Starting phenix.real_space_refine on Fri Apr 5 22:09:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dqk_27655/04_2024/8dqk_27655.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dqk_27655/04_2024/8dqk_27655.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dqk_27655/04_2024/8dqk_27655.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dqk_27655/04_2024/8dqk_27655.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dqk_27655/04_2024/8dqk_27655.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dqk_27655/04_2024/8dqk_27655.pdb" } resolution = 4.0 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= 1.000 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 21 5.16 5 C 3844 2.51 5 N 1002 2.21 5 O 1024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 264": "OE1" <-> "OE2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 453": "OD1" <-> "OD2" Residue "A TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 721": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 5891 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 733, 5891 Classifications: {'peptide': 733} Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 691} Chain breaks: 3 Time building chain proxies: 3.90, per 1000 atoms: 0.66 Number of scatterers: 5891 At special positions: 0 Unit cell: (83.83, 84.66, 107.9, 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 21 16.00 O 1024 8.00 N 1002 7.00 C 3844 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.46 Conformation dependent library (CDL) restraints added in 1.2 seconds 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1374 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 3 sheets defined 60.7% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 101 through 129 Proline residue: A 107 - end of helix Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 134 through 157 Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 169 through 176 Processing helix chain 'A' and resid 201 through 214 removed outlier: 3.548A pdb=" N THR A 205 " --> pdb=" O PRO A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 257 removed outlier: 4.087A pdb=" N THR A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) Proline residue: A 251 - end of helix Processing helix chain 'A' and resid 262 through 268 Processing helix chain 'A' and resid 279 through 302 Processing helix chain 'A' and resid 302 through 316 Processing helix chain 'A' and resid 405 through 422 removed outlier: 3.720A pdb=" N LEU A 420 " --> pdb=" O ARG A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 451 removed outlier: 4.485A pdb=" N PHE A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 484 Processing helix chain 'A' and resid 486 through 491 Processing helix chain 'A' and resid 579 through 585 removed outlier: 3.590A pdb=" N ALA A 583 " --> pdb=" O THR A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 592 removed outlier: 4.054A pdb=" N ALA A 590 " --> pdb=" O SER A 587 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA A 592 " --> pdb=" O TYR A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 610 Processing helix chain 'A' and resid 611 through 616 removed outlier: 3.912A pdb=" N PHE A 614 " --> pdb=" O ALA A 611 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS A 616 " --> pdb=" O ALA A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 643 removed outlier: 4.219A pdb=" N VAL A 636 " --> pdb=" O THR A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 686 Processing helix chain 'A' and resid 689 through 693 Processing helix chain 'A' and resid 698 through 711 Processing helix chain 'A' and resid 713 through 732 removed outlier: 4.366A pdb=" N PHE A 717 " --> pdb=" O PHE A 713 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N PHE A 720 " --> pdb=" O ILE A 716 " (cutoff:3.500A) Proline residue: A 725 - end of helix Processing helix chain 'A' and resid 740 through 765 Processing helix chain 'A' and resid 768 through 800 removed outlier: 4.159A pdb=" N TYR A 787 " --> pdb=" O SER A 783 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LEU A 788 " --> pdb=" O CYS A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 827 removed outlier: 3.666A pdb=" N VAL A 827 " --> pdb=" O ASP A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 833 No H-bonds generated for 'chain 'A' and resid 831 through 833' Processing helix chain 'A' and resid 834 through 857 removed outlier: 4.041A pdb=" N ILE A 838 " --> pdb=" O MET A 834 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE A 839 " --> pdb=" O ILE A 835 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE A 840 " --> pdb=" O THR A 836 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN A 844 " --> pdb=" O ILE A 840 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA A 849 " --> pdb=" O ILE A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 867 Processing helix chain 'A' and resid 868 through 889 Proline residue: A 882 - end of helix removed outlier: 4.404A pdb=" N LEU A 888 " --> pdb=" O ALA A 884 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY A 889 " --> pdb=" O LYS A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 893 Processing helix chain 'A' and resid 894 through 916 removed outlier: 4.618A pdb=" N VAL A 898 " --> pdb=" O THR A 894 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL A 900 " --> pdb=" O VAL A 896 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 95 through 99 Processing sheet with id=AA2, first strand: chain 'A' and resid 355 through 360 removed outlier: 6.507A pdb=" N LEU A 391 " --> pdb=" O LEU A 359 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N VAL A 392 " --> pdb=" O ASN A 222 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N CYS A 224 " --> pdb=" O VAL A 392 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL A 394 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL A 226 " --> pdb=" O VAL A 394 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ASP A 189 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N LEU A 430 " --> pdb=" O ASP A 189 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N PHE A 191 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N CYS A 503 " --> pdb=" O ASN A 429 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA A 458 " --> pdb=" O ARG A 506 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ARG A 649 " --> pdb=" O ALA A 458 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL A 460 " --> pdb=" O ARG A 649 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 435 through 436 removed outlier: 6.404A pdb=" N ARG A 465 " --> pdb=" O GLY A 660 " (cutoff:3.500A) 312 hydrogen bonds defined for protein. 903 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: 1.93 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1858 1.34 - 1.46: 1547 1.46 - 1.58: 2631 1.58 - 1.70: 0 1.70 - 1.81: 33 Bond restraints: 6069 Sorted by residual: bond pdb=" CA ARG A 348 " pdb=" CB ARG A 348 " ideal model delta sigma weight residual 1.529 1.560 -0.031 1.66e-02 3.63e+03 3.57e+00 bond pdb=" CB GLU A 668 " pdb=" CG GLU A 668 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.61e+00 bond pdb=" N LYS A 406 " pdb=" CA LYS A 406 " ideal model delta sigma weight residual 1.457 1.477 -0.019 1.29e-02 6.01e+03 2.19e+00 bond pdb=" C TYR A 881 " pdb=" N PRO A 882 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.09e+00 bond pdb=" CB ASN A 161 " pdb=" CG ASN A 161 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.88e-01 ... (remaining 6064 not shown) Histogram of bond angle deviations from ideal: 100.30 - 107.07: 222 107.07 - 113.84: 3340 113.84 - 120.61: 2517 120.61 - 127.39: 2102 127.39 - 134.16: 98 Bond angle restraints: 8279 Sorted by residual: angle pdb=" N VAL A 866 " pdb=" CA VAL A 866 " pdb=" C VAL A 866 " ideal model delta sigma weight residual 112.83 106.74 6.09 9.90e-01 1.02e+00 3.78e+01 angle pdb=" C ILE A 664 " pdb=" N ASN A 665 " pdb=" CA ASN A 665 " ideal model delta sigma weight residual 121.54 128.24 -6.70 1.91e+00 2.74e-01 1.23e+01 angle pdb=" N GLN A 279 " pdb=" CA GLN A 279 " pdb=" C GLN A 279 " ideal model delta sigma weight residual 112.12 108.00 4.12 1.34e+00 5.57e-01 9.47e+00 angle pdb=" CA ARG A 675 " pdb=" CB ARG A 675 " pdb=" CG ARG A 675 " ideal model delta sigma weight residual 114.10 119.97 -5.87 2.00e+00 2.50e-01 8.63e+00 angle pdb=" C VAL A 609 " pdb=" CA VAL A 609 " pdb=" CB VAL A 609 " ideal model delta sigma weight residual 111.88 107.99 3.89 1.37e+00 5.33e-01 8.05e+00 ... (remaining 8274 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 3222 17.97 - 35.93: 253 35.93 - 53.90: 25 53.90 - 71.86: 7 71.86 - 89.83: 3 Dihedral angle restraints: 3510 sinusoidal: 1379 harmonic: 2131 Sorted by residual: dihedral pdb=" CA TRP A 863 " pdb=" C TRP A 863 " pdb=" N LEU A 864 " pdb=" CA LEU A 864 " ideal model delta harmonic sigma weight residual -180.00 -151.85 -28.15 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA GLN A 405 " pdb=" C GLN A 405 " pdb=" N LYS A 406 " pdb=" CA LYS A 406 " ideal model delta harmonic sigma weight residual 180.00 161.95 18.05 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA ILE A 841 " pdb=" C ILE A 841 " pdb=" N PHE A 842 " pdb=" CA PHE A 842 " ideal model delta harmonic sigma weight residual 180.00 -163.17 -16.83 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 3507 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 663 0.044 - 0.088: 188 0.088 - 0.132: 55 0.132 - 0.176: 8 0.176 - 0.220: 3 Chirality restraints: 917 Sorted by residual: chirality pdb=" CB ILE A 427 " pdb=" CA ILE A 427 " pdb=" CG1 ILE A 427 " pdb=" CG2 ILE A 427 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA ASN A 665 " pdb=" N ASN A 665 " pdb=" C ASN A 665 " pdb=" CB ASN A 665 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.23e-01 chirality pdb=" CB ILE A 624 " pdb=" CA ILE A 624 " pdb=" CG1 ILE A 624 " pdb=" CG2 ILE A 624 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.07e-01 ... (remaining 914 not shown) Planarity restraints: 1043 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 217 " -0.035 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO A 218 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 218 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 218 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 166 " 0.033 5.00e-02 4.00e+02 5.06e-02 4.10e+00 pdb=" N PRO A 167 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 167 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 167 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 779 " -0.012 2.00e-02 2.50e+03 1.09e-02 2.97e+00 pdb=" CG TRP A 779 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP A 779 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP A 779 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 779 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 779 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 779 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 779 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 779 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 779 " -0.001 2.00e-02 2.50e+03 ... (remaining 1040 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 100 2.69 - 3.24: 6008 3.24 - 3.79: 9288 3.79 - 4.35: 11698 4.35 - 4.90: 18853 Nonbonded interactions: 45947 Sorted by model distance: nonbonded pdb=" OD1 ASN A 361 " pdb=" N HIS A 362 " model vdw 2.134 2.520 nonbonded pdb=" NE2 GLN A 777 " pdb=" O PHE A 878 " model vdw 2.144 2.520 nonbonded pdb=" O ALA A 606 " pdb=" OG1 THR A 610 " model vdw 2.247 2.440 nonbonded pdb=" N ILE A 664 " pdb=" OE2 GLU A 668 " model vdw 2.311 2.520 nonbonded pdb=" O ALA A 240 " pdb=" OG SER A 243 " model vdw 2.318 2.440 ... (remaining 45942 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: 1.910 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: 0.000 Extract box with map and model: 5.900 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 20.770 Find NCS groups from input model: 0.170 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5812 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 0.049 6069 Z= 0.192 Angle : 0.720 9.014 8279 Z= 0.398 Chirality : 0.045 0.220 917 Planarity : 0.005 0.052 1043 Dihedral : 12.564 89.826 2136 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.62 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.14 (0.32), residues: 725 helix: 0.74 (0.27), residues: 392 sheet: -0.64 (0.58), residues: 72 loop : -0.53 (0.40), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 779 HIS 0.005 0.001 HIS A 879 PHE 0.022 0.002 PHE A 773 TYR 0.029 0.002 TYR A 696 ARG 0.004 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: A 135 MET cc_start: 0.4370 (tpp) cc_final: 0.4125 (tpp) REVERT: A 308 LYS cc_start: 0.8552 (pptt) cc_final: 0.8210 (pptt) REVERT: A 493 MET cc_start: 0.4007 (ppp) cc_final: 0.2897 (ppp) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1850 time to fit residues: 19.6408 Evaluate side-chains 49 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 37 optimal weight: 0.0770 chunk 29 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 overall best weight: 6.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 GLN ** A 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 HIS ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 873 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 0.4789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 6069 Z= 0.510 Angle : 0.956 7.808 8279 Z= 0.521 Chirality : 0.054 0.195 917 Planarity : 0.009 0.103 1043 Dihedral : 5.788 22.184 802 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 29.33 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.28 % Favored : 95.45 % Rotamer: Outliers : 3.66 % Allowed : 9.70 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.33 (0.29), residues: 725 helix: -0.60 (0.24), residues: 396 sheet: -0.12 (0.63), residues: 68 loop : -1.32 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP A 779 HIS 0.011 0.003 HIS A 272 PHE 0.036 0.004 PHE A 267 TYR 0.033 0.004 TYR A 393 ARG 0.020 0.001 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 62 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: A 135 MET cc_start: 0.4500 (tpp) cc_final: 0.4203 (tpp) REVERT: A 212 ILE cc_start: 0.9119 (pt) cc_final: 0.8787 (mt) REVERT: A 232 MET cc_start: 0.7823 (mmm) cc_final: 0.7618 (mmm) REVERT: A 411 MET cc_start: 0.8559 (ptm) cc_final: 0.8232 (ptm) REVERT: A 493 MET cc_start: 0.5055 (ppp) cc_final: 0.4236 (ppp) REVERT: A 773 PHE cc_start: 0.7903 (t80) cc_final: 0.7541 (t80) outliers start: 23 outliers final: 11 residues processed: 82 average time/residue: 0.1712 time to fit residues: 18.8318 Evaluate side-chains 51 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 40 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 314 TYR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 784 CYS Chi-restraints excluded: chain A residue 879 HIS Chi-restraints excluded: chain A residue 887 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 36 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 873 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.5312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6069 Z= 0.272 Angle : 0.635 5.946 8279 Z= 0.339 Chirality : 0.044 0.146 917 Planarity : 0.005 0.048 1043 Dihedral : 4.950 19.638 802 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.45 % Favored : 96.41 % Rotamer: Outliers : 3.50 % Allowed : 12.88 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.31), residues: 725 helix: 0.19 (0.26), residues: 385 sheet: -0.10 (0.64), residues: 68 loop : -0.84 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 779 HIS 0.004 0.001 HIS A 698 PHE 0.031 0.002 PHE A 614 TYR 0.020 0.002 TYR A 654 ARG 0.006 0.001 ARG A 261 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 49 time to evaluate : 0.708 Fit side-chains revert: symmetry clash REVERT: A 135 MET cc_start: 0.4372 (tpp) cc_final: 0.4027 (tpp) REVERT: A 308 LYS cc_start: 0.8868 (pptt) cc_final: 0.8364 (tppt) REVERT: A 411 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8352 (ptm) REVERT: A 493 MET cc_start: 0.4736 (ppp) cc_final: 0.3896 (ppp) REVERT: A 773 PHE cc_start: 0.7968 (t80) cc_final: 0.7589 (t80) REVERT: A 826 TYR cc_start: 0.7232 (OUTLIER) cc_final: 0.6735 (m-80) outliers start: 22 outliers final: 15 residues processed: 64 average time/residue: 0.1802 time to fit residues: 16.4058 Evaluate side-chains 59 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 42 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 745 VAL Chi-restraints excluded: chain A residue 784 CYS Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 826 TYR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 879 HIS Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain A residue 900 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 GLN A 346 ASN ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 873 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.6136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6069 Z= 0.259 Angle : 0.624 8.336 8279 Z= 0.329 Chirality : 0.043 0.158 917 Planarity : 0.005 0.044 1043 Dihedral : 4.742 17.876 802 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.14 % Favored : 95.72 % Rotamer: Outliers : 3.82 % Allowed : 15.26 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.20 (0.31), residues: 725 helix: 0.51 (0.26), residues: 389 sheet: -0.55 (0.63), residues: 70 loop : -0.82 (0.40), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 779 HIS 0.005 0.001 HIS A 305 PHE 0.028 0.002 PHE A 614 TYR 0.016 0.002 TYR A 274 ARG 0.003 0.001 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 57 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: A 135 MET cc_start: 0.4491 (tpp) cc_final: 0.4199 (tpp) REVERT: A 212 ILE cc_start: 0.9203 (pt) cc_final: 0.8731 (mt) REVERT: A 232 MET cc_start: 0.7408 (mmm) cc_final: 0.6840 (mmm) REVERT: A 308 LYS cc_start: 0.8994 (pptt) cc_final: 0.8282 (tppt) REVERT: A 390 MET cc_start: 0.7425 (mmm) cc_final: 0.7069 (mmm) REVERT: A 411 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8338 (ptm) REVERT: A 493 MET cc_start: 0.4909 (ppp) cc_final: 0.4148 (ppp) REVERT: A 683 ILE cc_start: 0.8726 (pt) cc_final: 0.8489 (pt) REVERT: A 773 PHE cc_start: 0.7988 (t80) cc_final: 0.7593 (t80) REVERT: A 780 MET cc_start: 0.8561 (mmp) cc_final: 0.8346 (mmp) REVERT: A 826 TYR cc_start: 0.7312 (OUTLIER) cc_final: 0.6607 (m-80) REVERT: A 834 MET cc_start: 0.7985 (ppp) cc_final: 0.7583 (ppp) outliers start: 24 outliers final: 20 residues processed: 74 average time/residue: 0.1614 time to fit residues: 16.4859 Evaluate side-chains 69 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 47 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 745 VAL Chi-restraints excluded: chain A residue 784 CYS Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 826 TYR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 879 HIS Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 914 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 40 optimal weight: 9.9990 chunk 1 optimal weight: 0.8980 chunk 52 optimal weight: 0.0040 chunk 29 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 402 HIS ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 873 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.6175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6069 Z= 0.174 Angle : 0.567 5.859 8279 Z= 0.293 Chirality : 0.042 0.143 917 Planarity : 0.005 0.042 1043 Dihedral : 4.501 16.221 802 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.59 % Favored : 96.28 % Rotamer: Outliers : 3.18 % Allowed : 16.53 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.16 (0.32), residues: 725 helix: 0.77 (0.27), residues: 388 sheet: -0.14 (0.68), residues: 57 loop : -0.66 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 764 HIS 0.003 0.000 HIS A 698 PHE 0.022 0.001 PHE A 614 TYR 0.016 0.002 TYR A 746 ARG 0.003 0.000 ARG A 288 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 52 time to evaluate : 0.766 Fit side-chains revert: symmetry clash REVERT: A 135 MET cc_start: 0.4366 (tpp) cc_final: 0.4135 (tpp) REVERT: A 232 MET cc_start: 0.7309 (mmm) cc_final: 0.6717 (mmm) REVERT: A 308 LYS cc_start: 0.8967 (pptt) cc_final: 0.8344 (tppt) REVERT: A 390 MET cc_start: 0.7339 (mmm) cc_final: 0.6966 (mmm) REVERT: A 411 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8375 (ptm) REVERT: A 493 MET cc_start: 0.4765 (ppp) cc_final: 0.3999 (ppp) REVERT: A 773 PHE cc_start: 0.7926 (t80) cc_final: 0.7544 (t80) REVERT: A 826 TYR cc_start: 0.7317 (OUTLIER) cc_final: 0.6472 (m-80) outliers start: 20 outliers final: 16 residues processed: 65 average time/residue: 0.1532 time to fit residues: 14.2539 Evaluate side-chains 62 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 44 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 826 TYR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 879 HIS Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 914 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 63 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 32 optimal weight: 0.0670 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 overall best weight: 2.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 873 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.6756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6069 Z= 0.225 Angle : 0.591 6.166 8279 Z= 0.310 Chirality : 0.042 0.158 917 Planarity : 0.005 0.045 1043 Dihedral : 4.560 16.474 802 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.41 % Favored : 95.45 % Rotamer: Outliers : 3.97 % Allowed : 16.22 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.12 (0.32), residues: 725 helix: 0.69 (0.26), residues: 390 sheet: 0.12 (0.70), residues: 54 loop : -0.68 (0.39), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 779 HIS 0.003 0.001 HIS A 698 PHE 0.028 0.002 PHE A 614 TYR 0.014 0.002 TYR A 393 ARG 0.004 0.001 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 52 time to evaluate : 0.715 Fit side-chains revert: symmetry clash REVERT: A 109 ARG cc_start: 0.4240 (OUTLIER) cc_final: 0.3752 (ptt180) REVERT: A 232 MET cc_start: 0.7468 (mmm) cc_final: 0.6892 (mmm) REVERT: A 297 LYS cc_start: 0.7973 (mtmt) cc_final: 0.7770 (mtmm) REVERT: A 308 LYS cc_start: 0.9138 (pptt) cc_final: 0.8804 (pttp) REVERT: A 411 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8363 (ptm) REVERT: A 773 PHE cc_start: 0.8009 (t80) cc_final: 0.7607 (t80) REVERT: A 826 TYR cc_start: 0.7413 (OUTLIER) cc_final: 0.6529 (m-80) outliers start: 25 outliers final: 19 residues processed: 70 average time/residue: 0.1923 time to fit residues: 17.9416 Evaluate side-chains 65 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 43 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ARG Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 826 TYR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 914 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 7 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 42 optimal weight: 0.4980 chunk 32 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 873 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.6975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6069 Z= 0.200 Angle : 0.587 6.866 8279 Z= 0.301 Chirality : 0.042 0.147 917 Planarity : 0.005 0.044 1043 Dihedral : 4.528 15.006 802 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.41 % Favored : 95.45 % Rotamer: Outliers : 4.13 % Allowed : 18.12 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.21 (0.32), residues: 725 helix: 0.75 (0.26), residues: 393 sheet: -0.07 (0.69), residues: 55 loop : -0.57 (0.40), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 764 HIS 0.003 0.001 HIS A 698 PHE 0.022 0.001 PHE A 614 TYR 0.011 0.001 TYR A 274 ARG 0.011 0.001 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 47 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ARG cc_start: 0.4112 (OUTLIER) cc_final: 0.3674 (ptt180) REVERT: A 308 LYS cc_start: 0.9135 (pptt) cc_final: 0.8791 (pttp) REVERT: A 411 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8374 (ptm) REVERT: A 493 MET cc_start: 0.4332 (ppp) cc_final: 0.4039 (ppp) REVERT: A 773 PHE cc_start: 0.7937 (t80) cc_final: 0.7632 (t80) REVERT: A 826 TYR cc_start: 0.7444 (OUTLIER) cc_final: 0.6495 (m-80) REVERT: A 834 MET cc_start: 0.7873 (ppp) cc_final: 0.7386 (ppp) outliers start: 26 outliers final: 20 residues processed: 66 average time/residue: 0.1671 time to fit residues: 15.4509 Evaluate side-chains 65 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 42 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ARG Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 826 TYR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 879 HIS Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 914 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 42 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 34 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.7444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6069 Z= 0.240 Angle : 0.628 8.270 8279 Z= 0.321 Chirality : 0.042 0.142 917 Planarity : 0.005 0.044 1043 Dihedral : 4.614 16.240 802 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.69 % Favored : 95.17 % Rotamer: Outliers : 4.29 % Allowed : 17.81 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.14 (0.32), residues: 725 helix: 0.80 (0.26), residues: 387 sheet: -0.36 (0.68), residues: 62 loop : -0.70 (0.40), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 764 HIS 0.003 0.001 HIS A 642 PHE 0.023 0.002 PHE A 614 TYR 0.015 0.002 TYR A 393 ARG 0.006 0.001 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 47 time to evaluate : 0.727 Fit side-chains REVERT: A 109 ARG cc_start: 0.4214 (OUTLIER) cc_final: 0.3837 (ptt180) REVERT: A 232 MET cc_start: 0.7549 (mmm) cc_final: 0.7064 (mmm) REVERT: A 308 LYS cc_start: 0.9155 (pptt) cc_final: 0.8785 (pttp) REVERT: A 411 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8391 (ptm) REVERT: A 493 MET cc_start: 0.4544 (ppp) cc_final: 0.4241 (ppp) REVERT: A 666 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7524 (tt) REVERT: A 773 PHE cc_start: 0.8011 (t80) cc_final: 0.7571 (t80) REVERT: A 826 TYR cc_start: 0.7584 (OUTLIER) cc_final: 0.6519 (m-80) REVERT: A 834 MET cc_start: 0.7884 (ppp) cc_final: 0.7425 (ppp) outliers start: 27 outliers final: 22 residues processed: 67 average time/residue: 0.1671 time to fit residues: 15.5836 Evaluate side-chains 71 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 45 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ARG Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 826 TYR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 879 HIS Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 914 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.7512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6069 Z= 0.200 Angle : 0.621 9.924 8279 Z= 0.314 Chirality : 0.042 0.137 917 Planarity : 0.005 0.045 1043 Dihedral : 4.534 14.576 802 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.00 % Favored : 95.86 % Rotamer: Outliers : 3.66 % Allowed : 19.40 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.26 (0.32), residues: 725 helix: 0.89 (0.27), residues: 383 sheet: -0.48 (0.67), residues: 62 loop : -0.55 (0.40), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 764 HIS 0.003 0.001 HIS A 698 PHE 0.020 0.001 PHE A 614 TYR 0.012 0.002 TYR A 293 ARG 0.007 0.000 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 49 time to evaluate : 0.747 Fit side-chains revert: symmetry clash REVERT: A 109 ARG cc_start: 0.4286 (OUTLIER) cc_final: 0.3915 (ptt180) REVERT: A 232 MET cc_start: 0.7463 (mmm) cc_final: 0.7004 (mmm) REVERT: A 411 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8387 (ptm) REVERT: A 493 MET cc_start: 0.4469 (ppp) cc_final: 0.4200 (ppp) REVERT: A 666 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7501 (tp) REVERT: A 773 PHE cc_start: 0.7966 (t80) cc_final: 0.7583 (t80) REVERT: A 834 MET cc_start: 0.7842 (ppp) cc_final: 0.7527 (ppp) REVERT: A 864 LEU cc_start: 0.2104 (OUTLIER) cc_final: 0.1428 (tt) outliers start: 23 outliers final: 18 residues processed: 65 average time/residue: 0.1689 time to fit residues: 15.3017 Evaluate side-chains 66 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 44 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ARG Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 879 HIS Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 914 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 32 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 6 optimal weight: 0.0770 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.7683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6069 Z= 0.194 Angle : 0.614 7.947 8279 Z= 0.308 Chirality : 0.042 0.136 917 Planarity : 0.005 0.046 1043 Dihedral : 4.422 13.972 802 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.69 % Favored : 95.17 % Rotamer: Outliers : 3.50 % Allowed : 19.87 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.32), residues: 725 helix: 1.02 (0.27), residues: 378 sheet: -0.48 (0.67), residues: 62 loop : -0.45 (0.39), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 764 HIS 0.003 0.001 HIS A 698 PHE 0.020 0.001 PHE A 658 TYR 0.011 0.001 TYR A 393 ARG 0.010 0.001 ARG A 115 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 45 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: A 109 ARG cc_start: 0.4374 (OUTLIER) cc_final: 0.4080 (ptt180) REVERT: A 135 MET cc_start: 0.5893 (tmm) cc_final: 0.4224 (ttm) REVERT: A 232 MET cc_start: 0.7543 (mmm) cc_final: 0.7002 (mmm) REVERT: A 411 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8386 (ptm) REVERT: A 493 MET cc_start: 0.4467 (ppp) cc_final: 0.4174 (ppp) REVERT: A 623 GLU cc_start: 0.7710 (pp20) cc_final: 0.7435 (pp20) REVERT: A 666 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7612 (tp) REVERT: A 773 PHE cc_start: 0.7916 (t80) cc_final: 0.7556 (t80) REVERT: A 834 MET cc_start: 0.7815 (ppp) cc_final: 0.7539 (ppp) REVERT: A 864 LEU cc_start: 0.2296 (OUTLIER) cc_final: 0.1681 (tt) outliers start: 22 outliers final: 18 residues processed: 60 average time/residue: 0.1612 time to fit residues: 13.6795 Evaluate side-chains 66 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 44 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ARG Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 879 HIS Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 914 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 53 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 chunk 24 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.075522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.068301 restraints weight = 39995.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.069462 restraints weight = 27283.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.070290 restraints weight = 20319.513| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.8108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6069 Z= 0.233 Angle : 0.637 8.742 8279 Z= 0.324 Chirality : 0.042 0.136 917 Planarity : 0.005 0.046 1043 Dihedral : 4.585 15.649 802 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.41 % Favored : 95.45 % Rotamer: Outliers : 3.97 % Allowed : 19.55 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.29 (0.32), residues: 725 helix: 0.94 (0.27), residues: 379 sheet: -0.56 (0.67), residues: 62 loop : -0.53 (0.39), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 779 HIS 0.003 0.001 HIS A 698 PHE 0.020 0.002 PHE A 614 TYR 0.013 0.002 TYR A 274 ARG 0.007 0.001 ARG A 366 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1313.85 seconds wall clock time: 24 minutes 54.26 seconds (1494.26 seconds total)