Starting phenix.real_space_refine on Mon May 12 10:19:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zty_60476/05_2025/8zty_60476.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zty_60476/05_2025/8zty_60476.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zty_60476/05_2025/8zty_60476.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zty_60476/05_2025/8zty_60476.map" model { file = "/net/cci-nas-00/data/ceres_data/8zty_60476/05_2025/8zty_60476.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zty_60476/05_2025/8zty_60476.cif" } resolution = 2.85 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= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 56 5.49 5 S 27 5.16 5 C 5470 2.51 5 N 1529 2.21 5 O 1841 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 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: 8923 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 928, 7712 Classifications: {'peptide': 928} Link IDs: {'PTRANS': 21, 'TRANS': 906} Chain breaks: 13 Chain: "B" Number of atoms: 1211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1211 Classifications: {'RNA': 57} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 9, 'rna3p_pur': 22, 'rna3p_pyr': 18} Link IDs: {'rna2p': 17, 'rna3p': 39} Chain breaks: 1 Time building chain proxies: 5.43, per 1000 atoms: 0.61 Number of scatterers: 8923 At special positions: 0 Unit cell: (78.1, 91.3, 115.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 56 15.00 O 1841 8.00 N 1529 7.00 C 5470 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: 2.45 Conformation dependent library (CDL) restraints added in 848.3 milliseconds 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1814 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 5 sheets defined 70.3% alpha, 3.0% beta 8 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 3.03 Creating SS restraints... Processing helix chain 'A' and resid 68 through 75 Processing helix chain 'A' and resid 75 through 88 Processing helix chain 'A' and resid 93 through 105 Processing helix chain 'A' and resid 153 through 164 Processing helix chain 'A' and resid 180 through 203 Processing helix chain 'A' and resid 211 through 226 Processing helix chain 'A' and resid 232 through 241 Processing helix chain 'A' and resid 241 through 256 Processing helix chain 'A' and resid 263 through 283 removed outlier: 4.979A pdb=" N GLU A 280 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLU A 281 " --> pdb=" O GLN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 303 Processing helix chain 'A' and resid 314 through 318 Processing helix chain 'A' and resid 319 through 348 Processing helix chain 'A' and resid 355 through 387 Processing helix chain 'A' and resid 409 through 422 Processing helix chain 'A' and resid 429 through 450 Proline residue: A 443 - end of helix removed outlier: 3.907A pdb=" N HIS A 450 " --> pdb=" O ASN A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 462 removed outlier: 4.560A pdb=" N ASN A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 513 removed outlier: 3.885A pdb=" N ASP A 493 " --> pdb=" O THR A 489 " (cutoff:3.500A) Proline residue: A 503 - end of helix Processing helix chain 'A' and resid 520 through 526 removed outlier: 3.787A pdb=" N GLN A 526 " --> pdb=" O ASP A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 560 Processing helix chain 'A' and resid 582 through 599 Processing helix chain 'A' and resid 599 through 607 removed outlier: 4.321A pdb=" N GLN A 603 " --> pdb=" O VAL A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 623 removed outlier: 4.363A pdb=" N ASN A 622 " --> pdb=" O ILE A 618 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LYS A 623 " --> pdb=" O LEU A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 658 Processing helix chain 'A' and resid 670 through 690 Processing helix chain 'A' and resid 692 through 697 removed outlier: 3.676A pdb=" N ILE A 695 " --> pdb=" O LEU A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 730 Processing helix chain 'A' and resid 732 through 750 Processing helix chain 'A' and resid 752 through 774 removed outlier: 4.313A pdb=" N GLU A 774 " --> pdb=" O LEU A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 796 removed outlier: 3.694A pdb=" N LEU A 796 " --> pdb=" O LYS A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 828 Processing helix chain 'A' and resid 830 through 839 Processing helix chain 'A' and resid 841 through 845 removed outlier: 3.955A pdb=" N TYR A 844 " --> pdb=" O SER A 841 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LYS A 845 " --> pdb=" O ASP A 842 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 841 through 845' Processing helix chain 'A' and resid 847 through 857 removed outlier: 3.797A pdb=" N LEU A 854 " --> pdb=" O ASP A 850 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N HIS A 855 " --> pdb=" O ILE A 851 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TYR A 857 " --> pdb=" O LYS A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 876 Processing helix chain 'A' and resid 877 through 881 Processing helix chain 'A' and resid 882 through 907 Processing helix chain 'A' and resid 908 through 946 removed outlier: 3.503A pdb=" N ARG A 912 " --> pdb=" O LEU A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1020 Processing helix chain 'A' and resid 1022 through 1027 removed outlier: 3.770A pdb=" N ASN A1026 " --> pdb=" O PHE A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1044 Processing helix chain 'A' and resid 1047 through 1065 removed outlier: 3.539A pdb=" N ALA A1053 " --> pdb=" O LYS A1049 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER A1055 " --> pdb=" O LYS A1051 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU A1058 " --> pdb=" O VAL A1054 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1077 Processing helix chain 'A' and resid 1106 through 1118 Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 42 removed outlier: 3.928A pdb=" N VAL A 40 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 135 through 136 Processing sheet with id=AA3, first strand: chain 'A' and resid 464 through 466 Processing sheet with id=AA4, first strand: chain 'A' and resid 1067 through 1071 removed outlier: 4.264A pdb=" N THR A1070 " --> pdb=" O LYS A1085 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LYS A1085 " --> pdb=" O THR A1070 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1090 through 1092 471 hydrogen bonds defined for protein. 1380 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 3.01 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2551 1.34 - 1.46: 1734 1.46 - 1.57: 4761 1.57 - 1.69: 112 1.69 - 1.81: 46 Bond restraints: 9204 Sorted by residual: bond pdb=" CB PRO A 602 " pdb=" CG PRO A 602 " ideal model delta sigma weight residual 1.492 1.619 -0.127 5.00e-02 4.00e+02 6.41e+00 bond pdb=" CB GLN A 804 " pdb=" CG GLN A 804 " ideal model delta sigma weight residual 1.520 1.569 -0.049 3.00e-02 1.11e+03 2.65e+00 bond pdb=" CB ASP A 43 " pdb=" CG ASP A 43 " ideal model delta sigma weight residual 1.516 1.553 -0.037 2.50e-02 1.60e+03 2.22e+00 bond pdb=" CB GLU A 351 " pdb=" CG GLU A 351 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.91e+00 bond pdb=" CA ASP A 43 " pdb=" CB ASP A 43 " ideal model delta sigma weight residual 1.527 1.546 -0.019 1.61e-02 3.86e+03 1.40e+00 ... (remaining 9199 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 12432 2.27 - 4.54: 158 4.54 - 6.82: 40 6.82 - 9.09: 9 9.09 - 11.36: 3 Bond angle restraints: 12642 Sorted by residual: angle pdb=" CA PRO A 602 " pdb=" N PRO A 602 " pdb=" CD PRO A 602 " ideal model delta sigma weight residual 112.00 100.64 11.36 1.40e+00 5.10e-01 6.59e+01 angle pdb=" CA GLN A 804 " pdb=" CB GLN A 804 " pdb=" CG GLN A 804 " ideal model delta sigma weight residual 114.10 121.52 -7.42 2.00e+00 2.50e-01 1.38e+01 angle pdb=" CB GLN A 804 " pdb=" CG GLN A 804 " pdb=" CD GLN A 804 " ideal model delta sigma weight residual 112.60 118.86 -6.26 1.70e+00 3.46e-01 1.36e+01 angle pdb=" CA GLU A 365 " pdb=" CB GLU A 365 " pdb=" CG GLU A 365 " ideal model delta sigma weight residual 114.10 121.28 -7.18 2.00e+00 2.50e-01 1.29e+01 angle pdb=" CA GLU A 351 " pdb=" CB GLU A 351 " pdb=" CG GLU A 351 " ideal model delta sigma weight residual 114.10 120.85 -6.75 2.00e+00 2.50e-01 1.14e+01 ... (remaining 12637 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 5260 35.98 - 71.95: 396 71.95 - 107.93: 31 107.93 - 143.90: 1 143.90 - 179.88: 2 Dihedral angle restraints: 5690 sinusoidal: 2921 harmonic: 2769 Sorted by residual: dihedral pdb=" O4' C B 38 " pdb=" C1' C B 38 " pdb=" N1 C B 38 " pdb=" C2 C B 38 " ideal model delta sinusoidal sigma weight residual 232.00 52.12 179.88 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B 1 " pdb=" C1' U B 1 " pdb=" N1 U B 1 " pdb=" C2 U B 1 " ideal model delta sinusoidal sigma weight residual -160.00 -50.48 -109.52 1 1.50e+01 4.44e-03 5.69e+01 dihedral pdb=" CA ASP A 232 " pdb=" C ASP A 232 " pdb=" N ILE A 233 " pdb=" CA ILE A 233 " ideal model delta harmonic sigma weight residual -180.00 -152.49 -27.51 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 5687 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1175 0.049 - 0.098: 222 0.098 - 0.147: 40 0.147 - 0.196: 1 0.196 - 0.245: 1 Chirality restraints: 1439 Sorted by residual: chirality pdb=" CG LEU A 601 " pdb=" CB LEU A 601 " pdb=" CD1 LEU A 601 " pdb=" CD2 LEU A 601 " both_signs ideal model delta sigma weight residual False -2.59 -2.83 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CG LEU A 154 " pdb=" CB LEU A 154 " pdb=" CD1 LEU A 154 " pdb=" CD2 LEU A 154 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.47e-01 chirality pdb=" CA GLU A 322 " pdb=" N GLU A 322 " pdb=" C GLU A 322 " pdb=" CB GLU A 322 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.06e-01 ... (remaining 1436 not shown) Planarity restraints: 1389 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 601 " -0.085 5.00e-02 4.00e+02 1.22e-01 2.36e+01 pdb=" N PRO A 602 " 0.210 5.00e-02 4.00e+02 pdb=" CA PRO A 602 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 602 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 43 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.70e+00 pdb=" C ASP A 43 " 0.045 2.00e-02 2.50e+03 pdb=" O ASP A 43 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG A 44 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 585 " 0.004 2.00e-02 2.50e+03 1.54e-02 4.16e+00 pdb=" CG PHE A 585 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE A 585 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 585 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE A 585 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 585 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 585 " -0.001 2.00e-02 2.50e+03 ... (remaining 1386 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 379 2.71 - 3.26: 9091 3.26 - 3.80: 15957 3.80 - 4.35: 18941 4.35 - 4.90: 30299 Nonbonded interactions: 74667 Sorted by model distance: nonbonded pdb=" OE2 GLU A 672 " pdb=" O2' A B 29 " model vdw 2.161 3.040 nonbonded pdb=" O THR A 815 " pdb=" OG1 THR A 815 " model vdw 2.178 3.040 nonbonded pdb=" NZ LYS A 363 " pdb=" OP2 A B 26 " model vdw 2.216 3.120 nonbonded pdb=" O2' U B 46 " pdb=" O5' C B 47 " model vdw 2.237 3.040 nonbonded pdb=" OG SER A 145 " pdb=" OE1 GLU A 147 " model vdw 2.253 3.040 ... (remaining 74662 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.980 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:12.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6581 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.127 9204 Z= 0.135 Angle : 0.687 11.361 12642 Z= 0.349 Chirality : 0.038 0.245 1439 Planarity : 0.005 0.122 1389 Dihedral : 21.973 179.881 3876 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 5.14 % Allowed : 42.40 % Favored : 52.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.29), residues: 900 helix: 1.98 (0.21), residues: 590 sheet: -4.70 (0.67), residues: 10 loop : -1.36 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 435 HIS 0.011 0.001 HIS A 915 PHE 0.031 0.002 PHE A 585 TYR 0.031 0.001 TYR A 844 ARG 0.009 0.001 ARG A 149 Details of bonding type rmsd hydrogen bonds : bond 0.05385 ( 493) hydrogen bonds : angle 4.02875 ( 1424) covalent geometry : bond 0.00317 ( 9204) covalent geometry : angle 0.68742 (12642) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 180 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 TYR cc_start: 0.7507 (m-80) cc_final: 0.7279 (m-80) REVERT: A 150 ILE cc_start: 0.7667 (tp) cc_final: 0.7319 (tt) REVERT: A 156 GLN cc_start: 0.7734 (mm-40) cc_final: 0.7456 (tp-100) REVERT: A 219 ARG cc_start: 0.7212 (ttm-80) cc_final: 0.6878 (ttp-170) REVERT: A 368 PHE cc_start: 0.7517 (t80) cc_final: 0.7291 (t80) REVERT: A 432 LEU cc_start: 0.7464 (tt) cc_final: 0.7188 (tt) REVERT: A 511 GLU cc_start: 0.6984 (tm-30) cc_final: 0.6640 (tm-30) REVERT: A 648 MET cc_start: 0.6833 (ttm) cc_final: 0.6584 (tpp) REVERT: A 686 PHE cc_start: 0.6761 (t80) cc_final: 0.6463 (t80) REVERT: A 730 LEU cc_start: 0.7755 (mp) cc_final: 0.7493 (mt) REVERT: A 735 GLN cc_start: 0.6812 (OUTLIER) cc_final: 0.6564 (mt0) REVERT: A 797 TYR cc_start: 0.6986 (m-80) cc_final: 0.6751 (m-80) REVERT: A 1016 ARG cc_start: 0.6632 (ttm-80) cc_final: 0.6312 (mtt90) REVERT: A 1047 ASP cc_start: 0.6340 (p0) cc_final: 0.6049 (p0) outliers start: 45 outliers final: 37 residues processed: 221 average time/residue: 1.0353 time to fit residues: 246.2865 Evaluate side-chains 213 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 175 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 460 PHE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 632 PHE Chi-restraints excluded: chain A residue 658 TYR Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 729 LYS Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 748 CYS Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 782 GLU Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 849 LYS Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 1020 SER Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1070 THR Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1105 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 HIS A 355 ASN A 462 ASN ** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.177811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.164518 restraints weight = 12521.437| |-----------------------------------------------------------------------------| r_work (start): 0.4146 rms_B_bonded: 1.92 r_work: 0.4045 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9204 Z= 0.216 Angle : 0.663 8.262 12642 Z= 0.338 Chirality : 0.042 0.160 1439 Planarity : 0.004 0.049 1389 Dihedral : 19.789 179.762 1922 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 9.94 % Allowed : 33.60 % Favored : 56.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.69 (0.28), residues: 900 helix: 1.50 (0.21), residues: 598 sheet: -5.09 (0.65), residues: 10 loop : -1.56 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 435 HIS 0.003 0.001 HIS A 915 PHE 0.032 0.002 PHE A 585 TYR 0.017 0.002 TYR A1075 ARG 0.005 0.001 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.04054 ( 493) hydrogen bonds : angle 4.09397 ( 1424) covalent geometry : bond 0.00482 ( 9204) covalent geometry : angle 0.66294 (12642) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 207 time to evaluate : 0.844 Fit side-chains revert: symmetry clash REVERT: A 149 ARG cc_start: 0.7133 (ttt-90) cc_final: 0.6892 (ttt-90) REVERT: A 156 GLN cc_start: 0.7815 (mm-40) cc_final: 0.7564 (tp-100) REVERT: A 272 GLN cc_start: 0.6749 (OUTLIER) cc_final: 0.6176 (mp-120) REVERT: A 282 LEU cc_start: 0.7933 (tt) cc_final: 0.7593 (tt) REVERT: A 445 ARG cc_start: 0.7005 (tmm-80) cc_final: 0.6771 (tmm-80) REVERT: A 615 VAL cc_start: 0.6371 (OUTLIER) cc_final: 0.6078 (p) REVERT: A 710 GLU cc_start: 0.7385 (mp0) cc_final: 0.7150 (mp0) REVERT: A 757 SER cc_start: 0.7941 (t) cc_final: 0.7632 (t) REVERT: A 781 LYS cc_start: 0.6141 (pptt) cc_final: 0.5926 (pptt) REVERT: A 793 ASN cc_start: 0.7748 (t0) cc_final: 0.7531 (t0) REVERT: A 797 TYR cc_start: 0.7103 (m-80) cc_final: 0.6622 (m-80) REVERT: A 820 ARG cc_start: 0.6410 (OUTLIER) cc_final: 0.6102 (mtm-85) REVERT: A 919 ILE cc_start: 0.6622 (OUTLIER) cc_final: 0.5950 (mp) REVERT: A 924 ARG cc_start: 0.5993 (OUTLIER) cc_final: 0.5790 (tpt90) outliers start: 87 outliers final: 36 residues processed: 267 average time/residue: 0.9960 time to fit residues: 286.9306 Evaluate side-chains 240 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 199 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain A residue 460 PHE Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 632 PHE Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 658 TYR Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 820 ARG Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 849 LYS Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 924 ARG Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1057 SER Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1105 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 88 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 127 ASN A 454 HIS A 890 GLN A1023 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.177452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.164066 restraints weight = 12579.617| |-----------------------------------------------------------------------------| r_work (start): 0.4140 rms_B_bonded: 1.89 r_work: 0.4038 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3895 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9204 Z= 0.222 Angle : 0.669 9.676 12642 Z= 0.336 Chirality : 0.042 0.152 1439 Planarity : 0.004 0.041 1389 Dihedral : 19.561 179.449 1891 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 9.14 % Allowed : 34.29 % Favored : 56.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.42 (0.27), residues: 900 helix: 1.23 (0.20), residues: 602 sheet: -5.24 (0.61), residues: 10 loop : -1.53 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 435 HIS 0.005 0.001 HIS A 915 PHE 0.032 0.002 PHE A 585 TYR 0.019 0.002 TYR A1075 ARG 0.004 0.001 ARG A 415 Details of bonding type rmsd hydrogen bonds : bond 0.04009 ( 493) hydrogen bonds : angle 4.15599 ( 1424) covalent geometry : bond 0.00498 ( 9204) covalent geometry : angle 0.66885 (12642) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 204 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: A 36 ARG cc_start: 0.7623 (mmm160) cc_final: 0.7209 (ttm-80) REVERT: A 146 GLU cc_start: 0.7288 (tp30) cc_final: 0.6991 (tp30) REVERT: A 149 ARG cc_start: 0.7406 (ttt-90) cc_final: 0.6966 (ttt-90) REVERT: A 272 GLN cc_start: 0.6899 (OUTLIER) cc_final: 0.6213 (mp10) REVERT: A 445 ARG cc_start: 0.7108 (tmm-80) cc_final: 0.6898 (tmm-80) REVERT: A 573 ASN cc_start: 0.6286 (OUTLIER) cc_final: 0.6067 (OUTLIER) REVERT: A 585 PHE cc_start: 0.7670 (t80) cc_final: 0.7363 (t80) REVERT: A 588 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7933 (tt0) REVERT: A 710 GLU cc_start: 0.7605 (mp0) cc_final: 0.7334 (mp0) REVERT: A 757 SER cc_start: 0.7860 (t) cc_final: 0.7608 (t) REVERT: A 786 ASP cc_start: 0.6993 (p0) cc_final: 0.6764 (p0) REVERT: A 793 ASN cc_start: 0.7820 (t0) cc_final: 0.7575 (t0) REVERT: A 797 TYR cc_start: 0.7181 (m-80) cc_final: 0.6445 (m-80) REVERT: A 820 ARG cc_start: 0.6605 (OUTLIER) cc_final: 0.6280 (mtm-85) REVERT: A 882 ASP cc_start: 0.7895 (t0) cc_final: 0.7687 (t0) REVERT: A 895 ASP cc_start: 0.7238 (m-30) cc_final: 0.6974 (m-30) REVERT: A 919 ILE cc_start: 0.6428 (OUTLIER) cc_final: 0.5639 (mp) REVERT: A 1032 SER cc_start: 0.1657 (OUTLIER) cc_final: 0.1115 (m) outliers start: 80 outliers final: 45 residues processed: 260 average time/residue: 0.9930 time to fit residues: 278.4082 Evaluate side-chains 240 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 190 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 454 HIS Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 492 LYS Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 632 PHE Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 820 ARG Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 849 LYS Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 929 MET Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1105 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 34 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 85 optimal weight: 0.4980 chunk 79 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 0.0770 chunk 62 optimal weight: 0.6980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A1023 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.178680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.165711 restraints weight = 12583.495| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 1.94 r_work: 0.4061 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9204 Z= 0.158 Angle : 0.633 10.762 12642 Z= 0.318 Chirality : 0.039 0.143 1439 Planarity : 0.004 0.038 1389 Dihedral : 19.370 179.057 1883 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 9.03 % Allowed : 34.40 % Favored : 56.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.28), residues: 900 helix: 1.37 (0.21), residues: 602 sheet: -5.17 (0.66), residues: 10 loop : -1.57 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 435 HIS 0.011 0.001 HIS A 454 PHE 0.021 0.002 PHE A 585 TYR 0.014 0.001 TYR A 265 ARG 0.007 0.001 ARG A 934 Details of bonding type rmsd hydrogen bonds : bond 0.03728 ( 493) hydrogen bonds : angle 4.03794 ( 1424) covalent geometry : bond 0.00356 ( 9204) covalent geometry : angle 0.63346 (12642) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 196 time to evaluate : 0.934 Fit side-chains REVERT: A 149 ARG cc_start: 0.7109 (ttt-90) cc_final: 0.6727 (ttt-90) REVERT: A 272 GLN cc_start: 0.6783 (OUTLIER) cc_final: 0.6161 (mp-120) REVERT: A 281 GLU cc_start: 0.6451 (pp20) cc_final: 0.6231 (pp20) REVERT: A 585 PHE cc_start: 0.7666 (t80) cc_final: 0.7425 (t80) REVERT: A 588 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7878 (tt0) REVERT: A 647 TYR cc_start: 0.6672 (t80) cc_final: 0.6207 (t80) REVERT: A 685 SER cc_start: 0.7114 (OUTLIER) cc_final: 0.6762 (t) REVERT: A 710 GLU cc_start: 0.7389 (mp0) cc_final: 0.7100 (mp0) REVERT: A 797 TYR cc_start: 0.6923 (m-80) cc_final: 0.6493 (m-80) REVERT: A 919 ILE cc_start: 0.6101 (OUTLIER) cc_final: 0.5208 (mp) REVERT: A 1032 SER cc_start: 0.1609 (OUTLIER) cc_final: 0.1148 (m) REVERT: A 1057 SER cc_start: 0.6934 (OUTLIER) cc_final: 0.6625 (p) REVERT: A 1067 MET cc_start: 0.7126 (OUTLIER) cc_final: 0.6921 (ptp) outliers start: 79 outliers final: 39 residues processed: 249 average time/residue: 0.9698 time to fit residues: 261.4234 Evaluate side-chains 235 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 189 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 454 HIS Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 492 LYS Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 632 PHE Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 849 LYS Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 929 MET Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1057 SER Chi-restraints excluded: chain A residue 1067 MET Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1105 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 14 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 69 optimal weight: 0.0020 chunk 83 optimal weight: 0.3980 chunk 50 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A 454 HIS A 793 ASN A 865 GLN A 890 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.178516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.165366 restraints weight = 12511.519| |-----------------------------------------------------------------------------| r_work (start): 0.4158 rms_B_bonded: 1.96 r_work: 0.4059 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9204 Z= 0.168 Angle : 0.637 11.244 12642 Z= 0.320 Chirality : 0.040 0.143 1439 Planarity : 0.004 0.040 1389 Dihedral : 19.327 179.558 1883 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 8.69 % Allowed : 35.43 % Favored : 55.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.54 (0.27), residues: 900 helix: 1.35 (0.20), residues: 602 sheet: -5.18 (0.66), residues: 10 loop : -1.59 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 435 HIS 0.006 0.001 HIS A 915 PHE 0.025 0.002 PHE A 231 TYR 0.019 0.001 TYR A 844 ARG 0.006 0.001 ARG A 934 Details of bonding type rmsd hydrogen bonds : bond 0.03748 ( 493) hydrogen bonds : angle 4.05126 ( 1424) covalent geometry : bond 0.00378 ( 9204) covalent geometry : angle 0.63721 (12642) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 196 time to evaluate : 0.921 Fit side-chains REVERT: A 48 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7386 (pp) REVERT: A 57 LYS cc_start: 0.7780 (mptt) cc_final: 0.7399 (mptt) REVERT: A 149 ARG cc_start: 0.7169 (ttt-90) cc_final: 0.6834 (ttt-90) REVERT: A 154 LEU cc_start: 0.6506 (OUTLIER) cc_final: 0.6041 (tm) REVERT: A 272 GLN cc_start: 0.6811 (OUTLIER) cc_final: 0.6177 (mp-120) REVERT: A 281 GLU cc_start: 0.6477 (pp20) cc_final: 0.6269 (pp20) REVERT: A 585 PHE cc_start: 0.7711 (t80) cc_final: 0.7471 (t80) REVERT: A 588 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7909 (tt0) REVERT: A 685 SER cc_start: 0.7144 (OUTLIER) cc_final: 0.6778 (t) REVERT: A 710 GLU cc_start: 0.7422 (mp0) cc_final: 0.7134 (mp0) REVERT: A 797 TYR cc_start: 0.6954 (m-80) cc_final: 0.6611 (m-80) REVERT: A 811 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7272 (pm20) REVERT: A 919 ILE cc_start: 0.6118 (OUTLIER) cc_final: 0.5236 (mp) REVERT: A 1032 SER cc_start: 0.1613 (OUTLIER) cc_final: 0.1168 (m) REVERT: A 1067 MET cc_start: 0.7115 (OUTLIER) cc_final: 0.6765 (ptp) outliers start: 76 outliers final: 46 residues processed: 248 average time/residue: 0.9644 time to fit residues: 258.4705 Evaluate side-chains 246 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 191 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 492 LYS Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 632 PHE Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 849 LYS Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 929 MET Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1067 MET Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1105 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 39 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 43 optimal weight: 0.1980 chunk 80 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A 454 HIS A 793 ASN A1023 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.177747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.164719 restraints weight = 12472.992| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 1.92 r_work: 0.4052 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3909 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9204 Z= 0.188 Angle : 0.661 10.638 12642 Z= 0.334 Chirality : 0.041 0.154 1439 Planarity : 0.004 0.040 1389 Dihedral : 19.301 178.446 1883 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 9.94 % Allowed : 34.74 % Favored : 55.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.37 (0.27), residues: 900 helix: 1.23 (0.20), residues: 601 sheet: -5.22 (0.65), residues: 10 loop : -1.66 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 435 HIS 0.004 0.001 HIS A 915 PHE 0.020 0.002 PHE A 231 TYR 0.024 0.002 TYR A1046 ARG 0.006 0.001 ARG A 934 Details of bonding type rmsd hydrogen bonds : bond 0.03840 ( 493) hydrogen bonds : angle 4.13203 ( 1424) covalent geometry : bond 0.00424 ( 9204) covalent geometry : angle 0.66142 (12642) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 195 time to evaluate : 0.991 Fit side-chains REVERT: A 48 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7568 (pp) REVERT: A 57 LYS cc_start: 0.8020 (mptt) cc_final: 0.7656 (mptt) REVERT: A 79 PHE cc_start: 0.7969 (m-10) cc_final: 0.7702 (m-10) REVERT: A 149 ARG cc_start: 0.7394 (ttt-90) cc_final: 0.7039 (ttt-90) REVERT: A 272 GLN cc_start: 0.6921 (OUTLIER) cc_final: 0.6317 (mp-120) REVERT: A 281 GLU cc_start: 0.6635 (pp20) cc_final: 0.6396 (pp20) REVERT: A 585 PHE cc_start: 0.7844 (t80) cc_final: 0.7517 (t80) REVERT: A 588 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7987 (tt0) REVERT: A 685 SER cc_start: 0.7331 (OUTLIER) cc_final: 0.6942 (t) REVERT: A 710 GLU cc_start: 0.7852 (mp0) cc_final: 0.7557 (mp0) REVERT: A 797 TYR cc_start: 0.7219 (m-80) cc_final: 0.6809 (m-80) REVERT: A 919 ILE cc_start: 0.6302 (OUTLIER) cc_final: 0.5441 (mp) REVERT: A 1032 SER cc_start: 0.1969 (OUTLIER) cc_final: 0.1496 (m) REVERT: A 1057 SER cc_start: 0.7140 (OUTLIER) cc_final: 0.6842 (p) REVERT: A 1067 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.6974 (ptp) outliers start: 87 outliers final: 48 residues processed: 258 average time/residue: 0.9894 time to fit residues: 275.5358 Evaluate side-chains 246 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 190 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 492 LYS Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 632 PHE Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 849 LYS Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 929 MET Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1057 SER Chi-restraints excluded: chain A residue 1067 MET Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1105 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 45 optimal weight: 0.2980 chunk 42 optimal weight: 0.0770 chunk 54 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A 454 HIS A 654 GLN A 735 GLN A 793 ASN A 890 GLN A1023 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.178322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.165688 restraints weight = 12602.868| |-----------------------------------------------------------------------------| r_work (start): 0.4160 rms_B_bonded: 1.91 r_work: 0.4061 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3918 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9204 Z= 0.177 Angle : 0.670 10.801 12642 Z= 0.338 Chirality : 0.040 0.149 1439 Planarity : 0.004 0.046 1389 Dihedral : 19.217 178.337 1883 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 9.37 % Allowed : 36.23 % Favored : 54.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.36 (0.27), residues: 900 helix: 1.23 (0.20), residues: 601 sheet: -5.21 (0.66), residues: 10 loop : -1.69 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 435 HIS 0.005 0.001 HIS A 915 PHE 0.022 0.002 PHE A 713 TYR 0.021 0.002 TYR A 844 ARG 0.009 0.001 ARG A 934 Details of bonding type rmsd hydrogen bonds : bond 0.03780 ( 493) hydrogen bonds : angle 4.14206 ( 1424) covalent geometry : bond 0.00401 ( 9204) covalent geometry : angle 0.67046 (12642) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 191 time to evaluate : 0.865 Fit side-chains REVERT: A 48 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7559 (pp) REVERT: A 57 LYS cc_start: 0.7979 (mptt) cc_final: 0.7586 (mptt) REVERT: A 79 PHE cc_start: 0.7916 (m-10) cc_final: 0.7642 (m-10) REVERT: A 149 ARG cc_start: 0.7409 (ttt-90) cc_final: 0.7124 (ttt-90) REVERT: A 154 LEU cc_start: 0.6609 (OUTLIER) cc_final: 0.6140 (tm) REVERT: A 272 GLN cc_start: 0.6931 (OUTLIER) cc_final: 0.6336 (mp-120) REVERT: A 281 GLU cc_start: 0.6593 (pp20) cc_final: 0.6241 (pm20) REVERT: A 506 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.7395 (tt) REVERT: A 583 GLU cc_start: 0.7645 (tp30) cc_final: 0.7214 (tt0) REVERT: A 585 PHE cc_start: 0.7836 (t80) cc_final: 0.7489 (t80) REVERT: A 588 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7996 (tt0) REVERT: A 685 SER cc_start: 0.7338 (OUTLIER) cc_final: 0.6960 (t) REVERT: A 710 GLU cc_start: 0.7840 (mp0) cc_final: 0.7566 (mp0) REVERT: A 797 TYR cc_start: 0.7197 (m-80) cc_final: 0.6785 (m-80) REVERT: A 833 ILE cc_start: 0.6010 (OUTLIER) cc_final: 0.5782 (mp) REVERT: A 919 ILE cc_start: 0.6301 (OUTLIER) cc_final: 0.5394 (mp) REVERT: A 1032 SER cc_start: 0.1876 (OUTLIER) cc_final: 0.1443 (m) REVERT: A 1057 SER cc_start: 0.7134 (OUTLIER) cc_final: 0.6816 (p) REVERT: A 1067 MET cc_start: 0.7356 (OUTLIER) cc_final: 0.7036 (ptp) outliers start: 82 outliers final: 52 residues processed: 249 average time/residue: 0.9553 time to fit residues: 256.6358 Evaluate side-chains 250 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 187 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 460 PHE Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 492 LYS Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 632 PHE Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 654 GLN Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 849 LYS Chi-restraints excluded: chain A residue 857 TYR Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 929 MET Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1057 SER Chi-restraints excluded: chain A residue 1067 MET Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1105 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 74 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 85 optimal weight: 0.1980 chunk 66 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 58 optimal weight: 0.0770 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 HIS A 654 GLN A 735 GLN A 793 ASN A1023 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.179658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.166810 restraints weight = 12697.286| |-----------------------------------------------------------------------------| r_work (start): 0.4172 rms_B_bonded: 1.92 r_work: 0.4075 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9204 Z= 0.156 Angle : 0.666 10.712 12642 Z= 0.334 Chirality : 0.039 0.147 1439 Planarity : 0.004 0.042 1389 Dihedral : 19.109 177.824 1883 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 8.23 % Allowed : 37.37 % Favored : 54.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.54 (0.28), residues: 900 helix: 1.39 (0.21), residues: 602 sheet: -5.18 (0.67), residues: 10 loop : -1.70 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 435 HIS 0.006 0.001 HIS A 915 PHE 0.020 0.002 PHE A 231 TYR 0.024 0.002 TYR A1046 ARG 0.009 0.001 ARG A 934 Details of bonding type rmsd hydrogen bonds : bond 0.03636 ( 493) hydrogen bonds : angle 4.09956 ( 1424) covalent geometry : bond 0.00352 ( 9204) covalent geometry : angle 0.66590 (12642) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 195 time to evaluate : 0.887 Fit side-chains revert: symmetry clash REVERT: A 48 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7366 (pp) REVERT: A 57 LYS cc_start: 0.7761 (mptt) cc_final: 0.7347 (mptt) REVERT: A 149 ARG cc_start: 0.7193 (ttt-90) cc_final: 0.6920 (ttt-90) REVERT: A 154 LEU cc_start: 0.6558 (OUTLIER) cc_final: 0.6080 (tm) REVERT: A 272 GLN cc_start: 0.6815 (OUTLIER) cc_final: 0.6208 (mp-120) REVERT: A 281 GLU cc_start: 0.6400 (pp20) cc_final: 0.6112 (pm20) REVERT: A 506 ILE cc_start: 0.7567 (OUTLIER) cc_final: 0.7290 (OUTLIER) REVERT: A 533 PHE cc_start: 0.8390 (m-10) cc_final: 0.8188 (m-80) REVERT: A 583 GLU cc_start: 0.7310 (tp30) cc_final: 0.6934 (tt0) REVERT: A 585 PHE cc_start: 0.7742 (t80) cc_final: 0.7479 (t80) REVERT: A 588 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7919 (tt0) REVERT: A 685 SER cc_start: 0.7120 (OUTLIER) cc_final: 0.6731 (t) REVERT: A 710 GLU cc_start: 0.7507 (mp0) cc_final: 0.7235 (mp0) REVERT: A 797 TYR cc_start: 0.6889 (m-80) cc_final: 0.6511 (m-80) REVERT: A 1032 SER cc_start: 0.2119 (OUTLIER) cc_final: 0.1663 (m) REVERT: A 1057 SER cc_start: 0.6901 (OUTLIER) cc_final: 0.6600 (p) REVERT: A 1067 MET cc_start: 0.7107 (OUTLIER) cc_final: 0.6772 (ptp) outliers start: 72 outliers final: 41 residues processed: 246 average time/residue: 0.9573 time to fit residues: 254.5497 Evaluate side-chains 242 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 193 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 460 PHE Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 632 PHE Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 849 LYS Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 929 MET Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1057 SER Chi-restraints excluded: chain A residue 1067 MET Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1105 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 83 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 68 optimal weight: 0.0270 chunk 64 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.0770 chunk 21 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 HIS A 684 ASN A 735 GLN A 793 ASN A 890 GLN A1023 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.179599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.166752 restraints weight = 12597.658| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 1.93 r_work: 0.4078 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9204 Z= 0.162 Angle : 0.687 10.566 12642 Z= 0.343 Chirality : 0.040 0.144 1439 Planarity : 0.004 0.042 1389 Dihedral : 19.013 178.150 1876 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 7.31 % Allowed : 38.51 % Favored : 54.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.53 (0.28), residues: 900 helix: 1.38 (0.21), residues: 602 sheet: -5.22 (0.66), residues: 10 loop : -1.68 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 435 HIS 0.004 0.001 HIS A 915 PHE 0.020 0.002 PHE A 231 TYR 0.014 0.002 TYR A 647 ARG 0.008 0.001 ARG A 934 Details of bonding type rmsd hydrogen bonds : bond 0.03678 ( 493) hydrogen bonds : angle 4.13423 ( 1424) covalent geometry : bond 0.00369 ( 9204) covalent geometry : angle 0.68695 (12642) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 192 time to evaluate : 0.854 Fit side-chains revert: symmetry clash REVERT: A 35 MET cc_start: 0.4895 (tpt) cc_final: 0.4656 (tpt) REVERT: A 48 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7372 (pp) REVERT: A 57 LYS cc_start: 0.7736 (mptt) cc_final: 0.7347 (mptt) REVERT: A 69 GLU cc_start: 0.6977 (mp0) cc_final: 0.6747 (mp0) REVERT: A 149 ARG cc_start: 0.7187 (ttt-90) cc_final: 0.6917 (ttt-90) REVERT: A 150 ILE cc_start: 0.7885 (tp) cc_final: 0.7646 (tp) REVERT: A 154 LEU cc_start: 0.6614 (OUTLIER) cc_final: 0.6148 (tm) REVERT: A 272 GLN cc_start: 0.6823 (OUTLIER) cc_final: 0.6199 (mp-120) REVERT: A 281 GLU cc_start: 0.6425 (pp20) cc_final: 0.6169 (pm20) REVERT: A 365 GLU cc_start: 0.7347 (tm-30) cc_final: 0.6930 (tm-30) REVERT: A 506 ILE cc_start: 0.7546 (OUTLIER) cc_final: 0.7273 (OUTLIER) REVERT: A 583 GLU cc_start: 0.7332 (tp30) cc_final: 0.6963 (tt0) REVERT: A 585 PHE cc_start: 0.7746 (t80) cc_final: 0.7499 (t80) REVERT: A 588 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7915 (tt0) REVERT: A 685 SER cc_start: 0.7098 (OUTLIER) cc_final: 0.6749 (t) REVERT: A 710 GLU cc_start: 0.7500 (mp0) cc_final: 0.7190 (mp0) REVERT: A 797 TYR cc_start: 0.6915 (m-80) cc_final: 0.6533 (m-80) REVERT: A 1032 SER cc_start: 0.2071 (OUTLIER) cc_final: 0.1611 (m) REVERT: A 1057 SER cc_start: 0.6932 (OUTLIER) cc_final: 0.6623 (p) REVERT: A 1067 MET cc_start: 0.7111 (OUTLIER) cc_final: 0.6780 (ptp) outliers start: 64 outliers final: 43 residues processed: 235 average time/residue: 0.9759 time to fit residues: 247.6804 Evaluate side-chains 240 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 189 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 460 PHE Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 492 LYS Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 632 PHE Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 849 LYS Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1057 SER Chi-restraints excluded: chain A residue 1067 MET Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1105 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 0.0980 chunk 55 optimal weight: 0.4980 chunk 72 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 90 optimal weight: 0.0370 chunk 30 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 127 ASN ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 HIS A 684 ASN A 714 HIS A 735 GLN A 793 ASN A 890 GLN A1023 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.180677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.167628 restraints weight = 12510.994| |-----------------------------------------------------------------------------| r_work (start): 0.4185 rms_B_bonded: 1.96 r_work: 0.4086 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9204 Z= 0.153 Angle : 0.696 10.521 12642 Z= 0.348 Chirality : 0.039 0.142 1439 Planarity : 0.004 0.043 1389 Dihedral : 18.909 177.281 1876 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 6.63 % Allowed : 39.43 % Favored : 53.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.28), residues: 900 helix: 1.42 (0.21), residues: 603 sheet: -5.14 (0.67), residues: 10 loop : -1.64 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 435 HIS 0.005 0.000 HIS A 915 PHE 0.014 0.002 PHE A 585 TYR 0.024 0.002 TYR A1046 ARG 0.008 0.001 ARG A 934 Details of bonding type rmsd hydrogen bonds : bond 0.03597 ( 493) hydrogen bonds : angle 4.11015 ( 1424) covalent geometry : bond 0.00349 ( 9204) covalent geometry : angle 0.69614 (12642) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 188 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.4869 (tpt) cc_final: 0.4607 (tpt) REVERT: A 48 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7339 (pp) REVERT: A 57 LYS cc_start: 0.7749 (mptt) cc_final: 0.7346 (mptt) REVERT: A 69 GLU cc_start: 0.7015 (mp0) cc_final: 0.6762 (mp0) REVERT: A 149 ARG cc_start: 0.7157 (ttt-90) cc_final: 0.6864 (ttt-90) REVERT: A 154 LEU cc_start: 0.6480 (OUTLIER) cc_final: 0.6016 (tm) REVERT: A 272 GLN cc_start: 0.6811 (OUTLIER) cc_final: 0.6195 (mp-120) REVERT: A 365 GLU cc_start: 0.7355 (tm-30) cc_final: 0.6926 (tm-30) REVERT: A 506 ILE cc_start: 0.7602 (OUTLIER) cc_final: 0.7351 (OUTLIER) REVERT: A 533 PHE cc_start: 0.8344 (m-10) cc_final: 0.8140 (m-80) REVERT: A 583 GLU cc_start: 0.7340 (tp30) cc_final: 0.7116 (tt0) REVERT: A 585 PHE cc_start: 0.7761 (t80) cc_final: 0.7490 (t80) REVERT: A 588 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7902 (tt0) REVERT: A 648 MET cc_start: 0.6802 (ttm) cc_final: 0.6472 (tpp) REVERT: A 685 SER cc_start: 0.7094 (OUTLIER) cc_final: 0.6709 (t) REVERT: A 710 GLU cc_start: 0.7481 (mp0) cc_final: 0.7174 (mp0) REVERT: A 735 GLN cc_start: 0.6932 (OUTLIER) cc_final: 0.6459 (mt0) REVERT: A 797 TYR cc_start: 0.6986 (m-80) cc_final: 0.6714 (m-80) REVERT: A 1032 SER cc_start: 0.2006 (OUTLIER) cc_final: 0.1550 (m) REVERT: A 1057 SER cc_start: 0.6875 (OUTLIER) cc_final: 0.6542 (p) REVERT: A 1067 MET cc_start: 0.7115 (OUTLIER) cc_final: 0.6789 (ptp) outliers start: 58 outliers final: 41 residues processed: 227 average time/residue: 1.0014 time to fit residues: 246.0747 Evaluate side-chains 236 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 186 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 460 PHE Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 492 LYS Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 632 PHE Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 849 LYS Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1046 TYR Chi-restraints excluded: chain A residue 1057 SER Chi-restraints excluded: chain A residue 1067 MET Chi-restraints excluded: chain A residue 1105 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 3 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 0.3980 chunk 32 optimal weight: 0.4980 chunk 60 optimal weight: 0.3980 chunk 65 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A 153 ASN ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 HIS A 684 ASN A 793 ASN A 890 GLN A1023 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.180644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.167514 restraints weight = 12621.372| |-----------------------------------------------------------------------------| r_work (start): 0.4182 rms_B_bonded: 1.97 r_work: 0.4084 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.442 9204 Z= 0.370 Angle : 1.234 59.198 12642 Z= 0.728 Chirality : 0.048 0.763 1439 Planarity : 0.005 0.096 1389 Dihedral : 18.919 177.238 1875 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 6.29 % Allowed : 40.11 % Favored : 53.60 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % 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: 0.53 (0.28), residues: 900 helix: 1.39 (0.21), residues: 603 sheet: -5.13 (0.67), residues: 10 loop : -1.70 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 435 HIS 0.005 0.001 HIS A 915 PHE 0.014 0.002 PHE A 585 TYR 0.212 0.003 TYR A1046 ARG 0.007 0.001 ARG A 934 Details of bonding type rmsd hydrogen bonds : bond 0.03600 ( 493) hydrogen bonds : angle 4.11355 ( 1424) covalent geometry : bond 0.00793 ( 9204) covalent geometry : angle 1.23369 (12642) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6322.88 seconds wall clock time: 109 minutes 54.00 seconds (6594.00 seconds total)