Starting phenix.real_space_refine on Tue Apr 29 20:27:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zty_60476/04_2025/8zty_60476.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zty_60476/04_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_60476/04_2025/8zty_60476.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zty_60476/04_2025/8zty_60476.map" model { file = "/net/cci-nas-00/data/ceres_data/8zty_60476/04_2025/8zty_60476.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zty_60476/04_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-5669/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: 6.29, per 1000 atoms: 0.70 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: 2.42 Conformation dependent library (CDL) restraints added in 870.5 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: 3.00 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: 3.07 Time building geometry restraints manager: 2.87 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: 1.730 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.870 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.530 ------------------------------------------------------------------------------- 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 : 1.336 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: 1.1693 time to fit residues: 277.1735 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 : 0.977 ------------------------------------------------------------------------------- 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 = 45)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.164523 restraints weight = 12521.485| |-----------------------------------------------------------------------------| 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 : 0.933 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: 0.7563 (tp-100) REVERT: A 272 GLN cc_start: 0.6749 (OUTLIER) cc_final: 0.6176 (mp-120) REVERT: A 282 LEU cc_start: 0.7934 (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: 0.6370 (OUTLIER) cc_final: 0.6078 (p) REVERT: A 710 GLU cc_start: 0.7384 (mp0) cc_final: 0.7149 (mp0) REVERT: A 757 SER cc_start: 0.7941 (t) cc_final: 0.7632 (t) REVERT: A 781 LYS cc_start: 0.6140 (pptt) cc_final: 0.5925 (pptt) REVERT: A 793 ASN cc_start: 0.7748 (t0) cc_final: 0.7530 (t0) REVERT: A 797 TYR cc_start: 0.7103 (m-80) cc_final: 0.6622 (m-80) REVERT: A 820 ARG cc_start: 0.6411 (OUTLIER) cc_final: 0.6102 (mtm-85) REVERT: A 919 ILE cc_start: 0.6620 (OUTLIER) cc_final: 0.5949 (mp) REVERT: A 924 ARG cc_start: 0.5992 (OUTLIER) cc_final: 0.5790 (tpt90) outliers start: 87 outliers final: 36 residues processed: 267 average time/residue: 1.0019 time to fit residues: 288.8702 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 : 0.892 ------------------------------------------------------------------------------- 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: 0.9980 chunk 67 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 chunk 15 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A 890 GLN A1023 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.177716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.164480 restraints weight = 12600.409| |-----------------------------------------------------------------------------| r_work (start): 0.4146 rms_B_bonded: 1.86 r_work: 0.4044 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3901 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9204 Z= 0.211 Angle : 0.660 9.852 12642 Z= 0.331 Chirality : 0.042 0.147 1439 Planarity : 0.004 0.039 1389 Dihedral : 19.540 179.400 1891 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 9.37 % Allowed : 33.71 % Favored : 56.91 % 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: 0.48 (0.27), residues: 900 helix: 1.27 (0.20), residues: 602 sheet: -5.22 (0.62), residues: 10 loop : -1.51 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 435 HIS 0.004 0.001 HIS A 915 PHE 0.033 0.002 PHE A 585 TYR 0.018 0.002 TYR A1075 ARG 0.005 0.001 ARG A 438 Details of bonding type rmsd hydrogen bonds : bond 0.03935 ( 493) hydrogen bonds : angle 4.13547 ( 1424) covalent geometry : bond 0.00471 ( 9204) covalent geometry : angle 0.65989 (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 283 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 201 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: A 146 GLU cc_start: 0.7269 (tp30) cc_final: 0.6999 (tp30) REVERT: A 149 ARG cc_start: 0.7384 (ttt-90) cc_final: 0.6948 (ttt-90) REVERT: A 272 GLN cc_start: 0.6910 (OUTLIER) cc_final: 0.6235 (mp10) REVERT: A 585 PHE cc_start: 0.7661 (t80) cc_final: 0.7348 (t80) REVERT: A 588 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7935 (tt0) REVERT: A 710 GLU cc_start: 0.7612 (mp0) cc_final: 0.7344 (mp0) REVERT: A 786 ASP cc_start: 0.6970 (p0) cc_final: 0.6746 (p0) REVERT: A 793 ASN cc_start: 0.7809 (t0) cc_final: 0.7564 (t0) REVERT: A 797 TYR cc_start: 0.7168 (m-80) cc_final: 0.6438 (m-80) REVERT: A 820 ARG cc_start: 0.6573 (OUTLIER) cc_final: 0.6246 (mtm-85) REVERT: A 882 ASP cc_start: 0.7891 (t0) cc_final: 0.7687 (t0) REVERT: A 919 ILE cc_start: 0.6408 (OUTLIER) cc_final: 0.5580 (mp) REVERT: A 1032 SER cc_start: 0.1677 (OUTLIER) cc_final: 0.1090 (m) outliers start: 82 outliers final: 44 residues processed: 258 average time/residue: 1.5264 time to fit residues: 428.6145 Evaluate side-chains 239 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 190 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 425 ILE Chi-restraints excluded: chain A residue 451 LEU 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 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: 0.9980 chunk 66 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 62 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 A1023 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.178008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.165053 restraints weight = 12566.837| |-----------------------------------------------------------------------------| r_work (start): 0.4153 rms_B_bonded: 1.94 r_work: 0.4053 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.2165 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= 0.174 Angle : 0.640 11.082 12642 Z= 0.321 Chirality : 0.040 0.149 1439 Planarity : 0.004 0.040 1389 Dihedral : 19.390 179.206 1883 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 9.49 % Allowed : 33.60 % Favored : 56.91 % 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: 0.49 (0.27), residues: 900 helix: 1.31 (0.20), residues: 602 sheet: -5.23 (0.65), residues: 10 loop : -1.58 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 435 HIS 0.005 0.001 HIS A 915 PHE 0.021 0.002 PHE A 585 TYR 0.015 0.002 TYR A 265 ARG 0.007 0.001 ARG A 934 Details of bonding type rmsd hydrogen bonds : bond 0.03796 ( 493) hydrogen bonds : angle 4.06976 ( 1424) covalent geometry : bond 0.00391 ( 9204) covalent geometry : angle 0.64002 (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 280 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 197 time to evaluate : 1.124 Fit side-chains REVERT: A 57 LYS cc_start: 0.7815 (mptt) cc_final: 0.7396 (mptt) REVERT: A 149 ARG cc_start: 0.7142 (ttt-90) cc_final: 0.6747 (ttt-90) REVERT: A 272 GLN cc_start: 0.6807 (OUTLIER) cc_final: 0.6168 (mp-120) REVERT: A 281 GLU cc_start: 0.6454 (pp20) cc_final: 0.6234 (pp20) REVERT: A 585 PHE cc_start: 0.7665 (t80) cc_final: 0.7436 (t80) REVERT: A 588 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7885 (tt0) REVERT: A 685 SER cc_start: 0.7138 (OUTLIER) cc_final: 0.6789 (t) REVERT: A 710 GLU cc_start: 0.7405 (mp0) cc_final: 0.7124 (mp0) REVERT: A 786 ASP cc_start: 0.6791 (p0) cc_final: 0.6583 (p0) REVERT: A 797 TYR cc_start: 0.6936 (m-80) cc_final: 0.6511 (m-80) REVERT: A 811 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7246 (pm20) REVERT: A 919 ILE cc_start: 0.6143 (OUTLIER) cc_final: 0.5294 (mp) REVERT: A 1032 SER cc_start: 0.1614 (OUTLIER) cc_final: 0.1181 (m) REVERT: A 1057 SER cc_start: 0.6943 (OUTLIER) cc_final: 0.6628 (p) REVERT: A 1067 MET cc_start: 0.7137 (OUTLIER) cc_final: 0.6916 (ptp) outliers start: 83 outliers final: 44 residues processed: 253 average time/residue: 1.0313 time to fit residues: 281.9004 Evaluate side-chains 243 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 191 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 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 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 599 VAL 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 857 TYR 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 1057 SER Chi-restraints excluded: chain A residue 1067 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 14 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 63 optimal weight: 0.0470 chunk 69 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- 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 793 ASN A 865 GLN 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 = 0.4293 r_free = 0.4293 target = 0.177289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.164159 restraints weight = 12481.352| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 1.95 r_work: 0.4046 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.2378 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= 0.193 Angle : 0.659 10.520 12642 Z= 0.331 Chirality : 0.041 0.149 1439 Planarity : 0.004 0.042 1389 Dihedral : 19.374 178.411 1883 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 10.17 % Allowed : 34.17 % Favored : 55.66 % 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: 1.21 (0.20), residues: 602 sheet: -5.28 (0.64), residues: 10 loop : -1.63 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 435 HIS 0.005 0.001 HIS A 915 PHE 0.018 0.002 PHE A 585 TYR 0.025 0.002 TYR A1046 ARG 0.006 0.001 ARG A 934 Details of bonding type rmsd hydrogen bonds : bond 0.03882 ( 493) hydrogen bonds : angle 4.14059 ( 1424) covalent geometry : bond 0.00434 ( 9204) covalent geometry : angle 0.65869 (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 288 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 199 time to evaluate : 0.869 Fit side-chains REVERT: A 57 LYS cc_start: 0.7808 (mptt) cc_final: 0.7441 (mptt) REVERT: A 149 ARG cc_start: 0.7204 (ttt-90) cc_final: 0.6879 (ttt-90) REVERT: A 281 GLU cc_start: 0.6470 (pp20) cc_final: 0.6254 (pp20) REVERT: A 585 PHE cc_start: 0.7707 (t80) cc_final: 0.7481 (t80) REVERT: A 588 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7910 (tt0) REVERT: A 685 SER cc_start: 0.7168 (OUTLIER) cc_final: 0.6802 (t) REVERT: A 710 GLU cc_start: 0.7440 (mp0) cc_final: 0.7158 (mp0) REVERT: A 797 TYR cc_start: 0.6956 (m-80) cc_final: 0.6636 (m-80) REVERT: A 811 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7335 (pm20) REVERT: A 919 ILE cc_start: 0.6174 (OUTLIER) cc_final: 0.5355 (mp) REVERT: A 1032 SER cc_start: 0.1410 (OUTLIER) cc_final: 0.0914 (m) REVERT: A 1067 MET cc_start: 0.7121 (OUTLIER) cc_final: 0.6645 (ptp) outliers start: 89 outliers final: 50 residues processed: 261 average time/residue: 1.0726 time to fit residues: 301.0316 Evaluate side-chains 249 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 193 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 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 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 599 VAL 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 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 811 GLU Chi-restraints excluded: chain A residue 832 THR 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 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 1070 THR 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: 1.9990 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: 0.7980 chunk 80 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 684 ASN A 735 GLN A 793 ASN A1023 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.176139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.163406 restraints weight = 12418.778| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 1.89 r_work: 0.4038 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3895 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9204 Z= 0.223 Angle : 0.694 10.242 12642 Z= 0.350 Chirality : 0.043 0.155 1439 Planarity : 0.004 0.044 1389 Dihedral : 19.390 178.941 1883 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 9.14 % Allowed : 35.89 % Favored : 54.97 % 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: 0.13 (0.27), residues: 900 helix: 1.03 (0.20), residues: 600 sheet: -5.30 (0.63), residues: 10 loop : -1.69 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 435 HIS 0.005 0.001 HIS A 915 PHE 0.024 0.002 PHE A 713 TYR 0.019 0.002 TYR A1075 ARG 0.008 0.001 ARG A 934 Details of bonding type rmsd hydrogen bonds : bond 0.04083 ( 493) hydrogen bonds : angle 4.23336 ( 1424) covalent geometry : bond 0.00503 ( 9204) covalent geometry : angle 0.69403 (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 276 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 196 time to evaluate : 0.863 Fit side-chains REVERT: A 57 LYS cc_start: 0.8036 (mptt) cc_final: 0.7637 (mptt) REVERT: A 79 PHE cc_start: 0.8003 (m-10) cc_final: 0.7755 (m-10) REVERT: A 149 ARG cc_start: 0.7458 (ttt-90) cc_final: 0.7105 (ttt-90) REVERT: A 281 GLU cc_start: 0.6775 (pp20) cc_final: 0.6542 (pp20) REVERT: A 506 ILE cc_start: 0.7750 (OUTLIER) cc_final: 0.7498 (tp) REVERT: A 585 PHE cc_start: 0.7838 (t80) cc_final: 0.7507 (t80) REVERT: A 588 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.8007 (tt0) REVERT: A 647 TYR cc_start: 0.6883 (t80) cc_final: 0.6507 (t80) REVERT: A 685 SER cc_start: 0.7362 (OUTLIER) cc_final: 0.7007 (t) REVERT: A 710 GLU cc_start: 0.7855 (mp0) cc_final: 0.7573 (mp0) REVERT: A 797 TYR cc_start: 0.7194 (m-80) cc_final: 0.6761 (m-80) REVERT: A 810 GLN cc_start: 0.6298 (mm110) cc_final: 0.5800 (mt0) REVERT: A 919 ILE cc_start: 0.6455 (OUTLIER) cc_final: 0.5646 (mp) REVERT: A 1032 SER cc_start: 0.1540 (OUTLIER) cc_final: 0.1015 (m) REVERT: A 1067 MET cc_start: 0.7328 (OUTLIER) cc_final: 0.6875 (ptp) outliers start: 80 outliers final: 52 residues processed: 255 average time/residue: 1.0418 time to fit residues: 286.3689 Evaluate side-chains 248 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 190 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 299 LEU Chi-restraints excluded: chain A residue 347 SER 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 506 ILE Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 599 VAL 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 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 832 THR 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 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 1070 THR 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: 0.5980 chunk 42 optimal weight: 0.0270 chunk 54 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A 454 HIS A 654 GLN A 684 ASN A 735 GLN A 793 ASN A 890 GLN A1023 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.177613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.164774 restraints weight = 12568.639| |-----------------------------------------------------------------------------| r_work (start): 0.4152 rms_B_bonded: 1.91 r_work: 0.4053 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3911 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9204 Z= 0.183 Angle : 0.684 10.518 12642 Z= 0.344 Chirality : 0.041 0.153 1439 Planarity : 0.004 0.048 1389 Dihedral : 19.284 177.708 1883 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 8.57 % Allowed : 36.46 % Favored : 54.97 % 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: 0.22 (0.27), residues: 900 helix: 1.14 (0.20), residues: 598 sheet: -5.25 (0.65), residues: 10 loop : -1.74 (0.35), residues: 292 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 0.032 0.002 PHE A 491 TYR 0.024 0.002 TYR A1046 ARG 0.009 0.001 ARG A 934 Details of bonding type rmsd hydrogen bonds : bond 0.03852 ( 493) hydrogen bonds : angle 4.19217 ( 1424) covalent geometry : bond 0.00414 ( 9204) covalent geometry : angle 0.68369 (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 272 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 197 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: A 54 ASN cc_start: 0.7918 (p0) cc_final: 0.7646 (p0) REVERT: A 57 LYS cc_start: 0.8006 (mptt) cc_final: 0.7615 (mptt) REVERT: A 79 PHE cc_start: 0.7939 (m-10) cc_final: 0.7656 (m-10) REVERT: A 149 ARG cc_start: 0.7439 (ttt-90) cc_final: 0.7074 (ttt-90) REVERT: A 281 GLU cc_start: 0.6634 (pp20) cc_final: 0.6256 (pm20) REVERT: A 365 GLU cc_start: 0.7679 (tm-30) cc_final: 0.7278 (tm-30) REVERT: A 506 ILE cc_start: 0.7734 (OUTLIER) cc_final: 0.7441 (tt) REVERT: A 583 GLU cc_start: 0.7639 (tp30) cc_final: 0.7207 (tt0) REVERT: A 585 PHE cc_start: 0.7826 (t80) cc_final: 0.7517 (t80) REVERT: A 588 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7999 (tt0) REVERT: A 685 SER cc_start: 0.7334 (OUTLIER) cc_final: 0.6950 (t) REVERT: A 710 GLU cc_start: 0.7841 (mp0) cc_final: 0.7545 (mp0) REVERT: A 797 TYR cc_start: 0.7166 (m-80) cc_final: 0.6717 (m-80) REVERT: A 833 ILE cc_start: 0.6094 (OUTLIER) cc_final: 0.5879 (mp) REVERT: A 919 ILE cc_start: 0.6262 (OUTLIER) cc_final: 0.5333 (mp) REVERT: A 1032 SER cc_start: 0.1942 (OUTLIER) cc_final: 0.1483 (m) REVERT: A 1067 MET cc_start: 0.7320 (OUTLIER) cc_final: 0.7008 (ptp) outliers start: 75 outliers final: 49 residues processed: 248 average time/residue: 1.0296 time to fit residues: 275.1059 Evaluate side-chains 245 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 189 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 208 SER Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 347 SER 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 465 PHE 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 599 VAL 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 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 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 1046 TYR Chi-restraints excluded: chain A residue 1067 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 74 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 60 optimal weight: 0.3980 chunk 12 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 42 optimal weight: 0.0970 chunk 25 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 735 GLN A 793 ASN A1023 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.178850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.165999 restraints weight = 12646.785| |-----------------------------------------------------------------------------| r_work (start): 0.4165 rms_B_bonded: 1.92 r_work: 0.4065 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3922 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9204 Z= 0.163 Angle : 0.679 10.591 12642 Z= 0.340 Chirality : 0.040 0.148 1439 Planarity : 0.004 0.048 1389 Dihedral : 19.193 178.127 1883 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 7.20 % Allowed : 38.74 % Favored : 54.06 % 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 (0.28), residues: 900 helix: 1.28 (0.21), residues: 599 sheet: -5.25 (0.65), residues: 10 loop : -1.74 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 435 HIS 0.005 0.000 HIS A 915 PHE 0.028 0.002 PHE A 491 TYR 0.022 0.002 TYR A1046 ARG 0.009 0.001 ARG A 934 Details of bonding type rmsd hydrogen bonds : bond 0.03728 ( 493) hydrogen bonds : angle 4.13954 ( 1424) covalent geometry : bond 0.00369 ( 9204) covalent geometry : angle 0.67886 (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 260 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 197 time to evaluate : 0.945 Fit side-chains REVERT: A 54 ASN cc_start: 0.7931 (p0) cc_final: 0.7657 (p0) REVERT: A 57 LYS cc_start: 0.7966 (mptt) cc_final: 0.7583 (mptt) REVERT: A 79 PHE cc_start: 0.7899 (m-10) cc_final: 0.7604 (m-10) REVERT: A 149 ARG cc_start: 0.7395 (ttt-90) cc_final: 0.7069 (ttt-90) REVERT: A 207 GLN cc_start: 0.7319 (tt0) cc_final: 0.7074 (tt0) REVERT: A 281 GLU cc_start: 0.6596 (pp20) cc_final: 0.6302 (pm20) REVERT: A 365 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7279 (tm-30) REVERT: A 506 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7428 (OUTLIER) REVERT: A 514 LYS cc_start: 0.8377 (ptpp) cc_final: 0.7963 (ptpt) REVERT: A 583 GLU cc_start: 0.7658 (tp30) cc_final: 0.6921 (tt0) REVERT: A 585 PHE cc_start: 0.7824 (t80) cc_final: 0.7476 (t80) REVERT: A 588 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.8036 (tt0) REVERT: A 647 TYR cc_start: 0.6825 (t80) cc_final: 0.6254 (t80) REVERT: A 685 SER cc_start: 0.7312 (OUTLIER) cc_final: 0.6940 (t) REVERT: A 710 GLU cc_start: 0.7806 (mp0) cc_final: 0.7533 (mp0) REVERT: A 797 TYR cc_start: 0.7181 (m-80) cc_final: 0.6789 (m-80) REVERT: A 833 ILE cc_start: 0.6032 (OUTLIER) cc_final: 0.5814 (mp) REVERT: A 882 ASP cc_start: 0.7891 (t0) cc_final: 0.7670 (t0) REVERT: A 919 ILE cc_start: 0.6210 (OUTLIER) cc_final: 0.5180 (mp) REVERT: A 1032 SER cc_start: 0.2283 (OUTLIER) cc_final: 0.1874 (m) REVERT: A 1067 MET cc_start: 0.7278 (OUTLIER) cc_final: 0.6975 (ptp) outliers start: 63 outliers final: 40 residues processed: 239 average time/residue: 1.0514 time to fit residues: 270.4666 Evaluate side-chains 239 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 193 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 195 LYS 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 465 PHE 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 83 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 68 optimal weight: 0.0070 chunk 64 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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 684 ASN A 735 GLN A 793 ASN A 890 GLN A1023 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.178219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.165453 restraints weight = 12553.323| |-----------------------------------------------------------------------------| r_work (start): 0.4157 rms_B_bonded: 1.90 r_work: 0.4059 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3916 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.2496 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= 0.183 Angle : 0.699 10.122 12642 Z= 0.350 Chirality : 0.041 0.153 1439 Planarity : 0.004 0.051 1389 Dihedral : 19.162 178.200 1883 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 7.31 % Allowed : 38.97 % Favored : 53.71 % 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: 0.34 (0.28), residues: 900 helix: 1.23 (0.20), residues: 599 sheet: -5.27 (0.64), residues: 10 loop : -1.72 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 435 HIS 0.005 0.001 HIS A 915 PHE 0.029 0.002 PHE A 491 TYR 0.015 0.002 TYR A 647 ARG 0.010 0.001 ARG A 934 Details of bonding type rmsd hydrogen bonds : bond 0.03810 ( 493) hydrogen bonds : angle 4.21158 ( 1424) covalent geometry : bond 0.00417 ( 9204) covalent geometry : angle 0.69872 (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 262 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 198 time to evaluate : 0.876 Fit side-chains REVERT: A 35 MET cc_start: 0.5383 (tpt) cc_final: 0.5067 (tpt) REVERT: A 40 VAL cc_start: 0.7262 (OUTLIER) cc_final: 0.6936 (m) REVERT: A 54 ASN cc_start: 0.7953 (p0) cc_final: 0.7701 (p0) REVERT: A 57 LYS cc_start: 0.7975 (mptt) cc_final: 0.7603 (mptt) REVERT: A 79 PHE cc_start: 0.7903 (m-10) cc_final: 0.7587 (m-10) REVERT: A 149 ARG cc_start: 0.7424 (ttt-90) cc_final: 0.7092 (ttt-90) REVERT: A 156 GLN cc_start: 0.7906 (mm-40) cc_final: 0.7628 (tp-100) REVERT: A 164 LYS cc_start: 0.6823 (mppt) cc_final: 0.6614 (mppt) REVERT: A 281 GLU cc_start: 0.6629 (pp20) cc_final: 0.6377 (pm20) REVERT: A 365 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7301 (tm-30) REVERT: A 506 ILE cc_start: 0.7729 (OUTLIER) cc_final: 0.7418 (OUTLIER) REVERT: A 583 GLU cc_start: 0.7678 (tp30) cc_final: 0.7290 (tt0) REVERT: A 585 PHE cc_start: 0.7840 (t80) cc_final: 0.7512 (t80) REVERT: A 588 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.8033 (tt0) REVERT: A 685 SER cc_start: 0.7315 (OUTLIER) cc_final: 0.6940 (t) REVERT: A 710 GLU cc_start: 0.7803 (mp0) cc_final: 0.7540 (mp0) REVERT: A 714 HIS cc_start: 0.6886 (m-70) cc_final: 0.6666 (m-70) REVERT: A 757 SER cc_start: 0.7987 (t) cc_final: 0.7714 (t) REVERT: A 797 TYR cc_start: 0.7189 (m-80) cc_final: 0.6757 (m-80) REVERT: A 833 ILE cc_start: 0.6065 (OUTLIER) cc_final: 0.5820 (mp) REVERT: A 919 ILE cc_start: 0.6297 (OUTLIER) cc_final: 0.5366 (mp) REVERT: A 1032 SER cc_start: 0.2337 (OUTLIER) cc_final: 0.1874 (m) REVERT: A 1067 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.7056 (ptp) outliers start: 64 outliers final: 43 residues processed: 242 average time/residue: 1.0297 time to fit residues: 268.8790 Evaluate side-chains 246 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 196 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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 299 LEU Chi-restraints excluded: chain A residue 347 SER 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 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 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 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 874 ILE Chi-restraints excluded: chain A residue 919 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 25 optimal weight: 0.3980 chunk 50 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 A1023 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.178291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.165446 restraints weight = 12408.589| |-----------------------------------------------------------------------------| r_work (start): 0.4162 rms_B_bonded: 1.89 r_work: 0.4065 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3922 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9204 Z= 0.189 Angle : 0.720 10.039 12642 Z= 0.361 Chirality : 0.042 0.190 1439 Planarity : 0.004 0.052 1389 Dihedral : 19.131 178.109 1880 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 6.74 % Allowed : 40.11 % Favored : 53.14 % 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: 0.28 (0.27), residues: 900 helix: 1.16 (0.20), residues: 600 sheet: -5.23 (0.64), residues: 10 loop : -1.70 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 435 HIS 0.005 0.001 HIS A 915 PHE 0.022 0.002 PHE A 231 TYR 0.015 0.002 TYR A 647 ARG 0.010 0.001 ARG A 934 Details of bonding type rmsd hydrogen bonds : bond 0.03872 ( 493) hydrogen bonds : angle 4.22072 ( 1424) covalent geometry : bond 0.00430 ( 9204) covalent geometry : angle 0.71975 (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 253 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 194 time to evaluate : 0.995 Fit side-chains REVERT: A 35 MET cc_start: 0.5418 (tpt) cc_final: 0.5102 (tpt) REVERT: A 40 VAL cc_start: 0.7269 (OUTLIER) cc_final: 0.6939 (m) REVERT: A 54 ASN cc_start: 0.7987 (p0) cc_final: 0.7736 (p0) REVERT: A 57 LYS cc_start: 0.7972 (mptt) cc_final: 0.7607 (mptt) REVERT: A 79 PHE cc_start: 0.7886 (m-10) cc_final: 0.7589 (m-10) REVERT: A 149 ARG cc_start: 0.7448 (ttt-90) cc_final: 0.7108 (ttt-90) REVERT: A 156 GLN cc_start: 0.7895 (mm-40) cc_final: 0.7636 (tp-100) REVERT: A 281 GLU cc_start: 0.6654 (pp20) cc_final: 0.6357 (pm20) REVERT: A 365 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7300 (tm-30) REVERT: A 506 ILE cc_start: 0.7718 (OUTLIER) cc_final: 0.7413 (OUTLIER) REVERT: A 583 GLU cc_start: 0.7668 (tp30) cc_final: 0.7279 (tt0) REVERT: A 585 PHE cc_start: 0.7843 (t80) cc_final: 0.7526 (t80) REVERT: A 588 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8069 (tt0) REVERT: A 648 MET cc_start: 0.6894 (ttm) cc_final: 0.6472 (ttm) REVERT: A 685 SER cc_start: 0.7313 (OUTLIER) cc_final: 0.6936 (t) REVERT: A 710 GLU cc_start: 0.7803 (mp0) cc_final: 0.7537 (mp0) REVERT: A 714 HIS cc_start: 0.6855 (m-70) cc_final: 0.6639 (m-70) REVERT: A 757 SER cc_start: 0.7973 (t) cc_final: 0.7704 (t) REVERT: A 797 TYR cc_start: 0.7208 (m-80) cc_final: 0.6753 (m-80) REVERT: A 833 ILE cc_start: 0.6086 (OUTLIER) cc_final: 0.5838 (mp) REVERT: A 838 PHE cc_start: 0.5550 (OUTLIER) cc_final: 0.4459 (m-80) REVERT: A 919 ILE cc_start: 0.6230 (OUTLIER) cc_final: 0.5298 (mp) REVERT: A 1032 SER cc_start: 0.1920 (OUTLIER) cc_final: 0.1551 (m) REVERT: A 1067 MET cc_start: 0.7349 (OUTLIER) cc_final: 0.7050 (ptp) outliers start: 59 outliers final: 43 residues processed: 235 average time/residue: 1.0281 time to fit residues: 260.2551 Evaluate side-chains 244 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 193 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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 299 LEU Chi-restraints excluded: chain A residue 347 SER 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 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 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 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 838 PHE Chi-restraints excluded: chain A residue 849 LYS Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 919 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 3 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 58 optimal weight: 0.0770 chunk 86 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 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 = 0.4294 r_free = 0.4294 target = 0.176176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.163360 restraints weight = 12584.838| |-----------------------------------------------------------------------------| r_work (start): 0.4161 rms_B_bonded: 1.89 r_work: 0.4064 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3921 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9204 Z= 0.191 Angle : 0.722 9.969 12642 Z= 0.362 Chirality : 0.042 0.176 1439 Planarity : 0.004 0.052 1389 Dihedral : 19.122 178.211 1880 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 6.86 % Allowed : 39.66 % Favored : 53.49 % 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: 0.24 (0.27), residues: 900 helix: 1.13 (0.20), residues: 600 sheet: -5.23 (0.64), residues: 10 loop : -1.70 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 435 HIS 0.005 0.001 HIS A 915 PHE 0.021 0.002 PHE A 231 TYR 0.016 0.002 TYR A 265 ARG 0.010 0.001 ARG A 934 Details of bonding type rmsd hydrogen bonds : bond 0.03894 ( 493) hydrogen bonds : angle 4.24332 ( 1424) covalent geometry : bond 0.00434 ( 9204) covalent geometry : angle 0.72198 (12642) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7010.19 seconds wall clock time: 121 minutes 22.53 seconds (7282.53 seconds total)