms: 1.03 Number of scatterers: 6826 At special positions: 0 Unit cell: (72.336, 92.886, 101.106, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 46 16.00 O 1266 8.00 N 1179 7.00 C 4335 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 1.5 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: 1648 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 4 sheets defined 53.0% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 268 through 282 removed outlier: 3.894A pdb=" N LEU A 282 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 removed outlier: 4.156A pdb=" N THR A 350 " --> pdb=" O GLU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 371 removed outlier: 3.509A pdb=" N MET A 358 " --> pdb=" O ASP A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 383 removed outlier: 3.782A pdb=" N LYS A 383 " --> pdb=" O GLU A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.902A pdb=" N ALA A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N MET A 389 " --> pdb=" O PRO A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 389' Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 413 through 428 removed outlier: 4.242A pdb=" N ALA A 418 " --> pdb=" O THR A 414 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N GLN A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 433 Processing helix chain 'A' and resid 442 through 457 Processing helix chain 'A' and resid 486 through 494 Processing helix chain 'A' and resid 495 through 497 No H-bonds generated for 'chain 'A' and resid 495 through 497' Processing helix chain 'A' and resid 508 through 512 Processing helix chain 'A' and resid 513 through 530 Processing helix chain 'A' and resid 543 through 550 removed outlier: 3.873A pdb=" N PHE A 547 " --> pdb=" O ASP A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 579 removed outlier: 3.527A pdb=" N ILE A 574 " --> pdb=" O PHE A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 598 Processing helix chain 'A' and resid 610 through 614 Processing helix chain 'A' and resid 620 through 629 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: 3.673A pdb=" N PHE A 703 " --> pdb=" O GLN A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 722 removed outlier: 3.682A pdb=" N GLU A 721 " --> pdb=" O ASN A 718 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N THR A 722 " --> pdb=" O ILE A 719 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 718 through 722' Processing helix chain 'A' and resid 758 through 769 removed outlier: 3.672A pdb=" N ALA A 769 " --> pdb=" O ARG A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 788 Processing helix chain 'A' and resid 795 through 800 removed outlier: 4.054A 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 removed outlier: 3.517A pdb=" N PHE A 820 " --> pdb=" O SER A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 843 removed outlier: 3.801A pdb=" N MET A 843 " --> pdb=" O LEU A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 878 Processing helix chain 'A' and resid 880 through 893 Processing helix chain 'A' and resid 908 through 912 removed outlier: 3.762A pdb=" N LYS A 912 " --> pdb=" O ASN A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 919 removed outlier: 3.633A 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 940 through 947 Processing helix chain 'A' and resid 953 through 974 Processing helix chain 'A' and resid 977 through 982 removed outlier: 3.888A pdb=" N CYS A 980 " --> pdb=" O PRO A 977 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE A 982 " --> pdb=" O GLU A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1008 removed outlier: 4.035A pdb=" N CYS A1005 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A1006 " --> pdb=" O ALA A1002 " (cutoff:3.500A) 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 1079 Processing helix chain 'A' and resid 1101 through 1125 removed outlier: 3.788A pdb=" N ALA A1105 " --> pdb=" O GLU A1101 " (cutoff:3.500A) Proline residue: A1113 - end of helix Processing helix chain 'A' and resid 1133 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 472 through 473 removed outlier: 3.786A pdb=" N GLU A 472 " --> pdb=" O VAL A 469 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLY A 466 " --> pdb=" O PHE A 484 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE A 436 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N CYS A 485 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N VAL A 438 " --> pdb=" O CYS A 485 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N ASN A 435 " --> pdb=" O HIS A 503 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE A 505 " --> pdb=" O ASN A 435 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TYR A 437 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE A 504 " --> pdb=" O ILE A 536 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N MET A 538 " --> pdb=" O ILE A 504 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL A 506 " --> pdb=" O MET A 538 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL A 403 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N SER A 539 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE A 405 " --> pdb=" O SER A 539 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 567 through 568 removed outlier: 6.857A pdb=" N GLN A 567 " --> pdb=" O CYS A 777 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N THR A 779 " --> pdb=" O GLN A 567 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA A 655 " --> pdb=" O PHE A 731 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ILE A 733 " --> pdb=" O ALA A 655 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU A 657 " --> pdb=" O ILE A 733 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 737 through 738 Processing sheet with id=AA4, first strand: chain 'A' and resid 1062 through 1063 removed outlier: 7.939A pdb=" N CYS A1063 " --> pdb=" O ALA A1028 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU A1030 " --> pdb=" O CYS A1063 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LYS A1020 " --> pdb=" O LYS A1016 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A1016 " --> pdb=" O LYS A1020 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A1022 " --> pdb=" O VAL A1014 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A1014 " --> pdb=" O LEU A1022 " (cutoff:3.500A) 297 hydrogen bonds defined for protein. 846 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: 2.32 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1151 1.31 - 1.44: 1706 1.44 - 1.56: 4029 1.56 - 1.68: 0 1.68 - 1.81: 70 Bond restraints: 6956 Sorted by residual: bond pdb=" C ARG A 771 " pdb=" O ARG A 771 " ideal model delta sigma weight residual 1.236 1.342 -0.106 1.38e-02 5.25e+03 5.94e+01 bond pdb=" C PRO A 565 " pdb=" O PRO A 565 " ideal model delta sigma weight residual 1.234 1.187 0.047 1.14e-02 7.69e+03 1.67e+01 bond pdb=" C PRO A 774 " pdb=" O PRO A 774 " ideal model delta sigma weight residual 1.235 1.189 0.046 1.30e-02 5.92e+03 1.27e+01 bond pdb=" N ARG A 773 " pdb=" CA ARG A 773 " ideal model delta sigma weight residual 1.454 1.495 -0.041 1.30e-02 5.92e+03 1.00e+01 bond pdb=" N ARG A 771 " pdb=" CA ARG A 771 " ideal model delta sigma weight residual 1.456 1.495 -0.038 1.22e-02 6.72e+03 9.75e+00 ... (remaining 6951 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.08: 9298 3.08 - 6.15: 110 6.15 - 9.23: 13 9.23 - 12.30: 2 12.30 - 15.38: 1 Bond angle restraints: 9424 Sorted by residual: angle pdb=" CA ARG A 771 " pdb=" C ARG A 771 " pdb=" O ARG A 771 " ideal model delta sigma weight residual 119.59 134.97 -15.38 1.18e+00 7.18e-01 1.70e+02 angle pdb=" CA ARG A 771 " pdb=" C ARG A 771 " pdb=" N VAL A 772 " ideal model delta sigma weight residual 118.11 109.66 8.45 1.27e+00 6.20e-01 4.43e+01 angle pdb=" O ARG A 771 " pdb=" C ARG A 771 " pdb=" N VAL A 772 " ideal model delta sigma weight residual 122.25 115.11 7.14 1.19e+00 7.06e-01 3.60e+01 angle pdb=" O GLY A 770 " pdb=" C GLY A 770 " pdb=" N ARG A 771 " ideal model delta sigma weight residual 122.41 116.89 5.52 1.08e+00 8.57e-01 2.61e+01 angle pdb=" C LEU A 855 " pdb=" CA LEU A 855 " pdb=" CB LEU A 855 " ideal model delta sigma weight residual 117.23 110.42 6.81 1.36e+00 5.41e-01 2.51e+01 ... (remaining 9419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 3651 17.94 - 35.88: 477 35.88 - 53.82: 118 53.82 - 71.76: 22 71.76 - 89.69: 12 Dihedral angle restraints: 4280 sinusoidal: 1752 harmonic: 2528 Sorted by residual: dihedral pdb=" CD ARG A 771 " pdb=" NE ARG A 771 " pdb=" CZ ARG A 771 " pdb=" NH1 ARG A 771 " ideal model delta sinusoidal sigma weight residual 0.00 85.34 -85.34 1 1.00e+01 1.00e-02 8.82e+01 dihedral pdb=" CA ASN A1097 " pdb=" C ASN A1097 " pdb=" N PHE A1098 " pdb=" CA PHE A1098 " ideal model delta harmonic sigma weight residual 180.00 147.82 32.18 0 5.00e+00 4.00e-02 4.14e+01 dihedral pdb=" C VAL A 559 " pdb=" N VAL A 559 " pdb=" CA VAL A 559 " pdb=" CB VAL A 559 " ideal model delta harmonic sigma weight residual -122.00 -110.42 -11.58 0 2.50e+00 1.60e-01 2.15e+01 ... (remaining 4277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 984 0.085 - 0.170: 94 0.170 - 0.256: 5 0.256 - 0.341: 0 0.341 - 0.426: 1 Chirality restraints: 1084 Sorted by residual: chirality pdb=" CA VAL A 559 " pdb=" N VAL A 559 " pdb=" C VAL A 559 " pdb=" CB VAL A 559 " both_signs ideal model delta sigma weight residual False 2.44 2.87 -0.43 2.00e-01 2.50e+01 4.54e+00 chirality pdb=" CB VAL A 566 " pdb=" CA VAL A 566 " pdb=" CG1 VAL A 566 " pdb=" CG2 VAL A 566 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.41e+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 2.73 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 1081 not shown) Planarity restraints: 1217 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 771 " -1.106 9.50e-02 1.11e+02 4.96e-01 1.48e+02 pdb=" NE ARG A 771 " 0.064 2.00e-02 2.50e+03 pdb=" CZ ARG A 771 " 0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG A 771 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG A 771 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 770 " -0.050 2.00e-02 2.50e+03 9.86e-02 9.72e+01 pdb=" C GLY A 770 " 0.171 2.00e-02 2.50e+03 pdb=" O GLY A 770 " -0.064 2.00e-02 2.50e+03 pdb=" N ARG A 771 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 558 " 0.027 2.00e-02 2.50e+03 5.70e-02 3.25e+01 pdb=" C GLU A 558 " -0.098 2.00e-02 2.50e+03 pdb=" O GLU A 558 " 0.038 2.00e-02 2.50e+03 pdb=" N VAL A 559 " 0.033 2.00e-02 2.50e+03 ... (remaining 1214 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 189 2.70 - 3.25: 7112 3.25 - 3.80: 10872 3.80 - 4.35: 13543 4.35 - 4.90: 22800 Nonbonded interactions: 54516 Sorted by model distance: nonbonded pdb=" OG BSER A1070 " pdb=" OE1 GLN A1073 " model vdw 2.155 3.040 nonbonded pdb=" OG SER A 268 " pdb=" OD1 ASN A 270 " model vdw 2.209 3.040 nonbonded pdb=" O ILE A 444 " pdb=" OG SER A 448 " model vdw 2.225 3.040 nonbonded pdb=" OD1 ASP A 366 " pdb=" ND2 ASN A 370 " model vdw 2.254 3.120 nonbonded pdb=" OG1 THR A 414 " pdb=" OD2 ASP A 507 " model vdw 2.259 3.040 ... (remaining 54511 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: 1.040 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.900 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.080 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:3.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6022 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 : 0.004 0.106 6956 Z= 0.209 Angle : 0.782 15.379 9424 Z= 0.445 Chirality : 0.050 0.426 1084 Planarity : 0.016 0.496 1217 Dihedral : 17.516 89.694 2632 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.82 % Allowed : 8.41 % Favored : 90.77 % Rotamer: Outliers : 1.18 % Allowed : 22.05 % Favored : 76.77 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.21 (0.30), residues: 857 helix: 1.38 (0.27), residues: 394 sheet: -0.54 (0.60), residues: 80 loop : -1.74 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 756 HIS 0.003 0.001 HIS A 691 PHE 0.042 0.002 PHE A 672 TYR 0.014 0.001 TYR A 611 ARG 0.007 0.000 ARG A 771 Details of bonding type rmsd hydrogen bonds : bond 0.14492 ( 297) hydrogen bonds : angle 5.81428 ( 846) covalent geometry : bond 0.00358 ( 6956) covalent geometry : angle 0.78200 ( 9424) *********************** 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 172 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 164 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 170 average time/residue: 0.2048 time to fit residues: 45.1855 Evaluate side-chains 104 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 78 optimal weight: 0.5980 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 691 HIS A 911 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.082723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.061842 restraints weight = 52904.581| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 10.41 r_work: 0.3102 rms_B_bonded: 10.40 restraints_weight: 2.0000 r_work: 0.3268 rms_B_bonded: 6.46 restraints_weight: 4.0000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3254 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3254 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 6956 Z= 0.249 Angle : 0.849 9.264 9424 Z= 0.433 Chirality : 0.051 0.216 1084 Planarity : 0.008 0.197 1217 Dihedral : 5.027 32.700 936 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 0.93 % Allowed : 8.64 % Favored : 90.42 % Rotamer: Outliers : 3.94 % Allowed : 24.28 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.16 (0.30), residues: 857 helix: 1.35 (0.26), residues: 404 sheet: -0.52 (0.65), residues: 77 loop : -1.69 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1095 HIS 0.006 0.001 HIS A 803 PHE 0.013 0.002 PHE A 820 TYR 0.019 0.002 TYR A1009 ARG 0.018 0.001 ARG A 771 Details of bonding type rmsd hydrogen bonds : bond 0.04592 ( 297) hydrogen bonds : angle 5.14061 ( 846) covalent geometry : bond 0.00566 ( 6956) covalent geometry : angle 0.84946 ( 9424) *********************** 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 135 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 436 ILE cc_start: 0.9134 (mp) cc_final: 0.8710 (mm) REVERT: A 451 GLU cc_start: 0.9320 (mt-10) cc_final: 0.8907 (mp0) REVERT: A 629 MET cc_start: 0.8940 (mpp) cc_final: 0.8650 (mpp) REVERT: A 734 ASP cc_start: 0.8203 (t0) cc_final: 0.7856 (t0) REVERT: A 771 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8494 (mmm-85) REVERT: A 871 MET cc_start: 0.8803 (ttp) cc_final: 0.8487 (ttp) REVERT: A 957 MET cc_start: 0.8886 (mtm) cc_final: 0.8506 (ptp) REVERT: A 1112 LYS cc_start: 0.9288 (mmmm) cc_final: 0.9013 (mmmm) outliers start: 28 outliers final: 17 residues processed: 125 average time/residue: 0.1934 time to fit residues: 32.2222 Evaluate side-chains 108 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 663 TRP Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 771 ARG Chi-restraints excluded: chain A residue 946 PHE Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1082 ILE Chi-restraints excluded: chain A residue 1095 TRP Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1146 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 33 optimal weight: 8.9990 chunk 52 optimal weight: 0.2980 chunk 44 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 26 optimal weight: 0.0170 chunk 1 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 HIS A1094 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.085503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.065555 restraints weight = 37407.364| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 8.82 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3385 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3385 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6956 Z= 0.155 Angle : 0.819 9.831 9424 Z= 0.408 Chirality : 0.049 0.187 1084 Planarity : 0.006 0.076 1217 Dihedral : 4.820 30.442 934 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.82 % Allowed : 8.06 % Favored : 91.12 % Rotamer: Outliers : 3.15 % Allowed : 24.67 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.12 (0.30), residues: 857 helix: 1.34 (0.26), residues: 399 sheet: -0.66 (0.66), residues: 66 loop : -1.53 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1095 HIS 0.004 0.001 HIS A 803 PHE 0.016 0.002 PHE A 743 TYR 0.011 0.001 TYR A 479 ARG 0.011 0.001 ARG A 905 Details of bonding type rmsd hydrogen bonds : bond 0.04029 ( 297) hydrogen bonds : angle 4.79415 ( 846) covalent geometry : bond 0.00354 ( 6956) covalent geometry : angle 0.81869 ( 9424) *********************** 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 126 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 MET cc_start: 0.8347 (ttt) cc_final: 0.7603 (tmm) REVERT: A 436 ILE cc_start: 0.8952 (mp) cc_final: 0.8579 (mm) REVERT: A 508 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8289 (mm-30) REVERT: A 515 ASN cc_start: 0.9402 (OUTLIER) cc_final: 0.9084 (p0) REVERT: A 629 MET cc_start: 0.8763 (mpp) cc_final: 0.8446 (mpp) REVERT: A 638 GLU cc_start: 0.9173 (mp0) cc_final: 0.8759 (tp30) REVERT: A 734 ASP cc_start: 0.7385 (t0) cc_final: 0.6735 (t0) REVERT: A 771 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8480 (mmm-85) REVERT: A 810 LYS cc_start: 0.8980 (mptt) cc_final: 0.8732 (mttt) REVERT: A 861 ARG cc_start: 0.8133 (mmm160) cc_final: 0.7922 (mmm160) REVERT: A 871 MET cc_start: 0.8639 (ttp) cc_final: 0.8332 (ttp) REVERT: A 896 GLU cc_start: 0.8428 (mp0) cc_final: 0.8210 (mp0) REVERT: A 925 MET cc_start: 0.9295 (tmm) cc_final: 0.8950 (ptt) REVERT: A 957 MET cc_start: 0.8691 (mtm) cc_final: 0.8418 (ptp) outliers start: 22 outliers final: 14 residues processed: 119 average time/residue: 0.1730 time to fit residues: 28.6240 Evaluate side-chains 107 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 663 TRP Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 771 ARG Chi-restraints excluded: chain A residue 946 PHE Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1146 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 21 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 3 optimal weight: 0.0010 chunk 0 optimal weight: 20.0000 chunk 85 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 0.0370 chunk 35 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.5666 ------------------------------------------------------------------------------- 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 = 0.3828 r_free = 0.3828 target = 0.086386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.065794 restraints weight = 46614.118| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 9.85 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3400 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3400 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6956 Z= 0.143 Angle : 0.783 10.104 9424 Z= 0.392 Chirality : 0.048 0.268 1084 Planarity : 0.006 0.071 1217 Dihedral : 4.683 29.479 934 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.93 % Allowed : 8.06 % Favored : 91.00 % Rotamer: Outliers : 3.41 % Allowed : 24.15 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.20 (0.30), residues: 857 helix: 1.26 (0.26), residues: 399 sheet: -0.87 (0.62), residues: 71 loop : -1.52 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1095 HIS 0.004 0.001 HIS A 803 PHE 0.017 0.001 PHE A 743 TYR 0.015 0.001 TYR A 479 ARG 0.008 0.000 ARG A 905 Details of bonding type rmsd hydrogen bonds : bond 0.03713 ( 297) hydrogen bonds : angle 4.74056 ( 846) covalent geometry : bond 0.00328 ( 6956) covalent geometry : angle 0.78297 ( 9424) *********************** 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 130 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 MET cc_start: 0.8436 (ttt) cc_final: 0.7694 (tmm) REVERT: A 436 ILE cc_start: 0.8932 (mp) cc_final: 0.8539 (mm) REVERT: A 515 ASN cc_start: 0.9389 (OUTLIER) cc_final: 0.9141 (p0) REVERT: A 629 MET cc_start: 0.8739 (mpp) cc_final: 0.8517 (mpp) REVERT: A 641 GLU cc_start: 0.9420 (tm-30) cc_final: 0.9156 (pp20) REVERT: A 734 ASP cc_start: 0.7160 (t0) cc_final: 0.6435 (t0) REVERT: A 810 LYS cc_start: 0.9013 (mptt) cc_final: 0.8747 (mttt) REVERT: A 861 ARG cc_start: 0.8153 (mmm160) cc_final: 0.7925 (mmm160) REVERT: A 872 MET cc_start: 0.8108 (tmm) cc_final: 0.7873 (tmm) REVERT: A 896 GLU cc_start: 0.8413 (mp0) cc_final: 0.8086 (mp0) REVERT: A 957 MET cc_start: 0.8723 (mtm) cc_final: 0.8428 (ptp) outliers start: 24 outliers final: 17 residues processed: 118 average time/residue: 0.1690 time to fit residues: 27.8890 Evaluate side-chains 111 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 663 TRP Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 946 PHE Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1082 ILE Chi-restraints excluded: chain A residue 1146 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 12 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 40 optimal weight: 0.3980 chunk 23 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- 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 = 0.3779 r_free = 0.3779 target = 0.083067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.064195 restraints weight = 33419.914| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 7.93 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3364 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3364 r_free = 0.3364 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3364 r_free = 0.3364 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3364 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 6956 Z= 0.179 Angle : 0.796 12.981 9424 Z= 0.398 Chirality : 0.048 0.209 1084 Planarity : 0.006 0.067 1217 Dihedral : 4.742 29.194 934 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.82 % Allowed : 8.29 % Favored : 90.89 % Rotamer: Outliers : 3.67 % Allowed : 24.67 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.30), residues: 857 helix: 1.25 (0.26), residues: 402 sheet: -1.12 (0.61), residues: 71 loop : -1.52 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1095 HIS 0.005 0.001 HIS A 803 PHE 0.013 0.002 PHE A 743 TYR 0.014 0.001 TYR A 479 ARG 0.008 0.000 ARG A 905 Details of bonding type rmsd hydrogen bonds : bond 0.03710 ( 297) hydrogen bonds : angle 4.80536 ( 846) covalent geometry : bond 0.00420 ( 6956) covalent geometry : angle 0.79576 ( 9424) *********************** 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 117 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 GLU cc_start: 0.9178 (mt-10) cc_final: 0.8831 (mp0) REVERT: A 515 ASN cc_start: 0.9394 (OUTLIER) cc_final: 0.9142 (p0) REVERT: A 629 MET cc_start: 0.8775 (mpp) cc_final: 0.8566 (mpp) REVERT: A 638 GLU cc_start: 0.9319 (mp0) cc_final: 0.8819 (tp30) REVERT: A 810 LYS cc_start: 0.8951 (mptt) cc_final: 0.8678 (mttt) REVERT: A 861 ARG cc_start: 0.8240 (mmm160) cc_final: 0.8018 (mmm160) REVERT: A 871 MET cc_start: 0.8541 (ttp) cc_final: 0.8302 (ttp) REVERT: A 957 MET cc_start: 0.8778 (mtm) cc_final: 0.8418 (ptp) outliers start: 26 outliers final: 21 residues processed: 103 average time/residue: 0.1614 time to fit residues: 23.4500 Evaluate side-chains 105 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 663 TRP Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 946 PHE Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1082 ILE Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1146 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 65 optimal weight: 9.9990 chunk 60 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 4 optimal weight: 0.0970 chunk 22 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.3804 r_free = 0.3804 target = 0.083969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.065399 restraints weight = 33427.747| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 7.99 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3410 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3410 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6956 Z= 0.135 Angle : 0.784 13.931 9424 Z= 0.384 Chirality : 0.047 0.211 1084 Planarity : 0.005 0.067 1217 Dihedral : 4.636 28.746 934 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.82 % Allowed : 7.71 % Favored : 91.47 % Rotamer: Outliers : 3.54 % Allowed : 24.93 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.13 (0.30), residues: 857 helix: 1.33 (0.26), residues: 400 sheet: -1.16 (0.62), residues: 71 loop : -1.43 (0.34), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 663 HIS 0.004 0.001 HIS A 803 PHE 0.017 0.001 PHE A 743 TYR 0.015 0.001 TYR A 479 ARG 0.007 0.000 ARG A 905 Details of bonding type rmsd hydrogen bonds : bond 0.03544 ( 297) hydrogen bonds : angle 4.62379 ( 846) covalent geometry : bond 0.00308 ( 6956) covalent geometry : angle 0.78429 ( 9424) *********************** 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 123 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LEU cc_start: 0.9326 (tp) cc_final: 0.9037 (pp) REVERT: A 436 ILE cc_start: 0.8942 (mp) cc_final: 0.8609 (mm) REVERT: A 629 MET cc_start: 0.8679 (mpp) cc_final: 0.8470 (mpp) REVERT: A 638 GLU cc_start: 0.9290 (mp0) cc_final: 0.8802 (tp30) REVERT: A 810 LYS cc_start: 0.8954 (mptt) cc_final: 0.8635 (mttt) REVERT: A 871 MET cc_start: 0.8574 (ttp) cc_final: 0.8331 (ttp) REVERT: A 957 MET cc_start: 0.8791 (mtm) cc_final: 0.8433 (ptp) outliers start: 25 outliers final: 20 residues processed: 112 average time/residue: 0.1549 time to fit residues: 24.4471 Evaluate side-chains 112 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 663 TRP Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 946 PHE Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1082 ILE Chi-restraints excluded: chain A residue 1083 ASP Chi-restraints excluded: chain A residue 1096 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.0270 chunk 21 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 45 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 930 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.083986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.064873 restraints weight = 36852.617| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 8.56 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3400 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3400 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6956 Z= 0.132 Angle : 0.781 14.742 9424 Z= 0.382 Chirality : 0.047 0.183 1084 Planarity : 0.005 0.066 1217 Dihedral : 4.517 28.050 934 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.82 % Allowed : 8.06 % Favored : 91.12 % Rotamer: Outliers : 3.81 % Allowed : 25.46 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.14 (0.30), residues: 857 helix: 1.31 (0.26), residues: 400 sheet: -1.17 (0.62), residues: 71 loop : -1.42 (0.34), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1095 HIS 0.004 0.001 HIS A 803 PHE 0.017 0.001 PHE A 743 TYR 0.015 0.001 TYR A 479 ARG 0.006 0.000 ARG A 905 Details of bonding type rmsd hydrogen bonds : bond 0.03442 ( 297) hydrogen bonds : angle 4.57525 ( 846) covalent geometry : bond 0.00302 ( 6956) covalent geometry : angle 0.78127 ( 9424) *********************** 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 122 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LEU cc_start: 0.9315 (tp) cc_final: 0.9008 (pp) REVERT: A 436 ILE cc_start: 0.8961 (mp) cc_final: 0.8632 (mm) REVERT: A 638 GLU cc_start: 0.9306 (mp0) cc_final: 0.8811 (tp30) REVERT: A 663 TRP cc_start: 0.8448 (OUTLIER) cc_final: 0.7603 (p90) REVERT: A 670 MET cc_start: 0.8802 (ptp) cc_final: 0.7881 (ptp) REVERT: A 861 ARG cc_start: 0.8199 (mmm160) cc_final: 0.7994 (mmm160) REVERT: A 871 MET cc_start: 0.8580 (ttp) cc_final: 0.8343 (ttp) REVERT: A 896 GLU cc_start: 0.8443 (mp0) cc_final: 0.8054 (mp0) REVERT: A 957 MET cc_start: 0.8794 (mtm) cc_final: 0.8387 (ptp) outliers start: 27 outliers final: 22 residues processed: 109 average time/residue: 0.1702 time to fit residues: 26.5512 Evaluate side-chains 114 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 663 TRP Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 946 PHE Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1082 ILE Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1146 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 6 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 77 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 10 optimal weight: 0.0980 chunk 51 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 29 optimal weight: 0.1980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1087 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.084176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.063529 restraints weight = 50579.565| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 10.26 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3377 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3377 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6956 Z= 0.135 Angle : 0.799 14.504 9424 Z= 0.389 Chirality : 0.047 0.182 1084 Planarity : 0.005 0.067 1217 Dihedral : 4.506 27.636 934 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.82 % Allowed : 8.18 % Favored : 91.00 % Rotamer: Outliers : 3.41 % Allowed : 26.64 % Favored : 69.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.13 (0.30), residues: 857 helix: 1.34 (0.27), residues: 400 sheet: -1.18 (0.62), residues: 71 loop : -1.42 (0.34), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1095 HIS 0.004 0.001 HIS A 803 PHE 0.017 0.001 PHE A 743 TYR 0.015 0.001 TYR A 479 ARG 0.006 0.000 ARG A 905 Details of bonding type rmsd hydrogen bonds : bond 0.03383 ( 297) hydrogen bonds : angle 4.59443 ( 846) covalent geometry : bond 0.00311 ( 6956) covalent geometry : angle 0.79946 ( 9424) *********************** 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 118 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LEU cc_start: 0.9313 (tp) cc_final: 0.9023 (pp) REVERT: A 389 MET cc_start: 0.8463 (ttt) cc_final: 0.7649 (tmm) REVERT: A 436 ILE cc_start: 0.8939 (mp) cc_final: 0.8606 (mm) REVERT: A 638 GLU cc_start: 0.9334 (mp0) cc_final: 0.8818 (tp30) REVERT: A 663 TRP cc_start: 0.8518 (OUTLIER) cc_final: 0.7663 (p90) REVERT: A 861 ARG cc_start: 0.8255 (mmm160) cc_final: 0.8034 (mmm160) REVERT: A 871 MET cc_start: 0.8545 (ttp) cc_final: 0.8325 (ttp) REVERT: A 896 GLU cc_start: 0.8473 (mp0) cc_final: 0.8198 (mp0) REVERT: A 957 MET cc_start: 0.8828 (mtm) cc_final: 0.8473 (ptp) outliers start: 24 outliers final: 21 residues processed: 107 average time/residue: 0.1578 time to fit residues: 24.2320 Evaluate side-chains 111 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 663 TRP Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 946 PHE Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1098 PHE Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1146 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 81 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 66 optimal weight: 0.4980 chunk 31 optimal weight: 0.2980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3819 r_free = 0.3819 target = 0.084512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.063591 restraints weight = 50356.680| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 10.36 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3385 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3385 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6956 Z= 0.136 Angle : 0.799 15.159 9424 Z= 0.389 Chirality : 0.047 0.185 1084 Planarity : 0.005 0.066 1217 Dihedral : 4.438 27.035 934 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.82 % Allowed : 8.06 % Favored : 91.12 % Rotamer: Outliers : 3.02 % Allowed : 27.56 % Favored : 69.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.15 (0.30), residues: 857 helix: 1.30 (0.26), residues: 400 sheet: -1.13 (0.62), residues: 77 loop : -1.43 (0.34), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1095 HIS 0.004 0.001 HIS A 803 PHE 0.018 0.001 PHE A 743 TYR 0.015 0.001 TYR A 479 ARG 0.006 0.000 ARG A 905 Details of bonding type rmsd hydrogen bonds : bond 0.03343 ( 297) hydrogen bonds : angle 4.60773 ( 846) covalent geometry : bond 0.00315 ( 6956) covalent geometry : angle 0.79941 ( 9424) *********************** 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 117 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LEU cc_start: 0.9291 (tp) cc_final: 0.9012 (pp) REVERT: A 389 MET cc_start: 0.8491 (ttt) cc_final: 0.7718 (tmm) REVERT: A 436 ILE cc_start: 0.8924 (mp) cc_final: 0.8707 (mm) REVERT: A 638 GLU cc_start: 0.9310 (mp0) cc_final: 0.8806 (tp30) REVERT: A 641 GLU cc_start: 0.9387 (tm-30) cc_final: 0.9114 (tm-30) REVERT: A 663 TRP cc_start: 0.8501 (OUTLIER) cc_final: 0.7683 (p90) REVERT: A 740 MET cc_start: 0.8314 (ptt) cc_final: 0.7607 (pmm) REVERT: A 861 ARG cc_start: 0.8282 (mmm160) cc_final: 0.8051 (mmm160) REVERT: A 871 MET cc_start: 0.8529 (ttp) cc_final: 0.8315 (ttp) REVERT: A 896 GLU cc_start: 0.8437 (mp0) cc_final: 0.8155 (mp0) REVERT: A 957 MET cc_start: 0.8809 (mtm) cc_final: 0.8448 (ptp) outliers start: 21 outliers final: 19 residues processed: 109 average time/residue: 0.1854 time to fit residues: 28.3875 Evaluate side-chains 111 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 663 TRP Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 845 CYS Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 946 PHE Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1098 PHE Chi-restraints excluded: chain A residue 1146 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 26 optimal weight: 0.0070 chunk 56 optimal weight: 2.9990 chunk 72 optimal weight: 0.0040 chunk 25 optimal weight: 7.9990 chunk 63 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 40 optimal weight: 0.4980 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.4210 ------------------------------------------------------------------------------- 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 = 0.3829 r_free = 0.3829 target = 0.085162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.065694 restraints weight = 38252.749| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 8.79 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3423 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3423 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6956 Z= 0.131 Angle : 0.794 15.575 9424 Z= 0.384 Chirality : 0.047 0.191 1084 Planarity : 0.005 0.067 1217 Dihedral : 4.413 26.084 934 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.82 % Allowed : 7.71 % Favored : 91.47 % Rotamer: Outliers : 3.02 % Allowed : 27.17 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.15 (0.30), residues: 857 helix: 1.30 (0.26), residues: 399 sheet: -1.09 (0.63), residues: 77 loop : -1.43 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 338 HIS 0.004 0.001 HIS A 803 PHE 0.021 0.001 PHE A 743 TYR 0.012 0.001 TYR A 479 ARG 0.005 0.000 ARG A 905 Details of bonding type rmsd hydrogen bonds : bond 0.03354 ( 297) hydrogen bonds : angle 4.56793 ( 846) covalent geometry : bond 0.00298 ( 6956) covalent geometry : angle 0.79382 ( 9424) ********************** 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 115 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LEU cc_start: 0.9300 (tp) cc_final: 0.9015 (pp) REVERT: A 389 MET cc_start: 0.8503 (ttt) cc_final: 0.7766 (tmm) REVERT: A 436 ILE cc_start: 0.8912 (mp) cc_final: 0.8591 (mm) REVERT: A 638 GLU cc_start: 0.9283 (mp0) cc_final: 0.8734 (tp30) REVERT: A 641 GLU cc_start: 0.9373 (tm-30) cc_final: 0.9091 (tm-30) REVERT: A 663 TRP cc_start: 0.8423 (OUTLIER) cc_final: 0.7687 (p90) REVERT: A 740 MET cc_start: 0.8320 (ptt) cc_final: 0.7689 (pmm) REVERT: A 861 ARG cc_start: 0.8235 (mmm160) cc_final: 0.7995 (mmm160) REVERT: A 871 MET cc_start: 0.8505 (ttp) cc_final: 0.8301 (ttp) REVERT: A 896 GLU cc_start: 0.8360 (mp0) cc_final: 0.8083 (mp0) REVERT: A 957 MET cc_start: 0.8769 (mtm) cc_final: 0.8416 (ptp) outliers start: 21 outliers final: 17 residues processed: 106 average time/residue: 0.1479 time to fit residues: 22.4858 Evaluate side-chains 110 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 663 TRP Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 845 CYS Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 946 PHE Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1146 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 35 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 39 optimal weight: 0.0040 chunk 27 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 overall best weight: 1.1194 ------------------------------------------------------------------------------- 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 = 0.3804 r_free = 0.3804 target = 0.083838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.066281 restraints weight = 26479.189| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 6.96 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3433 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3433 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6956 Z= 0.141 Angle : 0.782 15.169 9424 Z= 0.383 Chirality : 0.047 0.187 1084 Planarity : 0.005 0.065 1217 Dihedral : 4.386 26.164 934 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.82 % Allowed : 8.06 % Favored : 91.12 % Rotamer: Outliers : 2.89 % Allowed : 27.17 % Favored : 69.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.11 (0.30), residues: 857 helix: 1.34 (0.26), residues: 400 sheet: -1.10 (0.63), residues: 77 loop : -1.42 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1095 HIS 0.004 0.001 HIS A 803 PHE 0.018 0.001 PHE A 743 TYR 0.015 0.001 TYR A 479 ARG 0.006 0.000 ARG A 905 Details of bonding type rmsd hydrogen bonds : bond 0.03382 ( 297) hydrogen bonds : angle 4.61960 ( 846) covalent geometry : bond 0.00329 ( 6956) covalent geometry : angle 0.78182 ( 9424) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3951.36 seconds wall clock time: 68 minutes 59.47 seconds (4139.47 seconds total)