Starting phenix.real_space_refine on Fri Mar 15 10:38:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2p_27145/03_2024/8d2p_27145_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2p_27145/03_2024/8d2p_27145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2p_27145/03_2024/8d2p_27145.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2p_27145/03_2024/8d2p_27145.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2p_27145/03_2024/8d2p_27145_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2p_27145/03_2024/8d2p_27145_updated.pdb" } resolution = 2.78 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= 0.004 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: 6 Type Number sf(0) Gaussians P 128 5.49 5 Mg 10 5.21 5 S 20 5.16 5 C 6655 2.51 5 N 2109 2.21 5 O 2514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 169": "OE1" <-> "OE2" Residue "A TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 805": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11436 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 8720 Classifications: {'peptide': 1105} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 59, 'TRANS': 1041} Chain breaks: 3 Chain: "B" Number of atoms: 2189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 2189 Unusual residues: {'GTP': 1} Classifications: {'RNA': 101, 'undetermined': 1} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 46, 'rna3p_pyr': 42} Link IDs: {'rna2p': 13, 'rna3p': 87, None: 1} Not linked: pdbres="GTP B 1 " pdbres=" G B 2 " Chain breaks: 1 Chain: "T" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 481 Classifications: {'DNA': 24} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 23} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' MG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "T" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 7.14, per 1000 atoms: 0.62 Number of scatterers: 11436 At special positions: 0 Unit cell: (94.05, 106.425, 130.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 20 16.00 P 128 15.00 Mg 10 11.99 O 2514 8.00 N 2109 7.00 C 6655 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.90 Conformation dependent library (CDL) restraints added in 1.7 seconds 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2074 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 7 sheets defined 43.4% alpha, 8.1% beta 41 base pairs and 80 stacking pairs defined. Time for finding SS restraints: 6.39 Creating SS restraints... Processing helix chain 'A' and resid 60 through 91 Processing helix chain 'A' and resid 105 through 115 Processing helix chain 'A' and resid 121 through 137 Processing helix chain 'A' and resid 148 through 153 Processing helix chain 'A' and resid 159 through 172 Processing helix chain 'A' and resid 181 through 191 Processing helix chain 'A' and resid 222 through 236 Processing helix chain 'A' and resid 240 through 250 Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'A' and resid 280 through 292 Processing helix chain 'A' and resid 307 through 318 Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 340 through 342 No H-bonds generated for 'chain 'A' and resid 340 through 342' Processing helix chain 'A' and resid 355 through 358 No H-bonds generated for 'chain 'A' and resid 355 through 358' Processing helix chain 'A' and resid 365 through 376 Processing helix chain 'A' and resid 382 through 390 Processing helix chain 'A' and resid 393 through 407 removed outlier: 5.446A pdb=" N SER A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 429 Processing helix chain 'A' and resid 442 through 455 Processing helix chain 'A' and resid 459 through 467 Processing helix chain 'A' and resid 487 through 507 Processing helix chain 'A' and resid 525 through 551 Processing helix chain 'A' and resid 559 through 570 Processing helix chain 'A' and resid 595 through 597 No H-bonds generated for 'chain 'A' and resid 595 through 597' Processing helix chain 'A' and resid 612 through 617 Processing helix chain 'A' and resid 622 through 628 Processing helix chain 'A' and resid 634 through 642 Processing helix chain 'A' and resid 654 through 668 Processing helix chain 'A' and resid 682 through 702 Processing helix chain 'A' and resid 712 through 720 removed outlier: 4.094A pdb=" N ALA A 716 " --> pdb=" O GLY A 712 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU A 717 " --> pdb=" O GLY A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 729 No H-bonds generated for 'chain 'A' and resid 726 through 729' Processing helix chain 'A' and resid 743 through 745 No H-bonds generated for 'chain 'A' and resid 743 through 745' Processing helix chain 'A' and resid 747 through 759 removed outlier: 3.607A pdb=" N HIS A 750 " --> pdb=" O ARG A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 776 Processing helix chain 'A' and resid 798 through 806 Processing helix chain 'A' and resid 808 through 819 removed outlier: 3.983A pdb=" N GLY A 811 " --> pdb=" O SER A 808 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA A 819 " --> pdb=" O SER A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 861 Processing helix chain 'A' and resid 865 through 875 Processing helix chain 'A' and resid 957 through 962 Processing helix chain 'A' and resid 982 through 985 No H-bonds generated for 'chain 'A' and resid 982 through 985' Processing helix chain 'A' and resid 989 through 997 Processing helix chain 'A' and resid 1026 through 1032 removed outlier: 4.172A pdb=" N TYR A1032 " --> pdb=" O MET A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1059 through 1069 removed outlier: 4.646A pdb=" N SER A1069 " --> pdb=" O ARG A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1085 Processing helix chain 'A' and resid 1094 through 1099 removed outlier: 4.362A pdb=" N CYS A1099 " --> pdb=" O ALA A1095 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 706 through 710 removed outlier: 3.881A pdb=" N SER A 512 " --> pdb=" O TRP A 13 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N VAL A 19 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N SER A 30 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ILE A 39 " --> pdb=" O SER A 30 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA A 824 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ILE A 46 " --> pdb=" O ALA A 824 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA A 826 " --> pdb=" O ILE A 46 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 295 through 298 Processing sheet with id= C, first strand: chain 'A' and resid 588 through 591 Processing sheet with id= D, first strand: chain 'A' and resid 846 through 849 Processing sheet with id= E, first strand: chain 'A' and resid 921 through 924 Processing sheet with id= F, first strand: chain 'A' and resid 1104 through 1106 removed outlier: 3.843A pdb=" N GLU A1011 " --> pdb=" O ILE A1106 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN A1050 " --> pdb=" O THR A1041 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 948 through 956 removed outlier: 3.738A pdb=" N GLY A1004 " --> pdb=" O VAL A 939 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG A 941 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N GLN A1002 " --> pdb=" O ARG A 941 " (cutoff:3.500A) 352 hydrogen bonds defined for protein. 993 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 106 hydrogen bonds 200 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 80 stacking parallelities Total time for adding SS restraints: 5.84 Time building geometry restraints manager: 6.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2585 1.33 - 1.45: 3122 1.45 - 1.57: 5902 1.57 - 1.69: 252 1.69 - 1.81: 28 Bond restraints: 11889 Sorted by residual: bond pdb=" C1' DC T 21 " pdb=" N1 DC T 21 " ideal model delta sigma weight residual 1.490 1.558 -0.068 3.00e-02 1.11e+03 5.12e+00 bond pdb=" C3' DC T 36 " pdb=" O3' DC T 36 " ideal model delta sigma weight residual 1.422 1.486 -0.064 3.00e-02 1.11e+03 4.58e+00 bond pdb=" C THR A 761 " pdb=" N PRO A 762 " ideal model delta sigma weight residual 1.335 1.357 -0.022 1.36e-02 5.41e+03 2.52e+00 bond pdb=" CG LEU A 872 " pdb=" CD1 LEU A 872 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.39e+00 bond pdb=" N1 DC T 21 " pdb=" C2 DC T 21 " ideal model delta sigma weight residual 1.399 1.428 -0.029 2.00e-02 2.50e+03 2.17e+00 ... (remaining 11884 not shown) Histogram of bond angle deviations from ideal: 99.36 - 106.32: 978 106.32 - 113.27: 6471 113.27 - 120.22: 4494 120.22 - 127.17: 4389 127.17 - 134.12: 392 Bond angle restraints: 16724 Sorted by residual: angle pdb=" CG ARG A 323 " pdb=" CD ARG A 323 " pdb=" NE ARG A 323 " ideal model delta sigma weight residual 112.00 122.57 -10.57 2.20e+00 2.07e-01 2.31e+01 angle pdb=" C3' U B 62 " pdb=" O3' U B 62 " pdb=" P C B 63 " ideal model delta sigma weight residual 120.20 125.97 -5.77 1.50e+00 4.44e-01 1.48e+01 angle pdb=" C4' U B 62 " pdb=" C3' U B 62 " pdb=" O3' U B 62 " ideal model delta sigma weight residual 113.00 118.66 -5.66 1.50e+00 4.44e-01 1.42e+01 angle pdb=" C LEU A 722 " pdb=" N ASP A 723 " pdb=" CA ASP A 723 " ideal model delta sigma weight residual 121.54 128.55 -7.01 1.91e+00 2.74e-01 1.35e+01 angle pdb=" C LEU A 416 " pdb=" N LEU A 417 " pdb=" CA LEU A 417 " ideal model delta sigma weight residual 121.54 128.53 -6.99 1.91e+00 2.74e-01 1.34e+01 ... (remaining 16719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.86: 6777 29.86 - 59.71: 374 59.71 - 89.57: 120 89.57 - 119.42: 3 119.42 - 149.28: 3 Dihedral angle restraints: 7277 sinusoidal: 4081 harmonic: 3196 Sorted by residual: dihedral pdb=" C5' GTP B 1 " pdb=" O5' GTP B 1 " pdb=" PA GTP B 1 " pdb=" O3A GTP B 1 " ideal model delta sinusoidal sigma weight residual 69.27 162.88 -93.61 1 2.00e+01 2.50e-03 2.55e+01 dihedral pdb=" C8 GTP B 1 " pdb=" C1' GTP B 1 " pdb=" N9 GTP B 1 " pdb=" O4' GTP B 1 " ideal model delta sinusoidal sigma weight residual 104.59 13.60 90.99 1 2.00e+01 2.50e-03 2.44e+01 dihedral pdb=" CA ILE A 592 " pdb=" C ILE A 592 " pdb=" N VAL A 593 " pdb=" CA VAL A 593 " ideal model delta harmonic sigma weight residual 180.00 157.55 22.45 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 7274 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1587 0.058 - 0.116: 293 0.116 - 0.175: 39 0.175 - 0.233: 8 0.233 - 0.291: 3 Chirality restraints: 1930 Sorted by residual: chirality pdb=" CG LEU A 84 " pdb=" CB LEU A 84 " pdb=" CD1 LEU A 84 " pdb=" CD2 LEU A 84 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CG LEU A1075 " pdb=" CB LEU A1075 " pdb=" CD1 LEU A1075 " pdb=" CD2 LEU A1075 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" C1' G B 30 " pdb=" O4' G B 30 " pdb=" C2' G B 30 " pdb=" N9 G B 30 " both_signs ideal model delta sigma weight residual False 2.46 2.21 0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 1927 not shown) Planarity restraints: 1714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 363 " 0.024 2.00e-02 2.50e+03 3.23e-02 1.82e+01 pdb=" CG PHE A 363 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 PHE A 363 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 PHE A 363 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 363 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE A 363 " 0.018 2.00e-02 2.50e+03 pdb=" CZ PHE A 363 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 800 " 0.009 2.00e-02 2.50e+03 1.96e-02 7.68e+00 pdb=" CG TYR A 800 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR A 800 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR A 800 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR A 800 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A 800 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 800 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 800 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 187 " -0.001 2.00e-02 2.50e+03 1.95e-02 7.60e+00 pdb=" CG TYR A 187 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR A 187 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR A 187 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR A 187 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 187 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 187 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 187 " -0.014 2.00e-02 2.50e+03 ... (remaining 1711 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 133 2.59 - 3.17: 8667 3.17 - 3.75: 20882 3.75 - 4.32: 28053 4.32 - 4.90: 42430 Nonbonded interactions: 100165 Sorted by model distance: nonbonded pdb="MG MG A1201 " pdb=" O HOH A1304 " model vdw 2.018 2.170 nonbonded pdb=" OD1 ASP A 590 " pdb="MG MG A1201 " model vdw 2.021 2.170 nonbonded pdb=" OP2 DC T 14 " pdb="MG MG A1201 " model vdw 2.036 2.170 nonbonded pdb=" OD1 ASN A 614 " pdb="MG MG A1201 " model vdw 2.045 2.170 nonbonded pdb="MG MG B 202 " pdb=" O HOH B 312 " model vdw 2.085 2.170 ... (remaining 100160 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.080 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: 6.850 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 41.570 Find NCS groups from input model: 0.260 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:14.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 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 : 0.005 0.068 11889 Z= 0.295 Angle : 0.806 10.570 16724 Z= 0.423 Chirality : 0.047 0.291 1930 Planarity : 0.008 0.108 1714 Dihedral : 18.654 149.279 5203 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: -1.23 (0.22), residues: 1097 helix: -0.68 (0.19), residues: 528 sheet: -0.70 (0.48), residues: 89 loop : -0.81 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 161 HIS 0.005 0.002 HIS A1037 PHE 0.069 0.003 PHE A 363 TYR 0.047 0.004 TYR A 800 ARG 0.014 0.001 ARG A 544 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.033 Fit side-chains REVERT: A 155 PRO cc_start: 0.7570 (Cg_endo) cc_final: 0.7300 (Cg_exo) REVERT: A 572 ASP cc_start: 0.7804 (t0) cc_final: 0.7578 (t0) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 1.6911 time to fit residues: 204.6291 Evaluate side-chains 84 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 51 optimal weight: 0.1980 chunk 31 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 71 optimal weight: 0.0070 chunk 110 optimal weight: 7.9990 overall best weight: 1.8404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11889 Z= 0.216 Angle : 0.536 5.857 16724 Z= 0.279 Chirality : 0.038 0.251 1930 Planarity : 0.005 0.066 1714 Dihedral : 19.378 151.851 3114 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.51 % Allowed : 6.99 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: -0.18 (0.24), residues: 1097 helix: 0.46 (0.22), residues: 535 sheet: -0.79 (0.48), residues: 89 loop : -0.52 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 161 HIS 0.004 0.001 HIS A1100 PHE 0.020 0.002 PHE A 282 TYR 0.015 0.002 TYR A 800 ARG 0.007 0.000 ARG A 659 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 96 time to evaluate : 1.002 Fit side-chains REVERT: A 261 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6950 (pm20) REVERT: A 470 ASP cc_start: 0.7346 (OUTLIER) cc_final: 0.7087 (p0) REVERT: A 516 GLU cc_start: 0.7360 (tt0) cc_final: 0.6499 (tm-30) REVERT: A 572 ASP cc_start: 0.7783 (t0) cc_final: 0.7337 (t0) REVERT: A 597 ASP cc_start: 0.7876 (m-30) cc_final: 0.7638 (m-30) outliers start: 23 outliers final: 7 residues processed: 106 average time/residue: 1.8425 time to fit residues: 207.4671 Evaluate side-chains 105 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain A residue 1064 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 37 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 109 optimal weight: 6.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11889 Z= 0.303 Angle : 0.586 6.643 16724 Z= 0.304 Chirality : 0.040 0.242 1930 Planarity : 0.006 0.066 1714 Dihedral : 19.410 150.609 3114 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.40 % Allowed : 8.74 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: -0.01 (0.24), residues: 1097 helix: 0.56 (0.22), residues: 536 sheet: -0.75 (0.48), residues: 91 loop : -0.38 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 387 HIS 0.008 0.001 HIS A1100 PHE 0.025 0.003 PHE A 363 TYR 0.013 0.002 TYR A 651 ARG 0.005 0.001 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 94 time to evaluate : 1.172 Fit side-chains REVERT: A 261 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7045 (pm20) REVERT: A 470 ASP cc_start: 0.7359 (OUTLIER) cc_final: 0.7150 (p0) REVERT: A 516 GLU cc_start: 0.7367 (tt0) cc_final: 0.6475 (tm-30) REVERT: A 572 ASP cc_start: 0.7900 (t0) cc_final: 0.7416 (t0) REVERT: A 753 ASP cc_start: 0.6929 (m-30) cc_final: 0.6391 (m-30) REVERT: A 801 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.6754 (mtp180) REVERT: A 1118 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.7145 (mtm-85) outliers start: 22 outliers final: 9 residues processed: 106 average time/residue: 1.7539 time to fit residues: 197.6936 Evaluate side-chains 100 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 801 ARG Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain A residue 1118 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 339 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 11889 Z= 0.524 Angle : 0.739 6.762 16724 Z= 0.382 Chirality : 0.048 0.261 1930 Planarity : 0.007 0.067 1714 Dihedral : 19.601 150.791 3114 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.95 % Allowed : 10.60 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: -0.44 (0.24), residues: 1097 helix: 0.14 (0.22), residues: 537 sheet: -0.86 (0.49), residues: 91 loop : -0.51 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 387 HIS 0.010 0.002 HIS A1100 PHE 0.026 0.004 PHE A 282 TYR 0.016 0.003 TYR A 800 ARG 0.007 0.001 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 92 time to evaluate : 1.138 Fit side-chains REVERT: A 121 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6258 (tm-30) REVERT: A 261 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7096 (pm20) REVERT: A 398 ASP cc_start: 0.6698 (OUTLIER) cc_final: 0.6002 (m-30) REVERT: A 470 ASP cc_start: 0.7346 (OUTLIER) cc_final: 0.7128 (p0) REVERT: A 572 ASP cc_start: 0.7989 (t0) cc_final: 0.7492 (t0) REVERT: A 753 ASP cc_start: 0.6631 (m-30) cc_final: 0.6132 (m-30) REVERT: A 1118 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7099 (mtm-85) outliers start: 27 outliers final: 14 residues processed: 107 average time/residue: 1.7187 time to fit residues: 195.2352 Evaluate side-chains 106 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 87 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 807 CYS Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1099 CYS Chi-restraints excluded: chain A residue 1118 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 87 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 100 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN A 472 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11889 Z= 0.225 Angle : 0.544 7.337 16724 Z= 0.284 Chirality : 0.038 0.252 1930 Planarity : 0.005 0.068 1714 Dihedral : 19.386 151.362 3114 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.40 % Allowed : 12.13 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 0.09 (0.25), residues: 1097 helix: 0.67 (0.22), residues: 535 sheet: -0.97 (0.47), residues: 91 loop : -0.29 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 387 HIS 0.003 0.001 HIS A 47 PHE 0.016 0.002 PHE A 282 TYR 0.013 0.002 TYR A 651 ARG 0.006 0.000 ARG A1088 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 91 time to evaluate : 1.083 Fit side-chains REVERT: A 121 GLU cc_start: 0.6965 (OUTLIER) cc_final: 0.6372 (tm-30) REVERT: A 261 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7040 (pm20) REVERT: A 470 ASP cc_start: 0.7313 (OUTLIER) cc_final: 0.7076 (p0) REVERT: A 572 ASP cc_start: 0.7872 (t0) cc_final: 0.7366 (t0) REVERT: A 753 ASP cc_start: 0.6712 (m-30) cc_final: 0.6166 (m-30) REVERT: A 1118 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.7187 (mtm-85) outliers start: 22 outliers final: 8 residues processed: 104 average time/residue: 1.7156 time to fit residues: 189.5330 Evaluate side-chains 98 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 86 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain A residue 1099 CYS Chi-restraints excluded: chain A residue 1118 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 chunk 54 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 113 optimal weight: 8.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN ** A1100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11889 Z= 0.245 Angle : 0.547 6.498 16724 Z= 0.285 Chirality : 0.038 0.246 1930 Planarity : 0.005 0.068 1714 Dihedral : 19.305 150.753 3114 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.51 % Allowed : 12.57 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 0.27 (0.25), residues: 1097 helix: 0.80 (0.22), residues: 535 sheet: -0.95 (0.47), residues: 91 loop : -0.17 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 387 HIS 0.003 0.001 HIS A1120 PHE 0.019 0.002 PHE A 282 TYR 0.014 0.002 TYR A 651 ARG 0.005 0.000 ARG A1088 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 91 time to evaluate : 1.072 Fit side-chains REVERT: A 121 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6299 (tm-30) REVERT: A 261 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7057 (pm20) REVERT: A 398 ASP cc_start: 0.6641 (OUTLIER) cc_final: 0.5932 (m-30) REVERT: A 470 ASP cc_start: 0.7286 (OUTLIER) cc_final: 0.7064 (p0) REVERT: A 572 ASP cc_start: 0.7889 (t0) cc_final: 0.7407 (t0) REVERT: A 753 ASP cc_start: 0.6698 (m-30) cc_final: 0.6164 (m-30) REVERT: A 1118 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.7189 (mtm-85) outliers start: 23 outliers final: 7 residues processed: 104 average time/residue: 1.8400 time to fit residues: 203.0907 Evaluate side-chains 96 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain A residue 1118 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 66 optimal weight: 0.1980 chunk 99 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11889 Z= 0.232 Angle : 0.535 6.251 16724 Z= 0.278 Chirality : 0.038 0.244 1930 Planarity : 0.005 0.068 1714 Dihedral : 19.262 150.738 3114 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.86 % Allowed : 13.66 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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 (0.25), residues: 1097 helix: 0.81 (0.22), residues: 541 sheet: -0.96 (0.47), residues: 91 loop : -0.16 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 387 HIS 0.003 0.001 HIS A 47 PHE 0.018 0.002 PHE A 282 TYR 0.014 0.002 TYR A 651 ARG 0.006 0.000 ARG A1088 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 1.058 Fit side-chains revert: symmetry clash REVERT: A 38 GLU cc_start: 0.6686 (OUTLIER) cc_final: 0.6134 (tt0) REVERT: A 121 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.6059 (tm-30) REVERT: A 261 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7047 (pm20) REVERT: A 398 ASP cc_start: 0.6634 (OUTLIER) cc_final: 0.5925 (m-30) REVERT: A 470 ASP cc_start: 0.7267 (OUTLIER) cc_final: 0.7056 (p0) REVERT: A 572 ASP cc_start: 0.7891 (t0) cc_final: 0.7403 (t0) REVERT: A 753 ASP cc_start: 0.6684 (m-30) cc_final: 0.6176 (m-30) REVERT: A 1118 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.7191 (mtm-85) outliers start: 17 outliers final: 8 residues processed: 98 average time/residue: 1.8090 time to fit residues: 188.0797 Evaluate side-chains 100 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain A residue 1118 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 23 optimal weight: 0.0060 chunk 22 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 overall best weight: 2.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11889 Z= 0.273 Angle : 0.560 6.232 16724 Z= 0.291 Chirality : 0.039 0.242 1930 Planarity : 0.005 0.068 1714 Dihedral : 19.287 150.731 3114 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.40 % Allowed : 13.44 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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 (0.25), residues: 1097 helix: 0.71 (0.22), residues: 541 sheet: -0.97 (0.47), residues: 91 loop : -0.16 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 387 HIS 0.004 0.001 HIS A 47 PHE 0.020 0.002 PHE A 282 TYR 0.015 0.002 TYR A 800 ARG 0.005 0.001 ARG A1088 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 88 time to evaluate : 0.990 Fit side-chains REVERT: A 38 GLU cc_start: 0.6725 (OUTLIER) cc_final: 0.6151 (tt0) REVERT: A 121 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.5757 (tm-30) REVERT: A 261 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7062 (pm20) REVERT: A 398 ASP cc_start: 0.6655 (OUTLIER) cc_final: 0.5945 (m-30) REVERT: A 470 ASP cc_start: 0.7256 (OUTLIER) cc_final: 0.7045 (p0) REVERT: A 572 ASP cc_start: 0.7883 (t0) cc_final: 0.7398 (t0) REVERT: A 753 ASP cc_start: 0.6703 (m-30) cc_final: 0.6200 (m-30) REVERT: A 880 ARG cc_start: 0.6730 (ptt180) cc_final: 0.6190 (ptt90) REVERT: A 1118 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7192 (mtm-85) outliers start: 22 outliers final: 12 residues processed: 99 average time/residue: 1.9347 time to fit residues: 202.7460 Evaluate side-chains 103 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 85 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1118 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 109 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11889 Z= 0.242 Angle : 0.541 6.160 16724 Z= 0.282 Chirality : 0.038 0.243 1930 Planarity : 0.005 0.068 1714 Dihedral : 19.265 150.795 3114 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.51 % Allowed : 13.44 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.25), residues: 1097 helix: 0.78 (0.22), residues: 541 sheet: -0.99 (0.47), residues: 91 loop : -0.12 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 387 HIS 0.003 0.001 HIS A 47 PHE 0.018 0.002 PHE A 282 TYR 0.014 0.002 TYR A 800 ARG 0.006 0.000 ARG A1088 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 90 time to evaluate : 1.045 Fit side-chains REVERT: A 38 GLU cc_start: 0.6689 (OUTLIER) cc_final: 0.6130 (tt0) REVERT: A 261 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7056 (pm20) REVERT: A 398 ASP cc_start: 0.6642 (OUTLIER) cc_final: 0.5934 (m-30) REVERT: A 470 ASP cc_start: 0.7239 (OUTLIER) cc_final: 0.7036 (p0) REVERT: A 572 ASP cc_start: 0.7887 (t0) cc_final: 0.7394 (t0) REVERT: A 645 LYS cc_start: 0.7287 (mmmt) cc_final: 0.6632 (mmmt) REVERT: A 647 SER cc_start: 0.7007 (OUTLIER) cc_final: 0.6806 (m) REVERT: A 753 ASP cc_start: 0.6710 (m-30) cc_final: 0.6207 (m-30) REVERT: A 801 ARG cc_start: 0.7188 (OUTLIER) cc_final: 0.6731 (mtp180) REVERT: A 880 ARG cc_start: 0.6748 (ptt180) cc_final: 0.6185 (ptt90) REVERT: A 1118 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7181 (mtm-85) outliers start: 23 outliers final: 12 residues processed: 102 average time/residue: 1.7653 time to fit residues: 191.0702 Evaluate side-chains 104 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 85 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 801 ARG Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1118 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11889 Z= 0.244 Angle : 0.541 6.064 16724 Z= 0.282 Chirality : 0.038 0.242 1930 Planarity : 0.005 0.068 1714 Dihedral : 19.257 150.719 3114 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.19 % Allowed : 13.66 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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 (0.25), residues: 1097 helix: 0.78 (0.22), residues: 541 sheet: -1.00 (0.47), residues: 91 loop : -0.11 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 387 HIS 0.003 0.001 HIS A1120 PHE 0.018 0.002 PHE A 282 TYR 0.015 0.002 TYR A 800 ARG 0.006 0.000 ARG A1088 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 88 time to evaluate : 1.091 Fit side-chains REVERT: A 38 GLU cc_start: 0.6687 (OUTLIER) cc_final: 0.6133 (tt0) REVERT: A 261 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7054 (pm20) REVERT: A 398 ASP cc_start: 0.6642 (OUTLIER) cc_final: 0.5933 (m-30) REVERT: A 572 ASP cc_start: 0.7885 (t0) cc_final: 0.7389 (t0) REVERT: A 645 LYS cc_start: 0.7278 (mmmt) cc_final: 0.6600 (mmmt) REVERT: A 753 ASP cc_start: 0.6712 (m-30) cc_final: 0.6208 (m-30) REVERT: A 801 ARG cc_start: 0.7211 (OUTLIER) cc_final: 0.6651 (mtp180) REVERT: A 880 ARG cc_start: 0.6748 (ptt180) cc_final: 0.6187 (ptt90) REVERT: A 1118 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7166 (mtm-85) outliers start: 20 outliers final: 10 residues processed: 97 average time/residue: 1.8364 time to fit residues: 188.9929 Evaluate side-chains 100 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 801 ARG Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1118 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN ** A1100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.163424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.127699 restraints weight = 11827.506| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.23 r_work: 0.3134 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 11889 Z= 0.376 Angle : 0.628 6.417 16724 Z= 0.326 Chirality : 0.042 0.244 1930 Planarity : 0.006 0.069 1714 Dihedral : 19.382 150.458 3114 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.19 % Allowed : 13.66 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: -0.01 (0.25), residues: 1097 helix: 0.50 (0.22), residues: 541 sheet: -1.02 (0.48), residues: 91 loop : -0.23 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 387 HIS 0.005 0.001 HIS A1120 PHE 0.024 0.003 PHE A 282 TYR 0.019 0.003 TYR A 800 ARG 0.005 0.001 ARG A1107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3874.12 seconds wall clock time: 69 minutes 12.77 seconds (4152.77 seconds total)