Starting phenix.real_space_refine on Sat Dec 28 03:41:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c3y_16415/12_2024/8c3y_16415.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c3y_16415/12_2024/8c3y_16415.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c3y_16415/12_2024/8c3y_16415.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c3y_16415/12_2024/8c3y_16415.map" model { file = "/net/cci-nas-00/data/ceres_data/8c3y_16415/12_2024/8c3y_16415.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c3y_16415/12_2024/8c3y_16415.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.051 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: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 4777 2.51 5 N 1319 2.21 5 O 1441 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7580 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 929, 7580 Classifications: {'peptide': 929} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 903} Chain breaks: 12 Time building chain proxies: 4.55, per 1000 atoms: 0.60 Number of scatterers: 7580 At special positions: 0 Unit cell: (74.88, 117.312, 107.328, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 1441 8.00 N 1319 7.00 C 4777 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 127 " distance=2.03 Simple disulfide: pdb=" SG CYS A 182 " - pdb=" SG CYS A 281 " distance=2.02 Simple disulfide: pdb=" SG CYS A 310 " - pdb=" SG CYS A 435 " distance=2.02 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 359 " distance=2.04 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 356 " distance=2.04 Simple disulfide: pdb=" SG CYS A 340 " - pdb=" SG CYS A 467 " distance=2.03 Simple disulfide: pdb=" SG CYS A 363 " - pdb=" SG CYS A 464 " distance=2.05 Simple disulfide: pdb=" SG CYS A 526 " - pdb=" SG CYS A 614 " distance=2.02 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 553 " distance=2.09 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 608 " distance=2.04 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS A 719 " distance=2.04 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 710 " distance=2.03 Simple disulfide: pdb=" SG CYS A 908 " - pdb=" SG CYS A1000 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 981.3 milliseconds 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1756 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 3 sheets defined 61.7% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 20 through 42 removed outlier: 3.853A pdb=" N LYS A 30 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASP A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ILE A 32 " --> pdb=" O PHE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 97 removed outlier: 3.966A pdb=" N ARG A 95 " --> pdb=" O PRO A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 137 through 142 Processing helix chain 'A' and resid 150 through 172 Processing helix chain 'A' and resid 179 through 197 Processing helix chain 'A' and resid 212 through 227 Processing helix chain 'A' and resid 227 through 232 removed outlier: 4.131A pdb=" N LEU A 231 " --> pdb=" O ASN A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 256 removed outlier: 5.536A pdb=" N GLU A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ASP A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 324 Processing helix chain 'A' and resid 327 through 330 Processing helix chain 'A' and resid 356 through 393 Proline residue: A 365 - end of helix Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 421 through 431 removed outlier: 4.190A pdb=" N GLU A 431 " --> pdb=" O LYS A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 523 Processing helix chain 'A' and resid 523 through 528 Processing helix chain 'A' and resid 571 through 593 Processing helix chain 'A' and resid 593 through 598 Processing helix chain 'A' and resid 604 through 631 removed outlier: 4.150A pdb=" N CYS A 608 " --> pdb=" O ASP A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 644 Processing helix chain 'A' and resid 648 through 654 removed outlier: 3.570A pdb=" N ASP A 652 " --> pdb=" O ASP A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 659 Processing helix chain 'A' and resid 666 through 686 Processing helix chain 'A' and resid 690 through 713 removed outlier: 3.932A pdb=" N ALA A 694 " --> pdb=" O LYS A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 719 removed outlier: 6.422A pdb=" N GLU A 717 " --> pdb=" O ASN A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 763 Processing helix chain 'A' and resid 764 through 769 Processing helix chain 'A' and resid 844 through 848 Processing helix chain 'A' and resid 869 through 892 Processing helix chain 'A' and resid 904 through 924 Processing helix chain 'A' and resid 931 through 952 Processing helix chain 'A' and resid 954 through 962 removed outlier: 3.882A pdb=" N ASN A 958 " --> pdb=" O ILE A 955 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N GLN A 959 " --> pdb=" O LYS A 956 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LYS A 960 " --> pdb=" O ASP A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 967 Processing helix chain 'A' and resid 971 through 994 removed outlier: 5.401A pdb=" N ASP A 984 " --> pdb=" O GLU A 980 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N GLN A 985 " --> pdb=" O ALA A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1040 Processing helix chain 'A' and resid 1058 through 1097 Processing helix chain 'A' and resid 1113 through 1126 Processing sheet with id=AA1, first strand: chain 'A' and resid 266 through 267 Processing sheet with id=AA2, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA3, first strand: chain 'A' and resid 503 through 509 removed outlier: 7.006A pdb=" N GLN A 539 " --> pdb=" O GLU A 556 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS A 552 " --> pdb=" O TYR A 543 " (cutoff:3.500A) 431 hydrogen bonds defined for protein. 1218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.27 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 1475 1.32 - 1.46: 2542 1.46 - 1.59: 3650 1.59 - 1.73: 17 1.73 - 1.87: 50 Bond restraints: 7734 Sorted by residual: bond pdb=" CB TYR A 644 " pdb=" CG TYR A 644 " ideal model delta sigma weight residual 1.512 1.427 0.085 2.20e-02 2.07e+03 1.50e+01 bond pdb=" NE ARG A 215 " pdb=" CZ ARG A 215 " ideal model delta sigma weight residual 1.326 1.368 -0.042 1.10e-02 8.26e+03 1.44e+01 bond pdb=" NE1 TRP A 589 " pdb=" CE2 TRP A 589 " ideal model delta sigma weight residual 1.370 1.329 0.041 1.10e-02 8.26e+03 1.42e+01 bond pdb=" CA TYR A 543 " pdb=" C TYR A 543 " ideal model delta sigma weight residual 1.530 1.488 0.041 1.11e-02 8.12e+03 1.37e+01 bond pdb=" CG ASP A 964 " pdb=" OD2 ASP A 964 " ideal model delta sigma weight residual 1.249 1.179 0.070 1.90e-02 2.77e+03 1.36e+01 ... (remaining 7729 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 8194 1.77 - 3.54: 1816 3.54 - 5.32: 308 5.32 - 7.09: 64 7.09 - 8.86: 13 Bond angle restraints: 10395 Sorted by residual: angle pdb=" C LEU A 841 " pdb=" N PRO A 842 " pdb=" CA PRO A 842 " ideal model delta sigma weight residual 119.66 125.64 -5.98 7.30e-01 1.88e+00 6.72e+01 angle pdb=" N ILE A1166 " pdb=" CA ILE A1166 " pdb=" C ILE A1166 " ideal model delta sigma weight residual 111.58 120.18 -8.60 1.06e+00 8.90e-01 6.58e+01 angle pdb=" C PRO A 842 " pdb=" N PRO A 843 " pdb=" CA PRO A 843 " ideal model delta sigma weight residual 119.56 127.30 -7.74 1.02e+00 9.61e-01 5.75e+01 angle pdb=" N ILE A 559 " pdb=" CA ILE A 559 " pdb=" C ILE A 559 " ideal model delta sigma weight residual 113.47 106.20 7.27 1.01e+00 9.80e-01 5.18e+01 angle pdb=" C MET A 952 " pdb=" N PRO A 953 " pdb=" CA PRO A 953 " ideal model delta sigma weight residual 120.03 127.09 -7.06 9.90e-01 1.02e+00 5.08e+01 ... (remaining 10390 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 4510 17.87 - 35.74: 156 35.74 - 53.61: 32 53.61 - 71.48: 12 71.48 - 89.35: 8 Dihedral angle restraints: 4718 sinusoidal: 2000 harmonic: 2718 Sorted by residual: dihedral pdb=" SG CYS A 605 " pdb=" CB CYS A 719 " pdb=" SG CYS A 719 " pdb=" CA CYS A 719 " ideal model delta sinusoidal sigma weight residual 79.00 3.44 75.56 1 2.00e+01 2.50e-03 1.80e+01 dihedral pdb=" CB CYS A 340 " pdb=" SG CYS A 340 " pdb=" SG CYS A 467 " pdb=" CB CYS A 467 " ideal model delta sinusoidal sigma weight residual -86.00 -55.46 -30.54 1 1.00e+01 1.00e-02 1.33e+01 dihedral pdb=" CB GLU A 515 " pdb=" CG GLU A 515 " pdb=" CD GLU A 515 " pdb=" OE1 GLU A 515 " ideal model delta sinusoidal sigma weight residual 0.00 -87.18 87.18 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 4715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 756 0.096 - 0.191: 262 0.191 - 0.287: 51 0.287 - 0.383: 4 0.383 - 0.479: 2 Chirality restraints: 1075 Sorted by residual: chirality pdb=" CB VAL A 839 " pdb=" CA VAL A 839 " pdb=" CG1 VAL A 839 " pdb=" CG2 VAL A 839 " both_signs ideal model delta sigma weight residual False -2.63 -3.11 0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" CB VAL A 472 " pdb=" CA VAL A 472 " pdb=" CG1 VAL A 472 " pdb=" CG2 VAL A 472 " both_signs ideal model delta sigma weight residual False -2.63 -3.06 0.43 2.00e-01 2.50e+01 4.63e+00 chirality pdb=" CA ILE A 647 " pdb=" N ILE A 647 " pdb=" C ILE A 647 " pdb=" CB ILE A 647 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.38e+00 ... (remaining 1072 not shown) Planarity restraints: 1344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 544 " 0.081 2.00e-02 2.50e+03 4.43e-02 3.92e+01 pdb=" CG TYR A 544 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 544 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR A 544 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR A 544 " -0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR A 544 " -0.029 2.00e-02 2.50e+03 pdb=" CZ TYR A 544 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 544 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 669 " 0.058 2.00e-02 2.50e+03 2.90e-02 2.11e+01 pdb=" CG TRP A 669 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP A 669 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP A 669 " -0.035 2.00e-02 2.50e+03 pdb=" NE1 TRP A 669 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 669 " -0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP A 669 " -0.039 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 669 " 0.019 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 669 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 669 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1017 " 0.371 9.50e-02 1.11e+02 1.66e-01 1.69e+01 pdb=" NE ARG A1017 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG A1017 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A1017 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A1017 " 0.012 2.00e-02 2.50e+03 ... (remaining 1341 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1479 2.76 - 3.30: 7897 3.30 - 3.83: 12979 3.83 - 4.37: 15979 4.37 - 4.90: 24659 Nonbonded interactions: 62993 Sorted by model distance: nonbonded pdb=" OD1 ASN A 686 " pdb=" OG1 THR A 689 " model vdw 2.226 3.040 nonbonded pdb=" OG SER A 20 " pdb=" ND2 ASN A 23 " model vdw 2.356 3.120 nonbonded pdb=" O LEU A 645 " pdb=" ND2 ASN A 646 " model vdw 2.362 3.120 nonbonded pdb=" NZ LYS A 745 " pdb=" OD1 ASP A1009 " model vdw 2.372 3.120 nonbonded pdb=" O PHE A 651 " pdb=" O PHE A 654 " model vdw 2.384 3.040 ... (remaining 62988 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.460 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 19.880 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 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 : 0.018 0.100 7734 Z= 1.150 Angle : 1.562 8.860 10395 Z= 1.101 Chirality : 0.097 0.479 1075 Planarity : 0.010 0.166 1344 Dihedral : 10.954 89.353 2920 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.65 % Favored : 96.02 % Rotamer: Outliers : 0.48 % Allowed : 1.45 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.25), residues: 904 helix: 0.93 (0.20), residues: 524 sheet: 0.59 (1.04), residues: 23 loop : -0.78 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.008 TRP A 669 HIS 0.007 0.002 HIS A 756 PHE 0.034 0.006 PHE A 615 TYR 0.081 0.008 TYR A 544 ARG 0.007 0.001 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 294 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 LYS cc_start: 0.5720 (mttt) cc_final: 0.5253 (tttm) REVERT: A 170 VAL cc_start: 0.7961 (m) cc_final: 0.7739 (m) REVERT: A 256 THR cc_start: 0.8987 (p) cc_final: 0.8710 (t) REVERT: A 291 ASN cc_start: 0.8715 (m-40) cc_final: 0.8486 (m-40) REVERT: A 514 LYS cc_start: 0.8747 (tttt) cc_final: 0.8189 (tptm) REVERT: A 647 ILE cc_start: 0.8356 (mt) cc_final: 0.8134 (mt) REVERT: A 883 GLU cc_start: 0.8457 (tt0) cc_final: 0.8059 (pp20) REVERT: A 912 ARG cc_start: 0.8786 (mtt180) cc_final: 0.8578 (ttm110) REVERT: A 991 LYS cc_start: 0.8769 (ptmt) cc_final: 0.8450 (ttmt) REVERT: A 1067 TYR cc_start: 0.9453 (t80) cc_final: 0.9000 (t80) REVERT: A 1084 LYS cc_start: 0.9275 (mttt) cc_final: 0.9064 (mmtt) outliers start: 4 outliers final: 0 residues processed: 298 average time/residue: 0.2997 time to fit residues: 111.3140 Evaluate side-chains 169 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 ASN A 364 ASN A 380 GLN A 621 GLN A 648 ASN ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 871 HIS A 958 ASN A 967 ASN A1070 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 7734 Z= 0.265 Angle : 0.738 9.364 10395 Z= 0.415 Chirality : 0.045 0.185 1075 Planarity : 0.005 0.059 1344 Dihedral : 4.845 20.575 995 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.21 % Favored : 96.68 % Rotamer: Outliers : 2.90 % Allowed : 10.64 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.27), residues: 904 helix: 1.60 (0.21), residues: 523 sheet: 0.20 (0.94), residues: 23 loop : -0.61 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 244 HIS 0.009 0.001 HIS A 18 PHE 0.023 0.002 PHE A 458 TYR 0.024 0.002 TYR A 643 ARG 0.009 0.001 ARG A1017 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 194 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.8635 (tp30) cc_final: 0.8328 (tp30) REVERT: A 180 GLU cc_start: 0.8190 (tt0) cc_final: 0.7858 (tt0) REVERT: A 243 TRP cc_start: 0.9021 (t60) cc_final: 0.8800 (t60) REVERT: A 256 THR cc_start: 0.8876 (p) cc_final: 0.8616 (t) REVERT: A 258 PHE cc_start: 0.8357 (m-80) cc_final: 0.8096 (m-80) REVERT: A 307 ASP cc_start: 0.8350 (m-30) cc_final: 0.8093 (m-30) REVERT: A 469 ASP cc_start: 0.8617 (m-30) cc_final: 0.8379 (t0) REVERT: A 883 GLU cc_start: 0.8324 (tt0) cc_final: 0.7976 (pp20) REVERT: A 912 ARG cc_start: 0.8802 (mtt180) cc_final: 0.8439 (ttm110) REVERT: A 915 TYR cc_start: 0.8884 (t80) cc_final: 0.8678 (t80) REVERT: A 1010 ASP cc_start: 0.8294 (p0) cc_final: 0.8075 (p0) outliers start: 24 outliers final: 16 residues processed: 208 average time/residue: 0.2640 time to fit residues: 70.4049 Evaluate side-chains 169 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1117 ASP Chi-restraints excluded: chain A residue 1126 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 56 optimal weight: 0.0980 chunk 23 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 82 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 702 HIS ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.4900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7734 Z= 0.265 Angle : 0.693 10.050 10395 Z= 0.379 Chirality : 0.044 0.155 1075 Planarity : 0.005 0.049 1344 Dihedral : 4.810 22.455 995 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.87 % Favored : 95.91 % Rotamer: Outliers : 4.35 % Allowed : 12.09 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.27), residues: 904 helix: 1.48 (0.22), residues: 515 sheet: 0.27 (0.96), residues: 23 loop : -0.62 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 244 HIS 0.004 0.001 HIS A 173 PHE 0.036 0.002 PHE A1118 TYR 0.027 0.002 TYR A1067 ARG 0.006 0.001 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.9178 (mmmt) cc_final: 0.8675 (mmmt) REVERT: A 99 LYS cc_start: 0.5634 (mmtt) cc_final: 0.5353 (mmtt) REVERT: A 163 LYS cc_start: 0.5457 (mttt) cc_final: 0.5042 (tttt) REVERT: A 194 ASP cc_start: 0.8760 (m-30) cc_final: 0.8212 (m-30) REVERT: A 256 THR cc_start: 0.8875 (p) cc_final: 0.8579 (t) REVERT: A 260 ASP cc_start: 0.5680 (t70) cc_final: 0.5427 (t70) REVERT: A 301 TRP cc_start: 0.9214 (m-10) cc_final: 0.8993 (m-10) REVERT: A 625 GLU cc_start: 0.6534 (mt-10) cc_final: 0.6321 (mt-10) REVERT: A 758 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8778 (tt0) REVERT: A 883 GLU cc_start: 0.8281 (tt0) cc_final: 0.7886 (pp20) REVERT: A 912 ARG cc_start: 0.8849 (mtt180) cc_final: 0.8437 (ttm110) REVERT: A 913 TYR cc_start: 0.8814 (m-80) cc_final: 0.8457 (m-10) REVERT: A 963 ASP cc_start: 0.8562 (m-30) cc_final: 0.7544 (t0) REVERT: A 1010 ASP cc_start: 0.8469 (p0) cc_final: 0.8214 (p0) REVERT: A 1014 GLN cc_start: 0.8541 (tt0) cc_final: 0.7624 (mm-40) REVERT: A 1018 TRP cc_start: 0.9048 (m-10) cc_final: 0.8343 (m100) REVERT: A 1072 LYS cc_start: 0.9493 (pttm) cc_final: 0.9257 (pttm) outliers start: 36 outliers final: 26 residues processed: 193 average time/residue: 0.2218 time to fit residues: 56.3494 Evaluate side-chains 172 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 651 PHE Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 758 GLN Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1064 CYS Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1117 ASP Chi-restraints excluded: chain A residue 1126 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 0.9980 chunk 62 optimal weight: 0.0980 chunk 43 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 0.0970 chunk 56 optimal weight: 0.0570 chunk 83 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 23 optimal weight: 0.4980 chunk 74 optimal weight: 7.9990 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS A 175 ASN A 393 HIS ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.5508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7734 Z= 0.188 Angle : 0.647 8.705 10395 Z= 0.351 Chirality : 0.043 0.173 1075 Planarity : 0.005 0.084 1344 Dihedral : 4.709 20.239 995 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.20 % Favored : 95.46 % Rotamer: Outliers : 3.99 % Allowed : 14.63 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.28), residues: 904 helix: 1.64 (0.22), residues: 510 sheet: 0.28 (1.03), residues: 21 loop : -0.75 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 244 HIS 0.003 0.001 HIS A 134 PHE 0.017 0.002 PHE A1118 TYR 0.025 0.002 TYR A1085 ARG 0.006 0.001 ARG A1017 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 173 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 LYS cc_start: 0.5379 (mttt) cc_final: 0.5112 (mttt) REVERT: A 165 GLU cc_start: 0.8545 (tp30) cc_final: 0.8267 (tp30) REVERT: A 167 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7562 (mp0) REVERT: A 256 THR cc_start: 0.8713 (p) cc_final: 0.8447 (t) REVERT: A 260 ASP cc_start: 0.5589 (t70) cc_final: 0.5363 (t70) REVERT: A 307 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7645 (t0) REVERT: A 638 ASP cc_start: 0.8406 (OUTLIER) cc_final: 0.7749 (p0) REVERT: A 883 GLU cc_start: 0.8220 (tt0) cc_final: 0.7796 (pp20) REVERT: A 912 ARG cc_start: 0.8652 (mtt180) cc_final: 0.8360 (ttm110) REVERT: A 917 ASP cc_start: 0.8302 (m-30) cc_final: 0.7955 (m-30) REVERT: A 963 ASP cc_start: 0.8599 (m-30) cc_final: 0.7582 (t0) REVERT: A 1014 GLN cc_start: 0.8461 (tt0) cc_final: 0.7560 (mm-40) REVERT: A 1018 TRP cc_start: 0.9038 (m-10) cc_final: 0.8329 (m-10) REVERT: A 1072 LYS cc_start: 0.9481 (pttm) cc_final: 0.9249 (pttm) REVERT: A 1126 ASN cc_start: 0.7957 (OUTLIER) cc_final: 0.7523 (t0) outliers start: 33 outliers final: 19 residues processed: 189 average time/residue: 0.2322 time to fit residues: 57.4950 Evaluate side-chains 172 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 651 PHE Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1064 CYS Chi-restraints excluded: chain A residue 1117 ASP Chi-restraints excluded: chain A residue 1126 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 66 optimal weight: 0.0570 chunk 36 optimal weight: 2.9990 chunk 75 optimal weight: 20.0000 chunk 61 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN ** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 ASN ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 702 HIS ** A 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.5896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7734 Z= 0.214 Angle : 0.656 9.294 10395 Z= 0.354 Chirality : 0.044 0.163 1075 Planarity : 0.005 0.052 1344 Dihedral : 4.678 20.432 995 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.42 % Favored : 95.24 % Rotamer: Outliers : 4.11 % Allowed : 16.08 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.28), residues: 904 helix: 1.47 (0.22), residues: 514 sheet: -0.21 (1.03), residues: 24 loop : -0.72 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP A 244 HIS 0.003 0.001 HIS A 18 PHE 0.027 0.002 PHE A 220 TYR 0.024 0.002 TYR A1085 ARG 0.009 0.001 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 162 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8656 (pp20) cc_final: 0.8228 (pp20) REVERT: A 165 GLU cc_start: 0.8581 (tp30) cc_final: 0.8366 (tp30) REVERT: A 256 THR cc_start: 0.8719 (p) cc_final: 0.8447 (t) REVERT: A 260 ASP cc_start: 0.5803 (t70) cc_final: 0.5595 (t70) REVERT: A 307 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7698 (t0) REVERT: A 625 GLU cc_start: 0.6508 (OUTLIER) cc_final: 0.5765 (mp0) REVERT: A 638 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.7736 (p0) REVERT: A 883 GLU cc_start: 0.8216 (tt0) cc_final: 0.7804 (pp20) REVERT: A 894 ARG cc_start: 0.7219 (ptt180) cc_final: 0.6864 (tmm-80) REVERT: A 912 ARG cc_start: 0.8807 (mtt180) cc_final: 0.8539 (ttm110) REVERT: A 917 ASP cc_start: 0.8441 (m-30) cc_final: 0.8168 (m-30) REVERT: A 963 ASP cc_start: 0.8603 (m-30) cc_final: 0.7622 (t0) REVERT: A 977 ASP cc_start: 0.8379 (m-30) cc_final: 0.8129 (m-30) REVERT: A 1014 GLN cc_start: 0.8480 (tt0) cc_final: 0.7570 (mm-40) REVERT: A 1018 TRP cc_start: 0.9036 (m-10) cc_final: 0.8442 (m-10) REVERT: A 1072 LYS cc_start: 0.9474 (pttm) cc_final: 0.9238 (pttm) REVERT: A 1126 ASN cc_start: 0.8012 (OUTLIER) cc_final: 0.7602 (t0) REVERT: A 1130 LYS cc_start: 0.8945 (mttt) cc_final: 0.8636 (tmtt) outliers start: 34 outliers final: 21 residues processed: 185 average time/residue: 0.2279 time to fit residues: 55.7433 Evaluate side-chains 165 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 651 PHE Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1064 CYS Chi-restraints excluded: chain A residue 1095 TYR Chi-restraints excluded: chain A residue 1117 ASP Chi-restraints excluded: chain A residue 1126 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 21 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 41 optimal weight: 0.0870 chunk 7 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 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 175 ASN ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.6146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7734 Z= 0.200 Angle : 0.643 11.622 10395 Z= 0.343 Chirality : 0.042 0.147 1075 Planarity : 0.004 0.039 1344 Dihedral : 4.648 21.211 995 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.76 % Favored : 94.91 % Rotamer: Outliers : 4.23 % Allowed : 18.02 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.28), residues: 904 helix: 1.48 (0.22), residues: 517 sheet: -0.67 (1.00), residues: 24 loop : -0.80 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP A 244 HIS 0.003 0.001 HIS A 134 PHE 0.023 0.002 PHE A 220 TYR 0.022 0.002 TYR A1085 ARG 0.006 0.001 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 162 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASN cc_start: 0.8483 (p0) cc_final: 0.8116 (p0) REVERT: A 256 THR cc_start: 0.8666 (p) cc_final: 0.8402 (t) REVERT: A 307 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.7610 (t0) REVERT: A 625 GLU cc_start: 0.6528 (OUTLIER) cc_final: 0.5522 (mp0) REVERT: A 638 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.7744 (p0) REVERT: A 693 GLU cc_start: 0.8022 (pm20) cc_final: 0.7789 (pm20) REVERT: A 712 ASP cc_start: 0.8658 (t70) cc_final: 0.8425 (t70) REVERT: A 715 THR cc_start: 0.9060 (OUTLIER) cc_final: 0.8757 (t) REVERT: A 883 GLU cc_start: 0.8212 (tt0) cc_final: 0.7778 (pp20) REVERT: A 894 ARG cc_start: 0.7232 (ptt180) cc_final: 0.6886 (tmm-80) REVERT: A 912 ARG cc_start: 0.8815 (mtt180) cc_final: 0.8562 (ttm110) REVERT: A 963 ASP cc_start: 0.8625 (m-30) cc_final: 0.7627 (t0) REVERT: A 1067 TYR cc_start: 0.9399 (t80) cc_final: 0.9163 (t80) REVERT: A 1072 LYS cc_start: 0.9435 (pttm) cc_final: 0.9208 (pttm) REVERT: A 1126 ASN cc_start: 0.8061 (OUTLIER) cc_final: 0.7679 (t0) REVERT: A 1130 LYS cc_start: 0.8981 (mttt) cc_final: 0.8666 (tmtt) outliers start: 35 outliers final: 22 residues processed: 184 average time/residue: 0.2293 time to fit residues: 55.3921 Evaluate side-chains 168 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 595 TYR Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 651 PHE Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 1064 CYS Chi-restraints excluded: chain A residue 1095 TYR Chi-restraints excluded: chain A residue 1117 ASP Chi-restraints excluded: chain A residue 1126 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 0.9980 chunk 50 optimal weight: 0.0970 chunk 65 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 88 optimal weight: 9.9990 chunk 55 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.6379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7734 Z= 0.203 Angle : 0.658 10.662 10395 Z= 0.353 Chirality : 0.043 0.239 1075 Planarity : 0.004 0.038 1344 Dihedral : 4.617 20.827 995 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.09 % Favored : 95.58 % Rotamer: Outliers : 3.87 % Allowed : 19.47 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.28), residues: 904 helix: 1.57 (0.22), residues: 515 sheet: -0.75 (0.99), residues: 24 loop : -0.86 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A 244 HIS 0.003 0.001 HIS A 18 PHE 0.019 0.002 PHE A 220 TYR 0.021 0.002 TYR A 643 ARG 0.005 0.001 ARG A 939 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.8276 (ttp80) cc_final: 0.7903 (ptt90) REVERT: A 98 ASN cc_start: 0.8461 (p0) cc_final: 0.8113 (p0) REVERT: A 164 TYR cc_start: 0.7927 (m-80) cc_final: 0.7506 (m-80) REVERT: A 256 THR cc_start: 0.8713 (p) cc_final: 0.8423 (t) REVERT: A 307 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7633 (t0) REVERT: A 507 ASN cc_start: 0.8791 (p0) cc_final: 0.8549 (p0) REVERT: A 625 GLU cc_start: 0.6436 (OUTLIER) cc_final: 0.5444 (mp0) REVERT: A 638 ASP cc_start: 0.8443 (OUTLIER) cc_final: 0.7759 (p0) REVERT: A 712 ASP cc_start: 0.8700 (t70) cc_final: 0.8277 (t70) REVERT: A 715 THR cc_start: 0.9005 (OUTLIER) cc_final: 0.8665 (t) REVERT: A 883 GLU cc_start: 0.8170 (tt0) cc_final: 0.7712 (pp20) REVERT: A 894 ARG cc_start: 0.7242 (ptt180) cc_final: 0.6941 (tmm-80) REVERT: A 912 ARG cc_start: 0.8799 (mtt180) cc_final: 0.8558 (ttm110) REVERT: A 963 ASP cc_start: 0.8630 (m-30) cc_final: 0.7619 (t0) REVERT: A 1017 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8167 (mtm180) REVERT: A 1072 LYS cc_start: 0.9392 (pttm) cc_final: 0.9184 (pttm) REVERT: A 1130 LYS cc_start: 0.8934 (mttt) cc_final: 0.8650 (tmtt) outliers start: 32 outliers final: 18 residues processed: 173 average time/residue: 0.2332 time to fit residues: 52.8537 Evaluate side-chains 162 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 651 PHE Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 1017 ARG Chi-restraints excluded: chain A residue 1095 TYR Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1117 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 0.0870 chunk 8 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 84 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 HIS ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 982 ASN A1014 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.6590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7734 Z= 0.199 Angle : 0.661 11.468 10395 Z= 0.352 Chirality : 0.043 0.207 1075 Planarity : 0.004 0.036 1344 Dihedral : 4.578 21.922 995 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.42 % Favored : 95.24 % Rotamer: Outliers : 2.78 % Allowed : 21.04 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.28), residues: 904 helix: 1.53 (0.22), residues: 511 sheet: -1.01 (0.96), residues: 24 loop : -0.84 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP A 244 HIS 0.003 0.001 HIS A 18 PHE 0.021 0.002 PHE A 654 TYR 0.029 0.002 TYR A 407 ARG 0.004 0.001 ARG A 939 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASN cc_start: 0.8444 (p0) cc_final: 0.8114 (p0) REVERT: A 256 THR cc_start: 0.8656 (p) cc_final: 0.8356 (t) REVERT: A 307 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.7681 (t0) REVERT: A 625 GLU cc_start: 0.6391 (OUTLIER) cc_final: 0.5467 (mp0) REVERT: A 638 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.7811 (p0) REVERT: A 883 GLU cc_start: 0.8161 (tt0) cc_final: 0.7716 (pp20) REVERT: A 894 ARG cc_start: 0.7291 (ptt180) cc_final: 0.7015 (tmm-80) REVERT: A 912 ARG cc_start: 0.8828 (mtt180) cc_final: 0.8624 (ttm110) REVERT: A 963 ASP cc_start: 0.8640 (m-30) cc_final: 0.7628 (t0) REVERT: A 1017 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8179 (mtm180) REVERT: A 1067 TYR cc_start: 0.9442 (t80) cc_final: 0.9189 (t80) REVERT: A 1072 LYS cc_start: 0.9375 (pttm) cc_final: 0.9165 (pttm) REVERT: A 1130 LYS cc_start: 0.8932 (mttt) cc_final: 0.8635 (tmtt) outliers start: 23 outliers final: 17 residues processed: 164 average time/residue: 0.2154 time to fit residues: 46.5297 Evaluate side-chains 158 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 651 PHE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 1017 ARG Chi-restraints excluded: chain A residue 1095 TYR Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1117 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 54 optimal weight: 0.0770 chunk 87 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.6816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7734 Z= 0.200 Angle : 0.685 11.855 10395 Z= 0.363 Chirality : 0.043 0.198 1075 Planarity : 0.004 0.035 1344 Dihedral : 4.576 22.213 995 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.65 % Favored : 95.02 % Rotamer: Outliers : 2.66 % Allowed : 21.52 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.28), residues: 904 helix: 1.52 (0.22), residues: 510 sheet: -0.99 (0.97), residues: 24 loop : -0.92 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP A 244 HIS 0.003 0.001 HIS A 146 PHE 0.022 0.002 PHE A 220 TYR 0.028 0.002 TYR A 407 ARG 0.003 0.001 ARG A 240 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.8233 (ttp80) cc_final: 0.7933 (ptt90) REVERT: A 98 ASN cc_start: 0.8300 (p0) cc_final: 0.7900 (p0) REVERT: A 227 ASN cc_start: 0.8482 (t0) cc_final: 0.8279 (t0) REVERT: A 256 THR cc_start: 0.8634 (p) cc_final: 0.8333 (t) REVERT: A 307 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7688 (t0) REVERT: A 625 GLU cc_start: 0.6366 (OUTLIER) cc_final: 0.5504 (mp0) REVERT: A 883 GLU cc_start: 0.8124 (tt0) cc_final: 0.7749 (tp30) REVERT: A 894 ARG cc_start: 0.7346 (ptt180) cc_final: 0.7072 (tmm-80) REVERT: A 912 ARG cc_start: 0.8818 (mtt180) cc_final: 0.8609 (ttm110) REVERT: A 963 ASP cc_start: 0.8607 (m-30) cc_final: 0.7589 (t0) REVERT: A 1067 TYR cc_start: 0.9479 (t80) cc_final: 0.9276 (t80) REVERT: A 1072 LYS cc_start: 0.9355 (pttm) cc_final: 0.9126 (pttm) REVERT: A 1084 LYS cc_start: 0.9499 (mmtt) cc_final: 0.9249 (mmtt) REVERT: A 1130 LYS cc_start: 0.8931 (mttt) cc_final: 0.8611 (tmtt) outliers start: 22 outliers final: 15 residues processed: 155 average time/residue: 0.2250 time to fit residues: 46.1028 Evaluate side-chains 156 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 1095 TYR Chi-restraints excluded: chain A residue 1117 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 0.0870 chunk 60 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 22 optimal weight: 0.0470 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.6958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7734 Z= 0.190 Angle : 0.698 12.002 10395 Z= 0.368 Chirality : 0.043 0.185 1075 Planarity : 0.004 0.038 1344 Dihedral : 4.520 21.946 995 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.31 % Favored : 95.35 % Rotamer: Outliers : 2.66 % Allowed : 21.40 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.27), residues: 904 helix: 1.47 (0.22), residues: 516 sheet: -0.90 (0.98), residues: 24 loop : -1.06 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.003 TRP A1018 HIS 0.003 0.000 HIS A 18 PHE 0.025 0.002 PHE A 651 TYR 0.026 0.002 TYR A 643 ARG 0.005 0.001 ARG A1017 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: 0.8045 (mmm) cc_final: 0.7609 (mmm) REVERT: A 98 ASN cc_start: 0.8292 (p0) cc_final: 0.7893 (p0) REVERT: A 164 TYR cc_start: 0.7859 (m-80) cc_final: 0.7438 (m-80) REVERT: A 227 ASN cc_start: 0.8428 (t0) cc_final: 0.8214 (t0) REVERT: A 256 THR cc_start: 0.8593 (p) cc_final: 0.8265 (t) REVERT: A 307 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7698 (t0) REVERT: A 625 GLU cc_start: 0.6347 (OUTLIER) cc_final: 0.5514 (mp0) REVERT: A 883 GLU cc_start: 0.8074 (tt0) cc_final: 0.7719 (tp30) REVERT: A 894 ARG cc_start: 0.7390 (ptt180) cc_final: 0.7111 (tmm-80) REVERT: A 912 ARG cc_start: 0.8798 (mtt180) cc_final: 0.8597 (ttm110) REVERT: A 963 ASP cc_start: 0.8672 (m-30) cc_final: 0.7658 (t0) REVERT: A 1067 TYR cc_start: 0.9497 (t80) cc_final: 0.9291 (t80) REVERT: A 1072 LYS cc_start: 0.9331 (pttm) cc_final: 0.9115 (pttm) REVERT: A 1084 LYS cc_start: 0.9492 (mmtt) cc_final: 0.9249 (mmtt) REVERT: A 1130 LYS cc_start: 0.8926 (mttt) cc_final: 0.8606 (tmtt) outliers start: 22 outliers final: 16 residues processed: 163 average time/residue: 0.2421 time to fit residues: 51.5635 Evaluate side-chains 159 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TYR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 1095 TYR Chi-restraints excluded: chain A residue 1117 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 9.9990 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 chunk 30 optimal weight: 0.5980 chunk 75 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 64 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.106869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.082785 restraints weight = 20878.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.086101 restraints weight = 11601.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.088342 restraints weight = 7998.477| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.7071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7734 Z= 0.217 Angle : 0.709 11.691 10395 Z= 0.374 Chirality : 0.043 0.173 1075 Planarity : 0.006 0.150 1344 Dihedral : 4.463 22.318 995 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.09 % Favored : 94.58 % Rotamer: Outliers : 2.42 % Allowed : 22.37 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.28), residues: 904 helix: 1.53 (0.22), residues: 513 sheet: -0.81 (0.97), residues: 24 loop : -0.90 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.003 TRP A1018 HIS 0.002 0.001 HIS A 134 PHE 0.023 0.002 PHE A 220 TYR 0.027 0.002 TYR A 407 ARG 0.004 0.001 ARG A 240 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2018.96 seconds wall clock time: 37 minutes 59.82 seconds (2279.82 seconds total)