Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 13:24:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dc2_27320/04_2023/8dc2_27320.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dc2_27320/04_2023/8dc2_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_27320/04_2023/8dc2_27320.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dc2_27320/04_2023/8dc2_27320.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dc2_27320/04_2023/8dc2_27320.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dc2_27320/04_2023/8dc2_27320.pdb" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 4.06 Conformation dependent library (CDL) restraints added in 846.9 milliseconds 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: 2.59 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: 2.75 Time building geometry restraints manager: 4.29 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: 4127 34.63 - 69.26: 198 69.26 - 103.89: 8 103.89 - 138.52: 1 138.52 - 173.15: 3 Dihedral angle restraints: 4337 sinusoidal: 2340 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 4334 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: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 2.320 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 27.060 Find NCS groups from input model: 0.160 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:13.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.290 ------------------------------------------------------------------------------- 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 : 17.638 173.155 3051 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 % 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 *********************** 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 : 0.783 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 134 average time/residue: 0.9734 time to fit residues: 139.4137 Evaluate side-chains 105 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.751 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 4.9990 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: 5.9990 chunk 22 optimal weight: 8.9990 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 140 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.052 7617 Z= 0.345 Angle : 0.615 6.809 10657 Z= 0.339 Chirality : 0.041 0.215 1214 Planarity : 0.004 0.035 1042 Dihedral : 18.959 169.714 1689 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 2.25 % 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: 1.01 (0.33), residues: 667 helix: 1.75 (0.29), residues: 334 sheet: 0.32 (0.61), residues: 69 loop : -0.62 (0.39), residues: 264 *********************** 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 121 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 107 time to evaluate : 0.830 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 113 average time/residue: 0.9249 time to fit residues: 112.4283 Evaluate side-chains 103 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 99 time to evaluate : 0.743 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.1287 time to fit residues: 1.4656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 56 optimal weight: 0.0570 chunk 46 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.1700 ------------------------------------------------------------------------------- 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 ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1531 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= 0.222 Angle : 0.550 6.000 10657 Z= 0.306 Chirality : 0.038 0.193 1214 Planarity : 0.003 0.027 1042 Dihedral : 18.838 170.107 1689 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 2.25 % 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: 1.00 (0.33), residues: 667 helix: 1.68 (0.29), residues: 339 sheet: 0.39 (0.60), residues: 70 loop : -0.59 (0.39), residues: 258 *********************** 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 128 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 114 time to evaluate : 0.826 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 3 residues processed: 119 average time/residue: 1.0033 time to fit residues: 127.9184 Evaluate side-chains 101 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 98 time to evaluate : 0.761 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.1211 time to fit residues: 1.1800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.3980 chunk 45 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- 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 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: 0.8211 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 7617 Z= 0.315 Angle : 0.591 4.895 10657 Z= 0.327 Chirality : 0.040 0.218 1214 Planarity : 0.003 0.029 1042 Dihedral : 18.990 167.806 1689 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer Outliers : 3.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.65 (0.28), residues: 343 sheet: 0.16 (0.61), residues: 67 loop : -0.70 (0.39), residues: 257 *********************** 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 117 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 98 time to evaluate : 0.779 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 107 average time/residue: 0.9539 time to fit residues: 109.6550 Evaluate side-chains 103 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 0.761 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 4 residues processed: 4 average time/residue: 0.3369 time to fit residues: 2.5827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 37 optimal weight: 0.0970 chunk 65 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1775 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= 0.241 Angle : 0.564 7.739 10657 Z= 0.312 Chirality : 0.039 0.199 1214 Planarity : 0.003 0.028 1042 Dihedral : 18.905 168.352 1689 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 3.22 % 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: 1.56 (0.28), residues: 351 sheet: 0.10 (0.60), residues: 69 loop : -0.60 (0.40), residues: 247 *********************** 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 125 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 105 time to evaluate : 0.780 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 7 residues processed: 114 average time/residue: 0.9325 time to fit residues: 114.1635 Evaluate side-chains 106 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 99 time to evaluate : 0.797 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.1158 time to fit residues: 1.1097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 17 optimal weight: 0.2980 chunk 72 optimal weight: 3.9990 chunk 60 optimal weight: 0.0050 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- 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 ** 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: 0.8151 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 7617 Z= 0.177 Angle : 0.557 12.806 10657 Z= 0.305 Chirality : 0.037 0.181 1214 Planarity : 0.003 0.028 1042 Dihedral : 18.781 170.226 1689 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer Outliers : 2.58 % 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: 0.96 (0.33), residues: 667 helix: 1.67 (0.29), residues: 349 sheet: 0.10 (0.59), residues: 69 loop : -0.66 (0.40), residues: 249 *********************** 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 126 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 0.796 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 117 average time/residue: 0.9767 time to fit residues: 122.2725 Evaluate side-chains 108 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 101 time to evaluate : 0.693 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.1117 time to fit residues: 1.2541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 52 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 452 GLN ** 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: 0.8204 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.034 7617 Z= 0.298 Angle : 0.615 12.299 10657 Z= 0.334 Chirality : 0.040 0.212 1214 Planarity : 0.003 0.029 1042 Dihedral : 18.951 168.220 1689 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer Outliers : 3.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.83 (0.33), residues: 667 helix: 1.54 (0.28), residues: 349 sheet: 0.14 (0.60), residues: 69 loop : -0.71 (0.40), residues: 249 *********************** 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 121 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 0.827 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 112 average time/residue: 0.9334 time to fit residues: 112.3266 Evaluate side-chains 108 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 0.749 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 4 average time/residue: 0.6059 time to fit residues: 3.6468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 6 optimal weight: 0.0770 chunk 56 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- 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: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 7617 Z= 0.219 Angle : 0.582 12.963 10657 Z= 0.318 Chirality : 0.039 0.196 1214 Planarity : 0.003 0.028 1042 Dihedral : 18.839 169.093 1689 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer Outliers : 2.42 % 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: 0.89 (0.33), residues: 667 helix: 1.68 (0.28), residues: 347 sheet: 0.14 (0.60), residues: 67 loop : -0.79 (0.40), residues: 253 *********************** 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 118 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 0.821 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 11 residues processed: 113 average time/residue: 0.9514 time to fit residues: 115.3624 Evaluate side-chains 110 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 99 time to evaluate : 0.759 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 4 average time/residue: 0.3897 time to fit residues: 2.8186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 43 optimal weight: 0.2980 overall best weight: 2.0588 ------------------------------------------------------------------------------- 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 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.034 7617 Z= 0.340 Angle : 0.666 11.805 10657 Z= 0.358 Chirality : 0.042 0.225 1214 Planarity : 0.004 0.030 1042 Dihedral : 19.062 166.500 1689 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer Outliers : 2.90 % 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: 0.65 (0.33), residues: 667 helix: 1.40 (0.28), residues: 350 sheet: 0.10 (0.61), residues: 69 loop : -0.83 (0.41), residues: 248 *********************** 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 116 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 98 time to evaluate : 0.830 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 13 residues processed: 110 average time/residue: 0.9767 time to fit residues: 115.3186 Evaluate side-chains 106 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 0.739 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 9 residues processed: 4 average time/residue: 0.6043 time to fit residues: 3.6630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 59 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN ** A 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2027 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= 0.266 Angle : 0.645 12.397 10657 Z= 0.343 Chirality : 0.041 0.205 1214 Planarity : 0.004 0.040 1042 Dihedral : 18.970 167.486 1689 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer Outliers : 2.09 % 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 (0.34), residues: 667 helix: 1.50 (0.29), residues: 347 sheet: 0.09 (0.62), residues: 69 loop : -0.87 (0.41), residues: 251 ********************** 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 111 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 0.801 Fit side-chains outliers start: 13 outliers final: 11 residues processed: 108 average time/residue: 0.9334 time to fit residues: 108.5902 Evaluate side-chains 108 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 0.692 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 2 average time/residue: 0.1536 time to fit residues: 1.3467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.092050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.078977 restraints weight = 15802.073| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.88 r_work: 0.3072 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 7617 Z= 0.198 Angle : 0.620 11.060 10657 Z= 0.330 Chirality : 0.039 0.182 1214 Planarity : 0.003 0.028 1042 Dihedral : 18.818 170.171 1689 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer Outliers : 2.09 % 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: 0.75 (0.34), residues: 667 helix: 1.57 (0.29), residues: 347 sheet: -0.05 (0.59), residues: 67 loop : -0.84 (0.41), residues: 253 =============================================================================== Job complete usr+sys time: 2463.54 seconds wall clock time: 44 minutes 47.08 seconds (2687.08 seconds total)