Starting phenix.real_space_refine on Mon Mar 11 06:37:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dc2_27320/03_2024/8dc2_27320.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dc2_27320/03_2024/8dc2_27320.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dc2_27320/03_2024/8dc2_27320.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dc2_27320/03_2024/8dc2_27320.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dc2_27320/03_2024/8dc2_27320.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dc2_27320/03_2024/8dc2_27320.pdb" } resolution = 2.99 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= 0.179 sd= 1.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 132 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 86 5.49 5 S 32 5.16 5 C 4326 2.51 5 N 1221 2.21 5 O 1631 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 8": "OE1" <-> "OE2" Residue "A TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 47": "OD1" <-> "OD2" Residue "A PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 397": "OD1" <-> "OD2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 412": "OD1" <-> "OD2" Residue "A ASP 618": "OD1" <-> "OD2" Residue "A PHE 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 709": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7296 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5483 Classifications: {'peptide': 673} Link IDs: {'PTRANS': 10, 'TRANS': 662} Chain breaks: 2 Chain: "B" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1069 Classifications: {'RNA': 51} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 5, 'rna3p_pur': 18, 'rna3p_pyr': 25} Link IDs: {'rna2p': 8, 'rna3p': 42} Chain: "C" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 542 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "D" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 202 Classifications: {'DNA': 10} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 9} Time building chain proxies: 4.89, per 1000 atoms: 0.67 Number of scatterers: 7296 At special positions: 0 Unit cell: (80.28, 92.545, 110.385, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 86 15.00 O 1631 8.00 N 1221 7.00 C 4326 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: 3.82 Conformation dependent library (CDL) restraints added in 1.0 seconds 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1286 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 3 sheets defined 57.1% alpha, 10.5% beta 33 base pairs and 58 stacking pairs defined. Time for finding SS restraints: 2.67 Creating SS restraints... Processing helix chain 'A' and resid 27 through 52 Processing helix chain 'A' and resid 56 through 64 Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 71 through 79 removed outlier: 3.607A pdb=" N THR A 76 " --> pdb=" O GLY A 72 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE A 78 " --> pdb=" O ALA A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 96 through 112 Processing helix chain 'A' and resid 124 through 131 Processing helix chain 'A' and resid 132 through 146 Processing helix chain 'A' and resid 162 through 177 removed outlier: 4.302A pdb=" N ASN A 177 " --> pdb=" O GLU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 195 Processing helix chain 'A' and resid 199 through 215 removed outlier: 4.049A pdb=" N ARG A 205 " --> pdb=" O ASN A 201 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER A 215 " --> pdb=" O GLU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 234 removed outlier: 3.944A pdb=" N LYS A 234 " --> pdb=" O ASP A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 298 Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.707A pdb=" N LYS A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 386 Processing helix chain 'A' and resid 395 through 408 Processing helix chain 'A' and resid 413 through 435 removed outlier: 3.530A pdb=" N LYS A 418 " --> pdb=" O SER A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 472 removed outlier: 3.882A pdb=" N ARG A 440 " --> pdb=" O ASP A 436 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS A 454 " --> pdb=" O ARG A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 482 Processing helix chain 'A' and resid 483 through 486 Processing helix chain 'A' and resid 487 through 523 removed outlier: 3.501A pdb=" N GLY A 523 " --> pdb=" O PHE A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 611 removed outlier: 3.639A pdb=" N ILE A 611 " --> pdb=" O MET A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 627 removed outlier: 4.280A pdb=" N ASN A 626 " --> pdb=" O THR A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 669 removed outlier: 3.786A pdb=" N VAL A 668 " --> pdb=" O LYS A 665 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG A 669 " --> pdb=" O HIS A 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 665 through 669' Processing helix chain 'A' and resid 680 through 695 removed outlier: 3.842A pdb=" N MET A 693 " --> pdb=" O ILE A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 702 Processing helix chain 'A' and resid 724 through 735 removed outlier: 3.567A pdb=" N LYS A 733 " --> pdb=" O VAL A 729 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS A 734 " --> pdb=" O ALA A 730 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLU A 735 " --> pdb=" O LYS A 731 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 246 through 250 removed outlier: 5.878A pdb=" N ASN A 317 " --> pdb=" O GLY A 300 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N SER A 302 " --> pdb=" O ASP A 315 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ASP A 315 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL A 304 " --> pdb=" O TYR A 313 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N TYR A 313 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS A 306 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLU A 311 " --> pdb=" O LYS A 306 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE A 312 " --> pdb=" O ILE A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 286 through 287 Processing sheet with id=AA3, first strand: chain 'A' and resid 388 through 391 removed outlier: 5.267A pdb=" N ILE A 348 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N PHE A 391 " --> pdb=" O THR A 346 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N THR A 346 " --> pdb=" O PHE A 391 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLY A 334 " --> pdb=" O ASN A 347 " (cutoff:3.500A) removed outlier: 9.447A pdb=" N LEU A 349 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 13.098A pdb=" N VAL A 332 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL A 333 " --> pdb=" O SER A 528 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N GLU A 530 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 9.108A pdb=" N ILE A 335 " --> pdb=" O GLU A 530 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL A 527 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL A 634 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU A 529 " --> pdb=" O VAL A 634 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N TYR A 718 " --> pdb=" O VAL A 631 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 720 " --> pdb=" O LEU A 633 " (cutoff:3.500A) 293 hydrogen bonds defined for protein. 834 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 83 hydrogen bonds 166 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 58 stacking parallelities Total time for adding SS restraints: 3.15 Time building geometry restraints manager: 4.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1697 1.33 - 1.45: 2004 1.45 - 1.57: 3690 1.57 - 1.69: 170 1.69 - 1.81: 56 Bond restraints: 7617 Sorted by residual: bond pdb=" CB GLU A 417 " pdb=" CG GLU A 417 " ideal model delta sigma weight residual 1.520 1.478 0.042 3.00e-02 1.11e+03 1.99e+00 bond pdb=" C3' DG D -8 " pdb=" O3' DG D -8 " ideal model delta sigma weight residual 1.422 1.463 -0.041 3.00e-02 1.11e+03 1.87e+00 bond pdb=" N SER A 158 " pdb=" CA SER A 158 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.71e+00 bond pdb=" CG GLU A 417 " pdb=" CD GLU A 417 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.66e+00 bond pdb=" CA SER A 158 " pdb=" CB SER A 158 " ideal model delta sigma weight residual 1.530 1.510 0.020 1.69e-02 3.50e+03 1.36e+00 ... (remaining 7612 not shown) Histogram of bond angle deviations from ideal: 98.42 - 105.54: 442 105.54 - 112.66: 4085 112.66 - 119.77: 2543 119.77 - 126.89: 3344 126.89 - 134.01: 243 Bond angle restraints: 10657 Sorted by residual: angle pdb=" C3' DG D -8 " pdb=" O3' DG D -8 " pdb=" P DA D -7 " ideal model delta sigma weight residual 120.20 123.90 -3.70 1.50e+00 4.44e-01 6.09e+00 angle pdb=" O3' U B -12 " pdb=" C3' U B -12 " pdb=" C2' U B -12 " ideal model delta sigma weight residual 113.70 117.04 -3.34 1.50e+00 4.44e-01 4.96e+00 angle pdb=" C3' U B -12 " pdb=" O3' U B -12 " pdb=" P G B -11 " ideal model delta sigma weight residual 120.20 123.48 -3.28 1.50e+00 4.44e-01 4.77e+00 angle pdb=" C SER A 158 " pdb=" CA SER A 158 " pdb=" CB SER A 158 " ideal model delta sigma weight residual 110.42 114.73 -4.31 1.99e+00 2.53e-01 4.69e+00 angle pdb=" C ASN A 338 " pdb=" CA ASN A 338 " pdb=" CB ASN A 338 " ideal model delta sigma weight residual 109.70 113.52 -3.82 1.81e+00 3.05e-01 4.45e+00 ... (remaining 10652 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.63: 4223 34.63 - 69.26: 289 69.26 - 103.89: 19 103.89 - 138.52: 1 138.52 - 173.15: 3 Dihedral angle restraints: 4535 sinusoidal: 2538 harmonic: 1997 Sorted by residual: dihedral pdb=" O4' U B 1 " pdb=" C1' U B 1 " pdb=" N1 U B 1 " pdb=" C2 U B 1 " ideal model delta sinusoidal sigma weight residual 232.00 58.85 173.15 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" CA MET A 607 " pdb=" C MET A 607 " pdb=" N ILE A 608 " pdb=" CA ILE A 608 " ideal model delta harmonic sigma weight residual 180.00 158.51 21.49 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA ILE A 157 " pdb=" C ILE A 157 " pdb=" N SER A 158 " pdb=" CA SER A 158 " ideal model delta harmonic sigma weight residual 180.00 158.88 21.12 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 4532 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 856 0.034 - 0.069: 268 0.069 - 0.103: 65 0.103 - 0.138: 24 0.138 - 0.172: 1 Chirality restraints: 1214 Sorted by residual: chirality pdb=" C3' U B -12 " pdb=" C4' U B -12 " pdb=" O3' U B -12 " pdb=" C2' U B -12 " both_signs ideal model delta sigma weight residual False -2.48 -2.31 -0.17 2.00e-01 2.50e+01 7.39e-01 chirality pdb=" CB THR A 165 " pdb=" CA THR A 165 " pdb=" OG1 THR A 165 " pdb=" CG2 THR A 165 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA ILE A 64 " pdb=" N ILE A 64 " pdb=" C ILE A 64 " pdb=" CB ILE A 64 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.90e-01 ... (remaining 1211 not shown) Planarity restraints: 1042 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG C -15 " 0.014 2.00e-02 2.50e+03 9.92e-03 2.95e+00 pdb=" N9 DG C -15 " -0.011 2.00e-02 2.50e+03 pdb=" C8 DG C -15 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DG C -15 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DG C -15 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG C -15 " -0.006 2.00e-02 2.50e+03 pdb=" O6 DG C -15 " 0.010 2.00e-02 2.50e+03 pdb=" N1 DG C -15 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DG C -15 " -0.024 2.00e-02 2.50e+03 pdb=" N2 DG C -15 " 0.013 2.00e-02 2.50e+03 pdb=" N3 DG C -15 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DG C -15 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 126 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.58e+00 pdb=" C THR A 126 " -0.028 2.00e-02 2.50e+03 pdb=" O THR A 126 " 0.010 2.00e-02 2.50e+03 pdb=" N TYR A 127 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C B -3 " -0.019 2.00e-02 2.50e+03 1.07e-02 2.57e+00 pdb=" N1 C B -3 " 0.025 2.00e-02 2.50e+03 pdb=" C2 C B -3 " 0.003 2.00e-02 2.50e+03 pdb=" O2 C B -3 " -0.001 2.00e-02 2.50e+03 pdb=" N3 C B -3 " -0.001 2.00e-02 2.50e+03 pdb=" C4 C B -3 " -0.005 2.00e-02 2.50e+03 pdb=" N4 C B -3 " -0.003 2.00e-02 2.50e+03 pdb=" C5 C B -3 " -0.003 2.00e-02 2.50e+03 pdb=" C6 C B -3 " 0.003 2.00e-02 2.50e+03 ... (remaining 1039 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 979 2.75 - 3.29: 7349 3.29 - 3.83: 13416 3.83 - 4.36: 15837 4.36 - 4.90: 24413 Nonbonded interactions: 61994 Sorted by model distance: nonbonded pdb=" OH TYR A 42 " pdb=" OD1 ASN A 140 " model vdw 2.216 2.440 nonbonded pdb=" NZ LYS A 155 " pdb=" O SER A 158 " model vdw 2.217 2.520 nonbonded pdb=" NE2 HIS A 612 " pdb=" OP1 DT C -8 " model vdw 2.289 2.520 nonbonded pdb=" O LEU A 121 " pdb=" ND2 ASN A 274 " model vdw 2.292 2.520 nonbonded pdb=" O2' U B -19 " pdb=" OP1 U B -16 " model vdw 2.301 2.440 ... (remaining 61989 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 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: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 2.080 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 28.050 Find NCS groups from input model: 0.180 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:11.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 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 0.042 7617 Z= 0.181 Angle : 0.544 5.898 10657 Z= 0.305 Chirality : 0.037 0.172 1214 Planarity : 0.003 0.029 1042 Dihedral : 19.786 173.155 3249 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.16 % Allowed : 0.16 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.33), residues: 667 helix: 1.96 (0.30), residues: 327 sheet: 0.43 (0.60), residues: 71 loop : -0.60 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 429 HIS 0.005 0.001 HIS A 4 PHE 0.017 0.001 PHE A 400 TYR 0.017 0.001 TYR A 133 ARG 0.003 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 133 time to evaluate : 0.766 Fit side-chains REVERT: A 174 MET cc_start: 0.6426 (mmp) cc_final: 0.6130 (mmt) REVERT: A 230 ASP cc_start: 0.7729 (t0) cc_final: 0.7519 (t0) REVERT: A 288 ASP cc_start: 0.7563 (t70) cc_final: 0.7332 (t70) REVERT: A 488 ASP cc_start: 0.8276 (p0) cc_final: 0.7965 (p0) REVERT: A 695 ASN cc_start: 0.7883 (OUTLIER) cc_final: 0.7545 (t0) outliers start: 1 outliers final: 0 residues processed: 134 average time/residue: 0.9415 time to fit residues: 134.9275 Evaluate side-chains 104 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 695 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 68 optimal weight: 6.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 ASN ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 7617 Z= 0.346 Angle : 0.619 6.742 10657 Z= 0.340 Chirality : 0.041 0.212 1214 Planarity : 0.004 0.035 1042 Dihedral : 21.981 169.895 1889 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.42 % Allowed : 11.76 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.99 (0.33), residues: 667 helix: 1.69 (0.29), residues: 337 sheet: 0.31 (0.61), residues: 69 loop : -0.59 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 185 HIS 0.005 0.002 HIS A 176 PHE 0.016 0.002 PHE A 613 TYR 0.021 0.002 TYR A 133 ARG 0.003 0.001 ARG A 240 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8015 (tp30) cc_final: 0.7735 (tp30) REVERT: A 206 MET cc_start: 0.7891 (mmm) cc_final: 0.7354 (mmt) REVERT: A 230 ASP cc_start: 0.7762 (t0) cc_final: 0.7435 (t0) REVERT: A 233 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8041 (pp) REVERT: A 288 ASP cc_start: 0.7814 (t70) cc_final: 0.7600 (t70) REVERT: A 363 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7194 (mt-10) REVERT: A 488 ASP cc_start: 0.8411 (p0) cc_final: 0.7963 (p0) REVERT: A 680 ASN cc_start: 0.8276 (t0) cc_final: 0.8047 (t0) outliers start: 15 outliers final: 5 residues processed: 111 average time/residue: 0.9631 time to fit residues: 114.7070 Evaluate side-chains 103 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 96 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 695 ASN Chi-restraints excluded: chain A residue 732 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 0.8980 chunk 21 optimal weight: 8.9990 chunk 56 optimal weight: 0.4980 chunk 46 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 68 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 176 HIS ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7617 Z= 0.218 Angle : 0.545 5.218 10657 Z= 0.303 Chirality : 0.038 0.191 1214 Planarity : 0.003 0.027 1042 Dihedral : 21.837 170.082 1889 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.06 % Allowed : 13.53 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.33), residues: 667 helix: 1.81 (0.29), residues: 336 sheet: 0.38 (0.60), residues: 70 loop : -0.60 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 185 HIS 0.004 0.001 HIS A 176 PHE 0.018 0.001 PHE A 613 TYR 0.018 0.002 TYR A 133 ARG 0.002 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 112 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7918 (tp30) cc_final: 0.7600 (tp30) REVERT: A 206 MET cc_start: 0.7885 (mmm) cc_final: 0.7346 (mmt) REVERT: A 230 ASP cc_start: 0.7778 (t0) cc_final: 0.7419 (t0) REVERT: A 233 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.7991 (pp) REVERT: A 288 ASP cc_start: 0.7799 (t70) cc_final: 0.7563 (t70) REVERT: A 363 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7475 (mm-30) REVERT: A 488 ASP cc_start: 0.8316 (p0) cc_final: 0.7943 (p0) REVERT: A 642 MET cc_start: 0.7863 (ttp) cc_final: 0.7426 (tpp) REVERT: A 680 ASN cc_start: 0.8236 (t0) cc_final: 0.8034 (t0) REVERT: A 695 ASN cc_start: 0.7855 (OUTLIER) cc_final: 0.7290 (t0) outliers start: 19 outliers final: 5 residues processed: 119 average time/residue: 1.0302 time to fit residues: 131.2473 Evaluate side-chains 107 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 99 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 695 ASN Chi-restraints excluded: chain A residue 732 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 32 optimal weight: 0.0470 chunk 45 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 169 GLN ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 7617 Z= 0.416 Angle : 0.655 5.912 10657 Z= 0.360 Chirality : 0.043 0.243 1214 Planarity : 0.004 0.030 1042 Dihedral : 22.133 168.798 1889 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.54 % Allowed : 16.43 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.33), residues: 667 helix: 1.49 (0.28), residues: 344 sheet: 0.09 (0.61), residues: 67 loop : -0.85 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP A 185 HIS 0.005 0.002 HIS A 482 PHE 0.019 0.002 PHE A 400 TYR 0.022 0.002 TYR A 133 ARG 0.005 0.001 ARG A 240 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 98 time to evaluate : 0.757 Fit side-chains REVERT: A 59 GLU cc_start: 0.8052 (tp30) cc_final: 0.7696 (tp30) REVERT: A 169 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7861 (tp40) REVERT: A 206 MET cc_start: 0.7922 (mmm) cc_final: 0.7440 (mmt) REVERT: A 230 ASP cc_start: 0.7851 (t0) cc_final: 0.7472 (t0) REVERT: A 233 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8088 (pp) REVERT: A 288 ASP cc_start: 0.7927 (t70) cc_final: 0.7700 (t70) REVERT: A 337 VAL cc_start: 0.8858 (t) cc_final: 0.8650 (p) REVERT: A 488 ASP cc_start: 0.8331 (p0) cc_final: 0.8002 (p0) REVERT: A 680 ASN cc_start: 0.8270 (t0) cc_final: 0.8046 (t0) REVERT: A 695 ASN cc_start: 0.7966 (OUTLIER) cc_final: 0.7359 (t0) outliers start: 22 outliers final: 8 residues processed: 108 average time/residue: 1.0109 time to fit residues: 116.8103 Evaluate side-chains 105 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 695 ASN Chi-restraints excluded: chain A residue 732 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 53 optimal weight: 0.0970 chunk 29 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 169 GLN ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7617 Z= 0.225 Angle : 0.560 6.752 10657 Z= 0.309 Chirality : 0.038 0.194 1214 Planarity : 0.003 0.029 1042 Dihedral : 21.900 167.242 1889 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.90 % Allowed : 18.36 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.33), residues: 667 helix: 1.64 (0.29), residues: 346 sheet: 0.16 (0.61), residues: 71 loop : -0.72 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 185 HIS 0.003 0.001 HIS A 341 PHE 0.016 0.001 PHE A 396 TYR 0.018 0.002 TYR A 133 ARG 0.001 0.000 ARG A 699 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 105 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7950 (tp30) cc_final: 0.7631 (tp30) REVERT: A 206 MET cc_start: 0.7918 (mmm) cc_final: 0.7397 (mmt) REVERT: A 230 ASP cc_start: 0.7823 (t0) cc_final: 0.7438 (t0) REVERT: A 233 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8018 (pp) REVERT: A 288 ASP cc_start: 0.7861 (t70) cc_final: 0.7616 (t70) REVERT: A 310 ASP cc_start: 0.8198 (m-30) cc_final: 0.7912 (m-30) REVERT: A 488 ASP cc_start: 0.8308 (p0) cc_final: 0.8002 (p0) REVERT: A 695 ASN cc_start: 0.7826 (t0) cc_final: 0.7332 (t0) outliers start: 18 outliers final: 9 residues processed: 115 average time/residue: 0.9225 time to fit residues: 114.0268 Evaluate side-chains 109 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 732 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 605 ASN ** A 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7617 Z= 0.204 Angle : 0.545 6.927 10657 Z= 0.303 Chirality : 0.038 0.189 1214 Planarity : 0.003 0.028 1042 Dihedral : 21.816 169.143 1887 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.38 % Allowed : 19.16 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.33), residues: 667 helix: 1.74 (0.29), residues: 346 sheet: 0.28 (0.62), residues: 69 loop : -0.73 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 185 HIS 0.002 0.001 HIS A 482 PHE 0.016 0.001 PHE A 400 TYR 0.018 0.001 TYR A 133 ARG 0.003 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 108 time to evaluate : 0.758 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7930 (tp30) cc_final: 0.7602 (tp30) REVERT: A 175 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7839 (tm-30) REVERT: A 206 MET cc_start: 0.7939 (mmm) cc_final: 0.7526 (mmt) REVERT: A 209 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8084 (mp) REVERT: A 230 ASP cc_start: 0.7753 (t0) cc_final: 0.7370 (t0) REVERT: A 233 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8000 (pp) REVERT: A 288 ASP cc_start: 0.7844 (t70) cc_final: 0.7595 (t70) REVERT: A 310 ASP cc_start: 0.8192 (m-30) cc_final: 0.7918 (m-30) REVERT: A 336 ASP cc_start: 0.8437 (t0) cc_final: 0.8101 (t0) REVERT: A 488 ASP cc_start: 0.8283 (p0) cc_final: 0.8013 (p0) REVERT: A 695 ASN cc_start: 0.7816 (t0) cc_final: 0.7275 (t0) outliers start: 21 outliers final: 10 residues processed: 120 average time/residue: 0.9492 time to fit residues: 121.9260 Evaluate side-chains 117 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 732 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7617 Z= 0.206 Angle : 0.555 7.800 10657 Z= 0.306 Chirality : 0.038 0.187 1214 Planarity : 0.003 0.028 1042 Dihedral : 21.783 169.468 1887 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.54 % Allowed : 18.84 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.33), residues: 667 helix: 1.71 (0.29), residues: 346 sheet: 0.26 (0.60), residues: 67 loop : -0.73 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 185 HIS 0.005 0.001 HIS A 341 PHE 0.017 0.001 PHE A 400 TYR 0.018 0.001 TYR A 133 ARG 0.002 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 106 time to evaluate : 0.773 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7904 (tp30) cc_final: 0.7537 (tp30) REVERT: A 175 GLU cc_start: 0.8305 (tm-30) cc_final: 0.7800 (tm-30) REVERT: A 206 MET cc_start: 0.7952 (mmm) cc_final: 0.7509 (mmt) REVERT: A 209 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8097 (mp) REVERT: A 230 ASP cc_start: 0.7814 (t0) cc_final: 0.7431 (t0) REVERT: A 233 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.7967 (pp) REVERT: A 250 MET cc_start: 0.8175 (tmm) cc_final: 0.7782 (tmt) REVERT: A 288 ASP cc_start: 0.7870 (t70) cc_final: 0.7623 (t70) REVERT: A 310 ASP cc_start: 0.8206 (m-30) cc_final: 0.7923 (m-30) REVERT: A 336 ASP cc_start: 0.8472 (t0) cc_final: 0.8186 (t0) REVERT: A 488 ASP cc_start: 0.8254 (p0) cc_final: 0.8009 (p0) REVERT: A 695 ASN cc_start: 0.7808 (t0) cc_final: 0.7236 (t0) outliers start: 22 outliers final: 11 residues processed: 121 average time/residue: 0.9650 time to fit residues: 125.1860 Evaluate side-chains 111 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 732 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 56 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 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 140 ASN ** A 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7617 Z= 0.319 Angle : 0.621 8.988 10657 Z= 0.340 Chirality : 0.041 0.223 1214 Planarity : 0.003 0.029 1042 Dihedral : 21.909 167.164 1887 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.38 % Allowed : 20.13 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.33), residues: 667 helix: 1.52 (0.29), residues: 350 sheet: 0.24 (0.61), residues: 69 loop : -0.78 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 185 HIS 0.003 0.001 HIS A 216 PHE 0.020 0.002 PHE A 400 TYR 0.022 0.002 TYR A 133 ARG 0.003 0.000 ARG A 240 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 102 time to evaluate : 0.709 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7989 (tp30) cc_final: 0.7630 (tp30) REVERT: A 175 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7928 (tm-30) REVERT: A 206 MET cc_start: 0.7984 (mmm) cc_final: 0.7544 (mmt) REVERT: A 209 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8098 (mp) REVERT: A 230 ASP cc_start: 0.7825 (t0) cc_final: 0.7431 (t0) REVERT: A 233 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8066 (pp) REVERT: A 288 ASP cc_start: 0.7934 (t70) cc_final: 0.7693 (t70) REVERT: A 488 ASP cc_start: 0.8306 (p0) cc_final: 0.8057 (p0) REVERT: A 604 PHE cc_start: 0.6640 (m-80) cc_final: 0.6355 (m-80) outliers start: 21 outliers final: 15 residues processed: 116 average time/residue: 0.9543 time to fit residues: 118.7375 Evaluate side-chains 113 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 693 MET Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 740 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 60 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN ** A 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 7617 Z= 0.294 Angle : 0.636 10.494 10657 Z= 0.343 Chirality : 0.041 0.210 1214 Planarity : 0.003 0.029 1042 Dihedral : 21.884 166.557 1887 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.38 % Allowed : 20.29 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.33), residues: 667 helix: 1.51 (0.28), residues: 348 sheet: 0.06 (0.59), residues: 67 loop : -0.84 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 185 HIS 0.006 0.001 HIS A 341 PHE 0.023 0.002 PHE A 396 TYR 0.021 0.002 TYR A 133 ARG 0.002 0.000 ARG A 240 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 99 time to evaluate : 0.791 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7957 (tp30) cc_final: 0.7572 (tp30) REVERT: A 175 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7836 (tm-30) REVERT: A 206 MET cc_start: 0.7964 (mmm) cc_final: 0.7519 (mmt) REVERT: A 209 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8090 (mp) REVERT: A 223 LYS cc_start: 0.8145 (ttmm) cc_final: 0.7939 (ttpt) REVERT: A 230 ASP cc_start: 0.7812 (t0) cc_final: 0.7504 (t0) REVERT: A 288 ASP cc_start: 0.7929 (t70) cc_final: 0.7677 (t70) REVERT: A 488 ASP cc_start: 0.8299 (p0) cc_final: 0.8059 (p0) REVERT: A 604 PHE cc_start: 0.6529 (m-80) cc_final: 0.6289 (m-80) REVERT: A 693 MET cc_start: 0.8310 (mmm) cc_final: 0.7956 (mmm) REVERT: A 695 ASN cc_start: 0.7909 (t0) cc_final: 0.7359 (t0) outliers start: 21 outliers final: 15 residues processed: 113 average time/residue: 0.9876 time to fit residues: 119.9013 Evaluate side-chains 115 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 99 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 740 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 0.2980 chunk 49 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 7617 Z= 0.292 Angle : 0.636 10.404 10657 Z= 0.342 Chirality : 0.041 0.213 1214 Planarity : 0.003 0.029 1042 Dihedral : 21.891 166.824 1887 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.90 % Allowed : 21.10 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.33), residues: 667 helix: 1.46 (0.29), residues: 342 sheet: -0.13 (0.58), residues: 69 loop : -0.79 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 185 HIS 0.004 0.001 HIS A 612 PHE 0.017 0.002 PHE A 400 TYR 0.021 0.002 TYR A 133 ARG 0.002 0.000 ARG A 240 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1334 Ramachandran restraints generated. 667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 99 time to evaluate : 0.819 Fit side-chains REVERT: A 59 GLU cc_start: 0.7960 (tp30) cc_final: 0.7573 (tp30) REVERT: A 175 GLU cc_start: 0.8357 (tm-30) cc_final: 0.8051 (tm-30) REVERT: A 206 MET cc_start: 0.7957 (mmm) cc_final: 0.7588 (mmt) REVERT: A 230 ASP cc_start: 0.7869 (t0) cc_final: 0.7412 (t0) REVERT: A 234 LYS cc_start: 0.8361 (mppt) cc_final: 0.8044 (mppt) REVERT: A 288 ASP cc_start: 0.7930 (t70) cc_final: 0.7674 (t70) REVERT: A 488 ASP cc_start: 0.8299 (p0) cc_final: 0.8068 (p0) REVERT: A 695 ASN cc_start: 0.7904 (t0) cc_final: 0.7341 (t0) outliers start: 18 outliers final: 17 residues processed: 111 average time/residue: 0.9418 time to fit residues: 112.1345 Evaluate side-chains 114 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 97 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 693 MET Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 740 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN ** A 522 ASN ** 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 = 0.3391 r_free = 0.3391 target = 0.091079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.077904 restraints weight = 15768.226| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.88 r_work: 0.3051 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7617 Z= 0.219 Angle : 0.613 10.700 10657 Z= 0.330 Chirality : 0.040 0.193 1214 Planarity : 0.003 0.027 1042 Dihedral : 21.783 168.748 1887 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.42 % Allowed : 21.90 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.33), residues: 667 helix: 1.49 (0.29), residues: 347 sheet: -0.02 (0.60), residues: 69 loop : -0.84 (0.40), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.004 TRP A 185 HIS 0.003 0.001 HIS A 612 PHE 0.017 0.001 PHE A 400 TYR 0.018 0.002 TYR A 133 ARG 0.002 0.000 ARG A 205 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2545.92 seconds wall clock time: 46 minutes 16.82 seconds (2776.82 seconds total)