Starting phenix.real_space_refine on Wed Sep 17 13:36:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zty_60476/09_2025/8zty_60476.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zty_60476/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8zty_60476/09_2025/8zty_60476.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zty_60476/09_2025/8zty_60476.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zty_60476/09_2025/8zty_60476.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zty_60476/09_2025/8zty_60476.map" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.94, per 1000 atoms: 0.22 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: 0.87 Conformation dependent library (CDL) restraints added in 286.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.13 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: 1.43 Time building geometry restraints manager: 1.15 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: 1.390 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.400 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:9.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.090 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.001 ARG A 149 TYR 0.031 0.001 TYR A 844 PHE 0.031 0.002 PHE A 585 TRP 0.027 0.002 TRP A 435 HIS 0.011 0.001 HIS A 915 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 9204) covalent geometry : angle 0.68742 (12642) hydrogen bonds : bond 0.05385 ( 493) hydrogen bonds : angle 4.02875 ( 1424) *********************** 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 : 0.246 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: 0.5111 time to fit residues: 121.1245 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 : 0.308 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.0170 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 298 HIS A 355 ASN A 735 GLN ** 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 = 0.4322 r_free = 0.4322 target = 0.180516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.167322 restraints weight = 12664.468| |-----------------------------------------------------------------------------| r_work (start): 0.4172 rms_B_bonded: 1.93 r_work: 0.4074 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9204 Z= 0.171 Angle : 0.616 8.316 12642 Z= 0.312 Chirality : 0.040 0.161 1439 Planarity : 0.004 0.048 1389 Dihedral : 19.632 179.488 1922 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 9.49 % Allowed : 33.94 % Favored : 56.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.28), residues: 900 helix: 1.74 (0.21), residues: 600 sheet: -5.09 (0.66), residues: 10 loop : -1.49 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 415 TYR 0.014 0.001 TYR A 928 PHE 0.030 0.002 PHE A 585 TRP 0.016 0.002 TRP A 435 HIS 0.004 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 9204) covalent geometry : angle 0.61612 (12642) hydrogen bonds : bond 0.03699 ( 493) hydrogen bonds : angle 3.92673 ( 1424) *********************** 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 280 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 197 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 36 ARG cc_start: 0.7569 (mmm160) cc_final: 0.7217 (ttm-80) REVERT: A 156 GLN cc_start: 0.7796 (mm-40) cc_final: 0.7544 (tp-100) REVERT: A 272 GLN cc_start: 0.6810 (OUTLIER) cc_final: 0.6357 (mp-120) REVERT: A 601 LEU cc_start: 0.7441 (mt) cc_final: 0.7216 (mp) REVERT: A 710 GLU cc_start: 0.7312 (mp0) cc_final: 0.7067 (mp0) REVERT: A 797 TYR cc_start: 0.7059 (m-80) cc_final: 0.6617 (m-80) REVERT: A 919 ILE cc_start: 0.6436 (OUTLIER) cc_final: 0.5807 (mp) REVERT: A 1043 VAL cc_start: 0.2903 (OUTLIER) cc_final: 0.1739 (m) outliers start: 83 outliers final: 37 residues processed: 259 average time/residue: 0.5033 time to fit residues: 140.3756 Evaluate side-chains 224 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 184 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 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 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 435 TRP 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 536 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 632 PHE 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 748 CYS 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 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 1043 VAL 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 95 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 127 ASN A 355 ASN A 735 GLN A 890 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.174895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.161711 restraints weight = 12462.060| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 1.93 r_work: 0.4025 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3878 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9204 Z= 0.284 Angle : 0.720 8.502 12642 Z= 0.368 Chirality : 0.046 0.163 1439 Planarity : 0.004 0.044 1389 Dihedral : 19.691 178.970 1889 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 10.40 % Allowed : 32.80 % Favored : 56.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.27), residues: 900 helix: 1.01 (0.20), residues: 601 sheet: -5.36 (0.57), residues: 10 loop : -1.60 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 149 TYR 0.027 0.002 TYR A1075 PHE 0.031 0.003 PHE A 585 TRP 0.014 0.002 TRP A 435 HIS 0.005 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00632 ( 9204) covalent geometry : angle 0.72034 (12642) hydrogen bonds : bond 0.04395 ( 493) hydrogen bonds : angle 4.32918 ( 1424) *********************** 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 296 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 205 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 40 VAL cc_start: 0.7405 (OUTLIER) cc_final: 0.7078 (t) REVERT: A 156 GLN cc_start: 0.7950 (mm-40) cc_final: 0.7645 (tp-100) REVERT: A 164 LYS cc_start: 0.6744 (mppt) cc_final: 0.6451 (mttp) REVERT: A 322 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6791 (pm20) REVERT: A 573 ASN cc_start: 0.6383 (OUTLIER) cc_final: 0.6038 (p0) REVERT: A 583 GLU cc_start: 0.7024 (tt0) cc_final: 0.6804 (tt0) REVERT: A 588 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7929 (tt0) REVERT: A 615 VAL cc_start: 0.6633 (OUTLIER) cc_final: 0.6355 (p) REVERT: A 710 GLU cc_start: 0.7722 (mp0) cc_final: 0.7459 (mp0) REVERT: A 746 PHE cc_start: 0.7976 (t80) cc_final: 0.7751 (t80) REVERT: A 786 ASP cc_start: 0.7023 (p0) cc_final: 0.6794 (p0) REVERT: A 793 ASN cc_start: 0.7905 (t0) cc_final: 0.7672 (t0) REVERT: A 797 TYR cc_start: 0.7234 (m-80) cc_final: 0.6509 (m-80) REVERT: A 810 GLN cc_start: 0.6350 (mm110) cc_final: 0.5753 (mt0) REVERT: A 833 ILE cc_start: 0.6324 (OUTLIER) cc_final: 0.5980 (mm) REVERT: A 874 ILE cc_start: 0.7176 (mp) cc_final: 0.6970 (OUTLIER) REVERT: A 888 LYS cc_start: 0.8098 (ttmm) cc_final: 0.7884 (ttpp) REVERT: A 919 ILE cc_start: 0.6646 (OUTLIER) cc_final: 0.5915 (mp) REVERT: A 1032 SER cc_start: 0.1464 (OUTLIER) cc_final: 0.0823 (m) REVERT: A 1080 HIS cc_start: 0.6719 (OUTLIER) cc_final: 0.6339 (m-70) outliers start: 91 outliers final: 43 residues processed: 270 average time/residue: 0.4872 time to fit residues: 141.6853 Evaluate side-chains 247 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 196 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 70 GLN Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 322 GLU 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 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 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 551 VAL Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 588 GLN 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 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 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 908 LEU Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 929 MET Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1080 HIS 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 7 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A 446 ASN A 454 HIS A1023 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.176409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.163243 restraints weight = 12653.389| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 1.92 r_work: 0.4037 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3894 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 9204 Z= 0.203 Angle : 0.661 8.501 12642 Z= 0.336 Chirality : 0.042 0.153 1439 Planarity : 0.004 0.044 1389 Dihedral : 19.497 178.673 1883 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 9.49 % Allowed : 34.17 % Favored : 56.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.27), residues: 900 helix: 1.09 (0.20), residues: 602 sheet: -5.31 (0.63), residues: 10 loop : -1.55 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 149 TYR 0.017 0.002 TYR A1075 PHE 0.033 0.002 PHE A 585 TRP 0.019 0.002 TRP A 435 HIS 0.005 0.001 HIS A 915 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 9204) covalent geometry : angle 0.66097 (12642) hydrogen bonds : bond 0.03992 ( 493) hydrogen bonds : angle 4.19153 ( 1424) *********************** 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 286 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 203 time to evaluate : 0.297 Fit side-chains REVERT: A 156 GLN cc_start: 0.7919 (mm-40) cc_final: 0.7637 (tp-100) REVERT: A 322 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6747 (pm20) REVERT: A 585 PHE cc_start: 0.7659 (t80) cc_final: 0.7372 (t80) REVERT: A 615 VAL cc_start: 0.6547 (OUTLIER) cc_final: 0.6272 (p) REVERT: A 710 GLU cc_start: 0.7748 (mp0) cc_final: 0.7468 (mp0) REVERT: A 757 SER cc_start: 0.7777 (t) cc_final: 0.7551 (t) REVERT: A 787 LYS cc_start: 0.6919 (tppp) cc_final: 0.6559 (tppp) REVERT: A 797 TYR cc_start: 0.7185 (m-80) cc_final: 0.6744 (m-80) REVERT: A 810 GLN cc_start: 0.6352 (mm110) cc_final: 0.5827 (mt0) REVERT: A 833 ILE cc_start: 0.6288 (OUTLIER) cc_final: 0.6013 (mm) REVERT: A 882 ASP cc_start: 0.7887 (t0) cc_final: 0.7675 (t0) REVERT: A 888 LYS cc_start: 0.8087 (ttmm) cc_final: 0.7885 (ttpp) REVERT: A 919 ILE cc_start: 0.6373 (OUTLIER) cc_final: 0.5523 (mp) REVERT: A 1032 SER cc_start: 0.1403 (OUTLIER) cc_final: 0.0957 (m) REVERT: A 1067 MET cc_start: 0.7413 (OUTLIER) cc_final: 0.6971 (ptp) outliers start: 83 outliers final: 48 residues processed: 264 average time/residue: 0.4531 time to fit residues: 129.3199 Evaluate side-chains 251 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 197 time to evaluate : 0.277 ------------------------------------------------------------------------------- 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 134 LEU Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 492 LYS Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 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 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 803 LEU 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 908 LEU Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 929 MET Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 2 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 74 optimal weight: 0.0170 chunk 67 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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 A1023 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.177455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.164677 restraints weight = 12519.946| |-----------------------------------------------------------------------------| r_work (start): 0.4153 rms_B_bonded: 1.89 r_work: 0.4056 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3912 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9204 Z= 0.181 Angle : 0.657 10.897 12642 Z= 0.331 Chirality : 0.041 0.214 1439 Planarity : 0.004 0.048 1389 Dihedral : 19.438 178.914 1883 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 9.14 % Allowed : 35.43 % Favored : 55.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.28), residues: 900 helix: 1.19 (0.21), residues: 598 sheet: -5.22 (0.66), residues: 10 loop : -1.56 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 934 TYR 0.016 0.002 TYR A 844 PHE 0.031 0.002 PHE A 604 TRP 0.019 0.002 TRP A 435 HIS 0.006 0.001 HIS A 915 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 9204) covalent geometry : angle 0.65711 (12642) hydrogen bonds : bond 0.03938 ( 493) hydrogen bonds : angle 4.16849 ( 1424) *********************** 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 276 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 196 time to evaluate : 0.218 Fit side-chains REVERT: A 57 LYS cc_start: 0.8031 (mptt) cc_final: 0.7695 (mptt) REVERT: A 79 PHE cc_start: 0.7965 (m-10) cc_final: 0.7729 (m-10) REVERT: A 146 GLU cc_start: 0.7261 (tp30) cc_final: 0.6943 (tp30) REVERT: A 150 ILE cc_start: 0.7956 (tp) cc_final: 0.7686 (tp) REVERT: A 156 GLN cc_start: 0.7897 (mm-40) cc_final: 0.7643 (tp-100) REVERT: A 322 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6746 (pm20) REVERT: A 585 PHE cc_start: 0.7735 (t80) cc_final: 0.7423 (t80) REVERT: A 588 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7882 (tt0) REVERT: A 615 VAL cc_start: 0.6516 (OUTLIER) cc_final: 0.6260 (p) REVERT: A 685 SER cc_start: 0.7307 (OUTLIER) cc_final: 0.6947 (t) REVERT: A 710 GLU cc_start: 0.7733 (mp0) cc_final: 0.7450 (mp0) REVERT: A 757 SER cc_start: 0.7761 (t) cc_final: 0.7537 (t) REVERT: A 797 TYR cc_start: 0.7162 (m-80) cc_final: 0.6680 (m-80) REVERT: A 810 GLN cc_start: 0.6325 (mm110) cc_final: 0.5804 (mt0) REVERT: A 833 ILE cc_start: 0.6117 (OUTLIER) cc_final: 0.5842 (mm) REVERT: A 882 ASP cc_start: 0.7879 (t0) cc_final: 0.7667 (t0) REVERT: A 888 LYS cc_start: 0.8091 (ttmm) cc_final: 0.7881 (ttpp) REVERT: A 919 ILE cc_start: 0.6267 (OUTLIER) cc_final: 0.5415 (mp) REVERT: A 1032 SER cc_start: 0.1845 (OUTLIER) cc_final: 0.1349 (m) REVERT: A 1067 MET cc_start: 0.7324 (OUTLIER) cc_final: 0.7004 (ptp) outliers start: 80 outliers final: 50 residues processed: 252 average time/residue: 0.4621 time to fit residues: 125.7566 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 : 0.327 ------------------------------------------------------------------------------- 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 88 ILE Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 492 LYS Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 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 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 803 LEU 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 893 ILE Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 929 MET Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 83 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 45 optimal weight: 0.2980 chunk 61 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 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 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 = 0.177355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.164365 restraints weight = 12551.456| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 1.91 r_work: 0.4053 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3910 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9204 Z= 0.182 Angle : 0.655 10.586 12642 Z= 0.332 Chirality : 0.041 0.149 1439 Planarity : 0.004 0.045 1389 Dihedral : 19.365 178.933 1883 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 8.80 % Allowed : 36.23 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.28), residues: 900 helix: 1.11 (0.20), residues: 605 sheet: -5.20 (0.66), residues: 10 loop : -1.61 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 934 TYR 0.016 0.002 TYR A 265 PHE 0.035 0.002 PHE A 604 TRP 0.022 0.002 TRP A 435 HIS 0.005 0.001 HIS A 915 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 9204) covalent geometry : angle 0.65530 (12642) hydrogen bonds : bond 0.03853 ( 493) hydrogen bonds : angle 4.14272 ( 1424) *********************** 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 272 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 195 time to evaluate : 0.335 Fit side-chains REVERT: A 57 LYS cc_start: 0.8006 (mptt) cc_final: 0.7644 (mptt) REVERT: A 79 PHE cc_start: 0.7969 (m-10) cc_final: 0.7693 (m-10) REVERT: A 146 GLU cc_start: 0.7286 (tp30) cc_final: 0.6962 (tp30) REVERT: A 150 ILE cc_start: 0.7936 (tp) cc_final: 0.7663 (tp) REVERT: A 156 GLN cc_start: 0.7905 (mm-40) cc_final: 0.7646 (tp-100) REVERT: A 272 GLN cc_start: 0.6944 (OUTLIER) cc_final: 0.6348 (mp-120) REVERT: A 322 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.6720 (pm20) REVERT: A 585 PHE cc_start: 0.7771 (t80) cc_final: 0.7476 (t80) REVERT: A 588 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7985 (tt0) REVERT: A 615 VAL cc_start: 0.6510 (OUTLIER) cc_final: 0.6247 (p) REVERT: A 685 SER cc_start: 0.7304 (OUTLIER) cc_final: 0.6943 (t) REVERT: A 710 GLU cc_start: 0.7869 (mp0) cc_final: 0.7578 (mp0) REVERT: A 757 SER cc_start: 0.7893 (t) cc_final: 0.7657 (t) REVERT: A 797 TYR cc_start: 0.7151 (m-80) cc_final: 0.6710 (m-80) REVERT: A 833 ILE cc_start: 0.6103 (OUTLIER) cc_final: 0.5806 (mp) REVERT: A 888 LYS cc_start: 0.8158 (ttmm) cc_final: 0.7938 (ttpp) REVERT: A 919 ILE cc_start: 0.6258 (OUTLIER) cc_final: 0.5369 (mp) REVERT: A 1032 SER cc_start: 0.1511 (OUTLIER) cc_final: 0.1022 (m) REVERT: A 1067 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.7091 (ptp) outliers start: 77 outliers final: 47 residues processed: 247 average time/residue: 0.4978 time to fit residues: 132.3222 Evaluate side-chains 244 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 188 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 217 MET Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 322 GLU 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 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 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 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 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 64 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 43 optimal weight: 0.0870 chunk 50 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 127 ASN A 454 HIS A 684 ASN A 714 HIS A 735 GLN A 793 ASN A1023 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.174639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.162058 restraints weight = 12613.268| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 1.87 r_work: 0.4051 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3909 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9204 Z= 0.201 Angle : 0.686 10.980 12642 Z= 0.346 Chirality : 0.042 0.152 1439 Planarity : 0.004 0.051 1389 Dihedral : 19.326 178.522 1883 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 9.14 % Allowed : 36.46 % Favored : 54.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.27), residues: 900 helix: 1.04 (0.20), residues: 605 sheet: -5.25 (0.64), residues: 10 loop : -1.64 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 934 TYR 0.023 0.002 TYR A 844 PHE 0.032 0.002 PHE A 604 TRP 0.026 0.002 TRP A 435 HIS 0.005 0.001 HIS A 915 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 9204) covalent geometry : angle 0.68584 (12642) hydrogen bonds : bond 0.03969 ( 493) hydrogen bonds : angle 4.21042 ( 1424) *********************** 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 269 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 189 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 57 LYS cc_start: 0.8033 (mptt) cc_final: 0.7648 (mptt) REVERT: A 79 PHE cc_start: 0.7942 (m-10) cc_final: 0.7682 (m-10) REVERT: A 146 GLU cc_start: 0.7268 (tp30) cc_final: 0.6976 (tp30) REVERT: A 150 ILE cc_start: 0.7955 (tp) cc_final: 0.7677 (tp) REVERT: A 156 GLN cc_start: 0.7886 (mm-40) cc_final: 0.7647 (tp-100) REVERT: A 322 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6703 (pm20) REVERT: A 585 PHE cc_start: 0.7807 (t80) cc_final: 0.7503 (t80) REVERT: A 588 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7994 (tt0) REVERT: A 615 VAL cc_start: 0.6542 (OUTLIER) cc_final: 0.6286 (p) REVERT: A 685 SER cc_start: 0.7324 (OUTLIER) cc_final: 0.6954 (t) REVERT: A 710 GLU cc_start: 0.7834 (mp0) cc_final: 0.7578 (mp0) REVERT: A 757 SER cc_start: 0.7882 (t) cc_final: 0.7647 (t) REVERT: A 786 ASP cc_start: 0.7017 (p0) cc_final: 0.6740 (p0) REVERT: A 797 TYR cc_start: 0.7177 (m-80) cc_final: 0.6728 (m-80) REVERT: A 833 ILE cc_start: 0.6123 (OUTLIER) cc_final: 0.5845 (mm) REVERT: A 888 LYS cc_start: 0.8142 (ttmm) cc_final: 0.7922 (ttpp) REVERT: A 919 ILE cc_start: 0.6371 (OUTLIER) cc_final: 0.5540 (mp) REVERT: A 1032 SER cc_start: 0.1593 (OUTLIER) cc_final: 0.1059 (m) REVERT: A 1067 MET cc_start: 0.7325 (OUTLIER) cc_final: 0.6990 (ptp) outliers start: 80 outliers final: 52 residues processed: 246 average time/residue: 0.4962 time to fit residues: 131.6767 Evaluate side-chains 244 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 184 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 217 MET Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 322 GLU 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 502 VAL 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 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 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 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 91 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 89 optimal weight: 0.2980 chunk 56 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4299 r_free = 0.4299 target = 0.177876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.164948 restraints weight = 12674.594| |-----------------------------------------------------------------------------| r_work (start): 0.4157 rms_B_bonded: 1.94 r_work: 0.4059 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9204 Z= 0.173 Angle : 0.677 11.032 12642 Z= 0.341 Chirality : 0.040 0.151 1439 Planarity : 0.004 0.048 1389 Dihedral : 19.246 178.446 1883 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 7.66 % Allowed : 37.94 % Favored : 54.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.28), residues: 900 helix: 1.15 (0.21), residues: 605 sheet: -5.21 (0.66), residues: 10 loop : -1.64 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 934 TYR 0.018 0.002 TYR A 844 PHE 0.031 0.002 PHE A 604 TRP 0.033 0.002 TRP A 435 HIS 0.005 0.001 HIS A 915 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 9204) covalent geometry : angle 0.67671 (12642) hydrogen bonds : bond 0.03837 ( 493) hydrogen bonds : angle 4.17845 ( 1424) *********************** 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 256 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 189 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 57 LYS cc_start: 0.7799 (mptt) cc_final: 0.7422 (mptt) REVERT: A 146 GLU cc_start: 0.6974 (tp30) cc_final: 0.6688 (tp30) REVERT: A 150 ILE cc_start: 0.7864 (tp) cc_final: 0.7586 (tp) REVERT: A 288 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6775 (mt) REVERT: A 322 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6642 (pm20) REVERT: A 365 GLU cc_start: 0.7363 (tm-30) cc_final: 0.6926 (tm-30) REVERT: A 514 LYS cc_start: 0.8180 (ptpt) cc_final: 0.7838 (ptpt) REVERT: A 533 PHE cc_start: 0.8371 (m-10) cc_final: 0.8129 (m-80) REVERT: A 583 GLU cc_start: 0.7290 (tp30) cc_final: 0.6788 (tt0) REVERT: A 585 PHE cc_start: 0.7730 (t80) cc_final: 0.7491 (t80) REVERT: A 588 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7927 (tt0) REVERT: A 615 VAL cc_start: 0.6355 (OUTLIER) cc_final: 0.6112 (p) REVERT: A 685 SER cc_start: 0.7119 (OUTLIER) cc_final: 0.6769 (t) REVERT: A 710 GLU cc_start: 0.7548 (mp0) cc_final: 0.7285 (mp0) REVERT: A 757 SER cc_start: 0.7675 (t) cc_final: 0.7427 (t) REVERT: A 786 ASP cc_start: 0.6850 (p0) cc_final: 0.6545 (p0) REVERT: A 797 TYR cc_start: 0.6876 (m-80) cc_final: 0.6392 (m-80) REVERT: A 888 LYS cc_start: 0.8101 (ttmm) cc_final: 0.7874 (ttpp) REVERT: A 919 ILE cc_start: 0.6138 (OUTLIER) cc_final: 0.5246 (mp) REVERT: A 1032 SER cc_start: 0.1740 (OUTLIER) cc_final: 0.1284 (m) REVERT: A 1067 MET cc_start: 0.7044 (OUTLIER) cc_final: 0.6684 (ptp) outliers start: 67 outliers final: 50 residues processed: 235 average time/residue: 0.5244 time to fit residues: 132.4638 Evaluate side-chains 243 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 185 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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 217 MET Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 460 PHE Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 492 LYS Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 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 685 SER Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 849 LYS Chi-restraints excluded: chain A residue 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 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 88 optimal weight: 0.9990 chunk 65 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A 454 HIS A 735 GLN A 793 ASN A 890 GLN A1023 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.174970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.162297 restraints weight = 12556.647| |-----------------------------------------------------------------------------| r_work (start): 0.4149 rms_B_bonded: 1.89 r_work: 0.4052 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3910 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9204 Z= 0.197 Angle : 0.714 10.648 12642 Z= 0.360 Chirality : 0.042 0.157 1439 Planarity : 0.004 0.045 1389 Dihedral : 19.231 178.551 1883 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 8.34 % Allowed : 37.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.28), residues: 900 helix: 1.04 (0.20), residues: 605 sheet: -5.22 (0.66), residues: 10 loop : -1.65 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 924 TYR 0.016 0.002 TYR A 928 PHE 0.030 0.002 PHE A 604 TRP 0.038 0.002 TRP A 435 HIS 0.004 0.001 HIS A 915 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 9204) covalent geometry : angle 0.71407 (12642) hydrogen bonds : bond 0.03939 ( 493) hydrogen bonds : angle 4.23467 ( 1424) *********************** 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 263 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 190 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 35 MET cc_start: 0.5388 (tpt) cc_final: 0.5070 (tpt) REVERT: A 57 LYS cc_start: 0.8008 (mptt) cc_final: 0.7652 (mptt) REVERT: A 79 PHE cc_start: 0.7918 (m-10) cc_final: 0.7622 (m-10) REVERT: A 146 GLU cc_start: 0.7276 (tp30) cc_final: 0.6989 (tp30) REVERT: A 150 ILE cc_start: 0.7927 (tp) cc_final: 0.7617 (tp) REVERT: A 164 LYS cc_start: 0.6813 (mppt) cc_final: 0.6608 (mppt) REVERT: A 322 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6682 (pm20) REVERT: A 365 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7283 (tm-30) REVERT: A 514 LYS cc_start: 0.8370 (ptpt) cc_final: 0.8117 (ptpp) REVERT: A 533 PHE cc_start: 0.8489 (m-10) cc_final: 0.8225 (m-80) REVERT: A 583 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7203 (tt0) REVERT: A 585 PHE cc_start: 0.7808 (t80) cc_final: 0.7493 (t80) REVERT: A 588 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7938 (tt0) REVERT: A 615 VAL cc_start: 0.6518 (OUTLIER) cc_final: 0.6256 (p) REVERT: A 648 MET cc_start: 0.6941 (ttm) cc_final: 0.6400 (ttm) REVERT: A 685 SER cc_start: 0.7306 (OUTLIER) cc_final: 0.6941 (t) REVERT: A 710 GLU cc_start: 0.7873 (mp0) cc_final: 0.7607 (mp0) REVERT: A 757 SER cc_start: 0.7876 (t) cc_final: 0.7638 (t) REVERT: A 797 TYR cc_start: 0.7181 (m-80) cc_final: 0.6745 (m-80) REVERT: A 838 PHE cc_start: 0.5540 (OUTLIER) cc_final: 0.4637 (m-80) REVERT: A 888 LYS cc_start: 0.8169 (ttmm) cc_final: 0.7950 (ttpp) REVERT: A 919 ILE cc_start: 0.6312 (OUTLIER) cc_final: 0.5445 (mp) REVERT: A 1032 SER cc_start: 0.1582 (OUTLIER) cc_final: 0.1010 (m) REVERT: A 1067 MET cc_start: 0.7368 (OUTLIER) cc_final: 0.7049 (ptp) outliers start: 73 outliers final: 52 residues processed: 240 average time/residue: 0.5178 time to fit residues: 133.3918 Evaluate side-chains 248 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 187 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 217 MET Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 322 GLU 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 502 VAL 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 583 GLU 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 615 VAL Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 632 PHE Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 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 838 PHE 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 893 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 924 ARG 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 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 19 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 42 optimal weight: 0.0870 chunk 16 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.4290 r_free = 0.4290 target = 0.175986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.163387 restraints weight = 12546.261| |-----------------------------------------------------------------------------| r_work (start): 0.4160 rms_B_bonded: 1.88 r_work: 0.4064 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: 0.6849 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9204 Z= 0.179 Angle : 0.710 10.794 12642 Z= 0.356 Chirality : 0.041 0.153 1439 Planarity : 0.005 0.056 1389 Dihedral : 19.182 178.519 1883 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 7.43 % Allowed : 38.17 % Favored : 54.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.28), residues: 900 helix: 1.09 (0.21), residues: 605 sheet: -5.21 (0.66), residues: 10 loop : -1.65 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 934 TYR 0.016 0.002 TYR A 647 PHE 0.030 0.002 PHE A 604 TRP 0.042 0.002 TRP A 435 HIS 0.004 0.000 HIS A 915 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 9204) covalent geometry : angle 0.70959 (12642) hydrogen bonds : bond 0.03888 ( 493) hydrogen bonds : angle 4.22084 ( 1424) ********************** 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 256 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 191 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 35 MET cc_start: 0.5373 (tpt) cc_final: 0.5059 (tpt) REVERT: A 57 LYS cc_start: 0.7994 (mptt) cc_final: 0.7636 (mptt) REVERT: A 79 PHE cc_start: 0.7883 (m-10) cc_final: 0.7575 (m-10) REVERT: A 146 GLU cc_start: 0.7264 (tp30) cc_final: 0.6977 (tp30) REVERT: A 150 ILE cc_start: 0.7903 (tp) cc_final: 0.7612 (tp) REVERT: A 154 LEU cc_start: 0.6726 (OUTLIER) cc_final: 0.6247 (tm) REVERT: A 322 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6649 (pm20) REVERT: A 365 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7275 (tm-30) REVERT: A 514 LYS cc_start: 0.8356 (ptpt) cc_final: 0.8102 (ptpp) REVERT: A 533 PHE cc_start: 0.8487 (m-10) cc_final: 0.8230 (m-80) REVERT: A 583 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7221 (tt0) REVERT: A 585 PHE cc_start: 0.7808 (t80) cc_final: 0.7502 (t80) REVERT: A 588 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.8031 (tt0) REVERT: A 615 VAL cc_start: 0.6489 (OUTLIER) cc_final: 0.6242 (p) REVERT: A 648 MET cc_start: 0.6876 (ttm) cc_final: 0.6397 (ttm) REVERT: A 685 SER cc_start: 0.7300 (OUTLIER) cc_final: 0.6933 (t) REVERT: A 710 GLU cc_start: 0.7857 (mp0) cc_final: 0.7578 (mp0) REVERT: A 757 SER cc_start: 0.7849 (t) cc_final: 0.7608 (t) REVERT: A 786 ASP cc_start: 0.7051 (p0) cc_final: 0.6710 (p0) REVERT: A 797 TYR cc_start: 0.7181 (m-80) cc_final: 0.6744 (m-80) REVERT: A 838 PHE cc_start: 0.5491 (OUTLIER) cc_final: 0.4656 (m-80) REVERT: A 888 LYS cc_start: 0.8183 (ttmm) cc_final: 0.7962 (ttpp) REVERT: A 919 ILE cc_start: 0.6229 (OUTLIER) cc_final: 0.5255 (mp) REVERT: A 1032 SER cc_start: 0.2043 (OUTLIER) cc_final: 0.1586 (m) REVERT: A 1057 SER cc_start: 0.7179 (OUTLIER) cc_final: 0.6876 (p) REVERT: A 1067 MET cc_start: 0.7323 (OUTLIER) cc_final: 0.7001 (ptp) outliers start: 65 outliers final: 49 residues processed: 235 average time/residue: 0.5237 time to fit residues: 132.3774 Evaluate side-chains 248 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 188 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 134 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 322 GLU 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 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 502 VAL 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 583 GLU 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 615 VAL Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 632 PHE Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 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 838 PHE 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 893 ILE 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 929 MET Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1057 SER Chi-restraints excluded: chain A residue 1067 MET Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1105 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 82 optimal weight: 2.9990 chunk 58 optimal weight: 0.0980 chunk 31 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 42 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 A 890 GLN A1023 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.176188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.163712 restraints weight = 12451.146| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 1.85 r_work: 0.4066 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3925 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.2472 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= 0.179 Angle : 0.720 10.687 12642 Z= 0.360 Chirality : 0.041 0.150 1439 Planarity : 0.004 0.050 1389 Dihedral : 19.089 178.617 1881 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 7.66 % Allowed : 38.51 % Favored : 53.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.28), residues: 900 helix: 1.10 (0.21), residues: 605 sheet: -5.19 (0.66), residues: 10 loop : -1.67 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 934 TYR 0.025 0.002 TYR A1046 PHE 0.029 0.002 PHE A 604 TRP 0.048 0.002 TRP A 435 HIS 0.004 0.000 HIS A 915 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 9204) covalent geometry : angle 0.72005 (12642) hydrogen bonds : bond 0.03841 ( 493) hydrogen bonds : angle 4.22607 ( 1424) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3446.07 seconds wall clock time: 59 minutes 41.23 seconds (3581.23 seconds total)